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|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement \\
\\  \\
Catastrophic failure (flooding) \\
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\\ |
| Physical volume vs. detectable volume ("virtual core") - SeaFlow, Sealable \\ | Ability to re-process primary data. | \\ | Pros: \\
&nbsp;\- Allows processing of undiluted sample \\
&nbsp;\- no need for sheath fluid \\
\\
Cons:&nbsp; \\
&nbsp;\- virtual core is harder to characterize then physical volume \\ |
| Sheath fluid, vs. undiluted sample | | | |
| fluorescent and calibration bits. \\ | Used for calibration on some (most) benchtop flowcytometers | | Cons: \\
&nbsp;\- hard to implement in "in situ" instrument \\ |
| Cell sorting: \\
&nbsp; - Mechanical sorting into "catcher tube". Enclosed path, one population. \\
\\
&nbsp;\- Electrostatic deflection | actively separate and isolate particles having specified properties. | seem to be complex to implement and currently does not required \\ | |
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&nbsp;\- Acoustic focusing (Ward) | This is physical sample focusing \\ | | |
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&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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<property name="body"><![CDATA[h3.

*{+}Bellingham's notes{+}*

Notes from telecon with the FlowCAM folks:

Attendees: Bellingham, Chavez, Klimov, Jac Fought, Harry Nelson (Fluid Imaging)
\\

Francisco:

160-170 codes for organisms quantified in 'standard' water analysis.&nbsp; larger by microscopy, smaller by flow cytometry, some \~um size in both.

Samples 250 ml in size.

Preserve material with glutaraldehyde, filter 25 ml of fluid.
\- microscopy done from filter
\- some fluid frozen w liquid N2 for cytometer (sent to U of Hawaii)

Catalog organisms to 200 um in size

Lots of small stuff - use staining to see bacteria, etc.

For the microscopy - use different magnifications and look over different areas

Harry:

We would probably use 10x objective for 100x magnification over 100um couvette (?) w lower limit of about 10um critter.

4x objective has lower effective size resolution of 40um.

Can use 20x objective w 50um couvette but 'takes a while'

Harry will send us all some sample images of organisms at the various resolutions.

User builds their own library, does not come with library.&nbsp; Library is used for classification.&nbsp; Have taxonomic photos, but not a library.

How many entries does it need?&nbsp; Depends.

Three step process - build a library, build a filter, build a template from the filters.&nbsp; Is dynamic - can add and subtract from them.&nbsp; Use the filter iteratively (first pass for organism 1, then for organism 2, etc.).

Could build some libraries ahead of time.

Chavez:

Can we also get size distribution of what is in sample?

Harry:

Yes, that just comes from pixels.&nbsp; Easily done.&nbsp; Can also use fluorescence, but if the sample is really concentrated then several organisms might be in field of view.

1/4 ml/min volumetric flow rate for 100 um couvette.

Outcome of&nbsp; the meeting is that Francisco sent them some preserved material.&nbsp; They are running it this week.&nbsp; We are going to get a copy of their software and work on developing a library for the resulting images, and use it to develop a classifier for the remainder of the data....

*{+}Additional notes from Klimov:+*

10x objective, 100x magnification, 10-20um resolved microorganisms, 100um flow cell. This is a most common configuration.
4x objective, 40x magnification, 25-30um resolved microorganisms, 200um flow cell.
25x objective, 250x magnification, 50um flow cell. For highest resolution but also slowest pumping rate.

It was not clear what is the actual optical resolution of the system with say 10x objective. It should be higher then specified resolved microorganism size, perhaps 1-2 um.
Harry said "10 um" is "many pixels", as can be seen in "sample pictures".

&nbsp;
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Centrifugal elutriation - pre-sort particles

Sampling statistics problem

Partec - flow microscope

Denis - showed SM data
PL: Could you acoustically control concentration in SM measurement volume, to prevent excessive particles?

Round table:

Influx sorting discussion with Camille

Scholin: interested in particle-field distribution, to guide adaptive sampling
CS: Which is more amenable to real-time sampling: scatter/fluor vs morphological?
PL: Need to decide size range. Answer is not always flow cytometry. Look at Shapiro's battery-powered microscope, for remote diagnostics

JB: How small can a flow cytometer be?
PL: lasers are really small now... a lot of cytometers had to be flexible - now more specialized, smaller versions available. HIV/AIDS applications in developing world are driving size/power downward.
CS: What are prospects for in situ cell sorting?
PL: Will show some slides... chip-based, not electrostatic, but mechanical. Working with Livermore guys

FC: Do you sort live material?
PL: Yes - sorting effects on living samples are largely unknown - work to be done . Typically pressurized to 60 psi

PL: Centrifuging technique seems pretty gentle. Acoustic tech hasn't made it into sorting applications yet.

FC: Anyone thought of breaking up cells and analyzing organelles?
PL: Done with e.g. tumor cells. Also lyse cells to extract chromosomes, then run through cytometer

PL: Can get fluorescent beads that bind to specific target - then measure beads in cytometer. Can get that fluoresce in different colors

SS: Can cells be sorted on basis of morphology?

CP: Could we sort environmental DNA?
PL: Need some kind of particle basis for cytometry
TO: Could this be a mass-spec application?
PL: Maybe\\

PL: No reason why a flow cytometer can't be very small - power is more challenging\\]]></property>
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<property name="body"><![CDATA[h2.



h2. Questions for Resolution Optics

\\

What is maximum recommended particle concentration? User manual says "In order to achieve accurate images, inline holography requires that a reasonable amount of the reference wave (unscattered light) reaches the camera sensor. Too many objects between the PS and the camera can reduce the amount of reference wave reaching the camera and will therefore result in poor reconstructions." {color:#ff0000}RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.{color}

What exactly is output of realtime processing? Predetermined stack of images? Configurable? {color:#ff0000}Can select single image depth for realtime processing. Can save other depths for later offline processing.{color}

Automated image depth determination? {color:#ff3300}This capability will be provided by RO's "Stingray" software, now in development{color}

Realtime particle classification?&nbsp; {color:#ff0000}Realtime particle size distribution, other statistics in one image plane provided by "Swordfish" software{color}

How does spatial resolution vary with image plane depth? {color:#ff0000}Highest resolution (1 micron) when target is against source window. Lowest resolution (4 microns) when target against camera window{color}

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?) {color:#ff0000}Smooth sapphire windows may discourage biofouling, but likely to be an issue. Particles stuck to window can be eliminated through software.{color}

What about embedded processing system? {color:#ff0000}RO is working on an embedded battery-powered version; maybe available September 2014?{color}

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption {color:#ff0000}5 Watts{color}
\- image storage (memory) capacity and total number of images possible {color:#ff0000}Depends on laptop drive capacity{color}
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\

ain outcome - MBARI can borrow a Submersible Microscope (older version) for 1.5 months maximum, starting "in April". Sergey or John might be able to visit MBARI to help us get started. Instrument is rated to 2000 meters, but currently has a 10 meter gigabit ethernet cable (R.O. might have a longer cable to loan us). Sample spacer is adjustable on this model.

h3. Notes from the telecon

Here are my actual notes of the meeting - please feel free to comment or correct.

Attendees:
Stephen Jones, Sergey Missan, George McMurtry, John Sampson
John Ryan, Brett Hobson, Francisco Chavez, Steve Haddock, Julio Harvey, Danelle Cline, Hans Thomas, Thom Maughan, Tom O'Reilly

Loaner SM instrument has same optical characteristics as newest version.

Spatial resolution varies with source-to-target distance. Best resolution is about 1 micron when close to source, 4 microns when close to camera.

Imaged volume is about 12 microliters: 2 x 2 mm FOV, 3 mm depth
Sampling rate is 16 fps, 190 microliters/sec
Single plane image transformation at 16 fps, i.e. can keep up in real time. Other planes can be processed later.

Check out the SM gallery

Software packages

Octopus: "manual" processing (hologram-to-image transform, measure size, etc)

Swordfish: High-speed real-time particle characterization (16 fps), historgrams, statistics

Stingray (in development): Automatic target tracking across image planes, morphological features, classifier. Problematic to track when targets overlap.

Particle concentration: if too many particles, there's not enough light for good reconstruction. But RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.

Sample spacer - adjustable in older model (the model we'd borrow), fixed at 8 mm in latest model.

Instrument has been deployed for up to 1 day at least.
Sapphire windows are smooth, but biofouling likely an issue for longer deployments.

To process, need reference holograms(s) - to options:
1. Collect clear-water reference at start of deployment, or
2. Alternate between reference and sample images during deployment (not sure how this works operationally - Tom)

Processing requires Windows laptop with Invidia gpu; raw data and images stored to laptop drive.

Instrument requires 12 V power, gigabit ethernet connection to laptop.

R.O. is working on an embedded, battery-powered data logger - maybe available in August or September 2014?

Camera: 2048 x 2048 pixel, 8 bits monochrome, 16 fps, up to 50 fps in binned mode
Holograms and images stored as png, tiff (other formats?)

Data can be analyzed with LabView, other software thanks to standard image formats.

Loaner instrument is rated to 2000 meters, but has 10 meter cable (R.O. might be able to loan us a longer one).

Loaner sample spacer can be adjusted.
Sergey or John Sampson may be able to come to MBARI to help set up and use the instrument.

Sergey will send document that describes method limitations.

Sergey has not seen any processing bottlenecks running at 16 fps for 24 hours.]]></property>
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[Telecon with Resolution Optics, 1/31/2014|CytometerTech:Submersible Microscope telecon January 31, 2014]\\

h3. Further information provided by Resolution Optics (John Samson, 2/1/2014)
[Submersible Microscope version 1.0.0 user guide|^Submersible-User-Guide-v1.0.0.pdf] (original version of the Submersible Microscope, which MBARI might borrow)

[Conventional and holographic microscopy compared|^ED-DIHMConventionalMicroscopyComparison.pdf]

[Limitations|^ED-Limitations.pdf]\\]]></property>
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<property name="body"><![CDATA[02/05/2014 /2013 MBARI Jarred Swalwell. Jarred was MBARI seminar speaker. Had discussions with Jarred at 9:00, 12:00, 16:00
&nbsp;
9:00 Klimov, Swalwell, O'Reilly
&nbsp;
Status: new electronics is done but have a noise on analog board from other (switching) board in a board stack. Due to limited resources, now working on components that can be used for existing systems SeaFlow (synergy). Need to solve:
Flowcell
Modified concept.
Laser (test, select)
Pump
Mechanics.
&nbsp;
"Unattended" Seaflow operation of a few days is pretty reliable. Generally shorter deployments (few days, a week) compare to CytoBot
&nbsp;
Rosette profiling pump may be a bit fast for cytometry. Need at least 3 minutes sampling same volume to get good population statistics
&nbsp;
May come out again in April
&nbsp;
Flow cell - hoping to use cheap $10 cell, as opposed to IFCB cell which costs $1000s
But have to frequently change the cell. Jarred uses MicroPump devices, pretty reliable.
Keep clean: consider hydrodynamics near flow cell walls.
&nbsp;
Testing new cheap 0.5Watt&nbsp; $500 Chinese-made laser - not too stable but can resolve prochlorococus. (ultrabright.com?) They also make $10k laser which is pretty stable so this is matter of price not technology.
&nbsp;
Could do embedded system with Arduino
&nbsp;
Camera - would like to take pictures of larger particles.
&nbsp;
&nbsp;
Round table discussion
&nbsp;
16:00-17:00 Klimov, O'Reilly, Maughan, Swalwell, Hamilton, Chavez
&nbsp;
Some of Francois' algorithms can be run in real-time
&nbsp;
FC: What about machine-learning approaches? E.g. make inferences from clustering and local environment.
&nbsp;
JS: Often have to specify centroids to Ribalet's algorithms at the beginning.
A lot of the clustering algorithms originated from medical applications (Fred Hutchinson Inst.). "Flowcast". Written in 'R', which is free (unlike MathLab)
&nbsp;
JS: Has done some acoustic applications. Drug-delivery via bubbles, infer bubble material properties from acoustic scatter
&nbsp;
JS: Note that size of virtual core can be adjusted. Larger VC results in poorer
&nbsp;
JS: Have processed 2012 data - will provide to Francisco/Jason
&nbsp;
Fluorescent beads tend to sink; so delivery rate is not constant, but this is not so important as long as some of them appear on cytogram for gating calibration
&nbsp;
On "real time": 3 min is sort of enough for cytogram, makes 1 file. Real flow rate is 15 mL/min, virtual core flow rate about 15-30 uL / min
&nbsp;
Plans: Fransico is asking what is good for Jarred: 1st, or 3-4 weeks of April?
Jarred: 1st week looks better.]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
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h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472 of their [recent paper|^Seaflow-Limnology-and-Oceanography.pdf]. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they are all detectable, and assume that each cell is individually detected (i.e. we don't see multiple cells counted as one).
\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) || N=100 (sigma=10%) \\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | 20000 s \\ | 4000 s \\ |
| p = 10^3 cell/ml \\ | 4000 s \\ | 2000 s \\ | 400 s \\ |
| p = 10^4 cell/ml \\ | 400 s \\ | 200 s \\ | 40 s \\ |
| p = 10^5 cell/ml \\ | 40 s \\ | 20 s \\ | 4 s \\ |
Note that the virtual core size (and hence OPP flow rate) is adjustable. The example value of \~15 uL/min corresponds to a virtual core diameter of \~6 microns (the physical stream diameter is \~200 microns). For a low number density, the virtual core diameter and OPP flow rate could be increased with only small risk of coincident counting, resulting in shorter counting times. Science likely wants to resolve several constituent populations with different number densities, in which case statistical uncertainties will vary with target population.&nbsp; ]]></property>
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<property name="body"><![CDATA[h2. 5/25/2013

&nbsp;Met with Alex Worden to discuss her cytometry applications, approaches

Attendees: Alex, Jim, Denis, Tom

h3.


h3. Tom's notes

Jarred is willing to give a talk when he visits Alex' lab in May.&nbsp; Will keep us apprised of the schedule
Jarred has grant to develop staining capability for Seaflow/(Sealabel?) \-&nbsp; measure grazing by diatoms, dinoflagellates, reproductive rates

Very important to engage UW collaborators at high intellectual level (as opposed to "contract labor").
UW has very extensive expertise in oligotrophic cytometry - informatics and biological. Too expensive/daunting to attempt to replicate that...

Big science problems:
Oligotrophic ocean: what picoplankton organisms are out there? How are the populations changing on various spatial and time-scales? Why are they changing?
Only a few cytometers able to resolve picoplankton
Need 488 nm excitation for phyto pigments

Diurnal growth cycles can now be extracted from Seaflow data, based on new modeling approach.
AUV advantages
realtime survey capability to inform ship sampling plan
3D measurement capability
Long-duration measurements during extended missions
Vehicle sensor payload provides contextual data (e.g. nutrient measurements important\!)

AW would use Cyto-AUV to write papers that utilizes the above advantages
&nbsp;
Instrument features:
Need 488 nm excitation
Must resolve pico\- and nanoplankton (0.2 - 20 micron)
imaging probably not useful - can't discriminate between very small (< 3 micron) organisms, e.g. grazers
staining is useful (e.g. for fungi, bacteria, DNA measurement) but not necessary
in-situ calibration w/ beads is critical

Measurement approaches:
Need 10% sigma or better on counting. Note that large counting errors can be amplified when deriving other quantities (e.g. growth rates). Note that medical applications usually require 1% sigma or better (10,000 count)
Always add calibration beads to sample to verify alignment, detection, etc (except for DNA samples)
Usually able to use single configuration for given seawater sample (detectors have 4-decade dynamic range). May need to change configuration for different water mass (e.g. open-ocean vs eddy?)
Not sure how large cells affect Seaflow measurements
BD Influx measurements are typically 10 minutes (25 microliters/minute)
AW lab does not "gate" on fluorescence or scatter - keep all raw data (may not be practical for coastal waters)
Current focus on cells smaller than 5 micron in open ocean, but including larger cells may be important in some environments
Prochlorococcus and synechococcus are readily identifiable - eukaryotes more problematic

Major challenges:
Time consuming, expensive to collect sparse 3D datasets from CTD casts. Seaflow is vast improvement, but surface water only.
Data analysis (see below)

Data analysis challenges:
Cytometer signatures depend on many factors; diverse organism populations, nutrients, depth, etc...
Lots of human judgement, calibration, tweaking required to analyze data - difficult to automate (look at Ribalet et al PNAS paper on bio-diversity index)
UW team has enormous experience and knowledge - biological combined with informatic

Potential alternatives to cytometry - Raman is talked about, no one appears to have used it yet.

h3. Denis' notes

Application:
\-&nbsp;&nbsp;&nbsp; What groups of organisms are over there? Cytometer on AUV could provide a yo-yo capability, 3D and so on, this means presence.
\-&nbsp;&nbsp;&nbsp; Day-night dynamics.
\-&nbsp;&nbsp;&nbsp; Characterize food web is good information is microbiology

Observational challenges:
\-&nbsp;&nbsp;&nbsp; Total throughput from sampling to real data, is very low (presently), sometimes takes years if sample are analyzed in the lab.&nbsp; This also puts a limit on a numbers of samples.
\-&nbsp;&nbsp;&nbsp; Presence is very low (presently), limited number of ship cruises

Target organisms and mixed populations
\-&nbsp;&nbsp;&nbsp; Not really concerned with high dynamic range on sizes (<5um?).
\-&nbsp;&nbsp;&nbsp; Discriminate between groups of organisms, using optical methods, Ch A and accessory pigments.

Features:
\-&nbsp;&nbsp;&nbsp; Imaging. Value of imaging is limited, organisms below 5um appear as "blobs", can not distinguish. Low Value.
\-&nbsp;&nbsp;&nbsp; Real time processing. Normally cytometer is used during cruises by Worden group. On ship, adaptive sampling strategy is used, and decisions on cruise plan are made based on CTD and cytometer data, if it possible at all, and a team have enough bandwidth to do so. High Value.
\-&nbsp;&nbsp;&nbsp; Bacterial communities need staining.
\-&nbsp;&nbsp;&nbsp; Population identification. Gating is not used, instead, trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach. This works well in "blue water". Coastal zones with much more silt etc.,&nbsp; is a different story.

Value of integration with mobile platform
\-&nbsp;&nbsp;&nbsp; adaptive behavior, contextual data; real-time data, reconnaissance, surviving;&nbsp; persistent presence, high-res. All High Value.

Procedure:
\-&nbsp;&nbsp;&nbsp; Typically, sample is split in 2, with calibration bids, and without, and both run thru cytometer.
\-&nbsp;&nbsp;&nbsp; Beads are needed to calibrate optics for sensitivity and alignment.
\-&nbsp;&nbsp;&nbsp; Typical sampling rage is 25uL/mil, so it takes 10 min to analyze 250 uL; ~ 1000 eukaryotes, number of cyano bacteria's ~ 100x higher.
\-&nbsp;&nbsp;&nbsp; Statistical errors: <10% is good.
\-&nbsp;&nbsp;&nbsp; As a "rule of thumb", about 10k cells needs to be accumulated in flow cytometry, in order to compute growth rate, which is difficult.
\-&nbsp;&nbsp;&nbsp; Gain control: manual, interactive. Use to need gain control adjustment before running some samples, or to resolve different species in the same sample. Now, with 4 orders of dynamic range, only occasional adjustment for regions of ocean are being made.&nbsp;

Data analysis.
\-&nbsp;&nbsp;&nbsp; Not a static process. Interactive process requiring involvement of skillful individual such as scientist.
\-&nbsp;&nbsp;&nbsp; Signatures of groups of organisms are not static, that is why very helpful to use calibration beads.
\-&nbsp;&nbsp;&nbsp; There is a lot of knowledge went into data processing in established groups, would be very hard to replicate that.
\-&nbsp;&nbsp;&nbsp; Interdisciplinary field between biology and computation => high value.

Trends:
\-&nbsp;&nbsp;&nbsp; Imaging cytometry
\-&nbsp;&nbsp;&nbsp; Smaller particles
\-&nbsp;&nbsp;&nbsp; Certain interest to Raman, but nobody did it yet.

&nbsp;
\\

h2. 3/27/2013

Sorry these notes are delayed. Denis have I missed anything important?

Attendees: Denis, Tom

Note that Dorota's "Taxa" table is now online.

Reviewed instrument comparison tables on project Confluence page.
Consider LISST Holo to be an imaging cytometer; should be included with other existing cytometers
Condense some table rows into a single row, with more descriptive text in each cell

Good start on science applications/requirements page

DK: We are a month behind schedule specified in our proposal - hoped to have "literature search" complete by March 1.
DK: As we read articles and attach them, it is useful to markup the PDF file with notes

Alex is available next week - review nature of her lab's work beforehand

Action items:
Denis to review new technologies described in "perspectives" section of Cytotechnology article.
Tom to continue instrument comparison tables, filling out science applications/requirements page
All: prepare to interview Worden by reading her lab's publications and posters (e.g. this one)
&nbsp;
\\

h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\

h2. 3/7/2013 - telecon with Holomic LLC

&nbsp;Pre-call:

Denis - the cell phone cytometer is not prssure-tolerant.
Holomic achieves high optical efficiency; can we achieve that?

Ketaki Sood (marketing) , Nevan Karlovac (CEO), Ozcan (scientist)
O'Reilly, Bellingham, Klimov

JGB: Gave MBARI background. Autonomy. Increasing emphasis on microbiology. Physical sampling.
Mentioned summer intern program.

Ozcan: what about broad-field microscopy?
JGB: tricky in situ. Contextual sensors for water samples

JGB: What are max flow rates that prototype can sustain?
Holomic: Low so far, Microliters per minute...

Holomic: Current software gives particle counts, not size
Also wide-field fluorescent microscope

DK: Unattended operation is key. Low power, size

Holomic hasn't focused on low power
Holomic: would require significant funding to build instrument for MBARI
JGB: MBARI engineering is capable of significant contribution
Holomic: formulate your requirments, parameters, etc. Holomic sells products. Cell phone cytometer is not yet a product.
JGB: Oceanographic market is quite small.
How important is continuous sampling?
Holomic: Will keep MBARI in mind as they develop the cytometers

Post call:
Need to develop requirements
\- particle densities (concentration)
\- organism
\- flow rates, integration time
\- sensitivity, chlorophyll concentration
\- excitation/fluorescent wavelengths

Compare to BD, Seaflow
Need to talk with Alex, Scholin, about the above
Example: want to resolve organisms that generate signal detected by EcoPuck; want equivalent sensitivity
Send them a thank-you email, invite them to visit

For next Tuesday:
Target organisms and sizes
How to detect (fluorescence, polarization..)
Characteristics
Natural concentrations

JGB: John Ryan is a good resource for the above
Meet again in 1.5 weeks - March 19
Ask Dorota what organisms BOGS tracks; she's compiling a table

Ask Ryan and Chavez; what organisms would you look for with flow cytometer?

Denis and Tom to interview
\\

h2. 2/26/2013

&nbsp;Action items for next meeting

Contact Zhu about cell phone cytometer; latest developments, availability of device - Tom
Look at Zhu et al paper to determine feasibility of reproducing device - Denis
Consider potential embedded imaging intern project - Tom
Review capabilities of Sosik's Imaging Flow Cytobot - Jim

Note: Post-doc candidate Eric Rehm will visit MBARI on March 18-19

Let's explore possible Becton-Dickinson tour when Alex returns (she has several contacts there).

JGB: Cell phones for robotics are very interesting and promising - high capability, low-cost sensors, computing power
Post-doc Eric Rehm will visit on March 18-19

DK: Note that theoretical imaging limit is about 1 micron
DK: Variable bandpass filter via electronic control/piezo-electric control
JGB: Could pulse multiple frequencies on a given particle to measure multiple parameters

Could flow channel be designed to segregate/orient particles based on pressure gradient?

Flow "panel" rather than "stream"?

Investigate flow cytobot - what have they achieved?

Look at citations of Zhu et al:
Microfluidic diagnostics for the developing world:
[http://pubs.rsc.org/en/Content/ArticleLanding/2012/LC/C2LC90022J]

Millipore Scepter: $3.5K - gives similar data as LISST, which is much more expensive

Approaches:
Coulter
Imaging
Flow cytometer

Ask Zhu et al if device is available

Think about intern project

Denis will look into reproducing cell phone camera

Review flow cytobot work

Becton-Dickinson tour/contact?

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;&nbsp;

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Oceanographic cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

[Some non-oceanographic instruments|CytometerTech:Some non-oceanographic instruments]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

[Visit by Peter Lopez, 9/10/2014|CytometerTech:Visit by Peter Lopez 9-10-2014]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Howard Shapiro's web page|http://www.shapirolab.com/]

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles suspended in an electrolyte fluid, based on changing electrical properties. The technique does not rely on optical sources or sensors.The particles are pumped through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap. Variant techniques that utilize the Coulter principle include [Scanning ION Occlusion Sensing|http://en.wikipedia.org/wiki/Scanning_Ion_Occlusion_Sensing] and [CASY|http://en.wikipedia.org/wiki/CASY_cell_counting_technology].

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species

What MBARI science applications could benefit even with the above limitations?



The [Millipore Scepter|http://www.millipore.com/catalogue/module/c85360] hand-held Coulter counter for medical applications is available for $3.5K. Note that the channeled sampling tip apparently must be replaced after each sample. Here is a [blog|http://ucflow.blogspot.com/2011/10/counting-cells-with-emd-millipore.html] describing its use. (pointed out by Ken Johnson)]]></property>
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging \\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ??? \\ | Pros:&nbsp; \\
\- LISST-HOLO adapted to Dorado \\
\\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado \\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\

Trends:

Continue to decrease in size and energy consumption.

Use of smaller laser diodes/ solid state lasers.

Increase in detection and precision measurements

Lower cost especially for medical and bio sciences


&nbsp;
Challenges

Limited dynamic range vs. unpredictable wide range population composition

Trade-off between size range, concentration range, and throughput is really optimized for \*narrow range\* of those parameters

If detection volume is set to be able to resolve pulses from small particles, then statistics on larger cells with low concentration is becoming unacceptably slow

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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cell/ml \\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cell/ml \\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cell/ml \\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Washington coast 1998 _Pseudo-nitzschia_ bloom, 18000 cell/ml ([Ref|http://www.coexploration.org/habs/ppt/HAB_online99/sld007.htm]) \\
Washington coast 1997 Pseudo-nitzschia bloom, 13000 cell/ml ([Trainer et al 1998|http://www.ncbi.nlm.nih.gov/pubmed/10223627]) \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | From [Li et al (2009)|http://www.sciencemag.org/content/326/5952/539.full]: \\
Nanophytoplankton: 2-20 um, 450 cell/ml \\
Picophytoplankton: 0.5-2 um, 2500 cell/ml \\
Bacterioplankton:&nbsp; (size?), 2x10^5 cell/ml \\ | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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<property name="body"><![CDATA[1. If a cytometer were available on an AUV, how would you use it?

&nbsp; &nbsp;&nbsp; - what science question would you address? What paper would you write?

&nbsp;&nbsp;&nbsp;&nbsp; - what observational challenges do you face?


&nbsp;&nbsp;&nbsp;&nbsp; - coastal zones vs. open ocean, eddies, midwater vs. surface

2.&nbsp; Range of target organisms in mixed populations?

&nbsp; &nbsp;&nbsp; - size range

&nbsp;&nbsp;&nbsp;&nbsp; - concentration range

&nbsp;&nbsp;&nbsp;&nbsp; - methods of discrimination (optical, fluorescent properties, etc)


3. Which features are more or less important?

&nbsp;&nbsp;&nbsp;&nbsp; - value of imaging (on-demand, occasional, primary)

&nbsp;&nbsp;&nbsp;&nbsp; - value of physical sorting, pick-and-accumulate

&nbsp; &nbsp;&nbsp; - real time or post processing

&nbsp; &nbsp;&nbsp; - fluorescent labeling

&nbsp;&nbsp;&nbsp;&nbsp; - traditional gating vs. computational population ID (how to find rare and hidden populations)

4. Value of new features of integration on autonomous mobile platform?

&nbsp; &nbsp;&nbsp; - adaptive behavior, contextual sensors data

&nbsp; &nbsp;&nbsp; - real-time data for reconnaissance and surveying&nbsp;&nbsp;

&nbsp; &nbsp;&nbsp; - persistent presence, high-res
\\

5. Any new trends in cytometry, alternative approaches, etc or you aware of? ]]></property>
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Zhu et al [2013], Cost-effective and rapid blood analysis on a cell-phone, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594636/


Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

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Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
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\\  !figure.jpg|width=619,height=450!\\
\\

[Cytometer movie|http://pubs.acs.org/doi/suppl/10.1021/ac201587a/suppl_file/ac201587a_si_001.avi]

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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).
\\

The prototype CytoSub instrument was integrated with AutoSub by Alex Cunningham's team at the Environmental Optics Lab in Glasgow, in 2002 ([presentation|^Cunningham-CytoSub-slides.ppt], [paper1|^CytoSub-AutoSub.pdf], [paper2|^CytoSub-AutoSub-2.pdf]). The prototype has since been refined to today's commercial CytoSub, with smaller size, better performance, and imaging capability. But CytoSub hasn't been deployed on another AUV since AutoSub (according to CytoSense CEO George Dubelaar).&nbsp;

More technical info from CytoSense Dominic Stuart:

Flow Rates
Our sample pump has a range of 0.07ul/s up to 18ul/s or 0.1ul/s up to 30ul/s (depending on the tubing used in our sample pump). However the big speeds of 18 - 30ul/sec are usualy only used for flushing purposes or searching for very big organisms. The speed of the sample pump affects 2 things.

1. Particles/second
If you increase the sample pump speed, you will push more sample through the machine which means that the amount of particles per second increases. Our current system can process up to 5000 particles/second (small particles and a standard 3 detector system). If the concentration is too high, the sample pump speed needs to be lowered for the system to handle the datastream.

2. The Sample core
The sample pump pushes the sample into the CytoSense. When it reaches the injector, the sheath fluid "pulls" The sample fluid through the cuvette where the laser scans each particle one by one. The sample core is aligned by the sheath fluid. In the center of the sample core, the optics are the most sensitive and this is the "sweet-spot" where you would like the particles you are analyzing.

If you increase the sample pump speed, the sample core gets wider, this means that the position of the particles in the laser beam are not always optimal and you can notice shifts in your data for small particles (this is less important for big particles because a part of them will always be in the center).

3. Conclusion
It really comes down to:
a) What are the size ranges you are interested in? (bigger things, are generally less abundant and sample core width is also less important, and can be analyzed at higher flow speeds)
What we would suggest, if you would like to have a broad analysis of your sample, is to perform say 3 measurements at different speeds and trigger levels. This results in 3 data files where you get the best of both worlds (accurate data for your small particles and enough big particles). Roughly:

Sample speed 0.07 - 4 ul/sec - Picoplankton, bacteria
Sample speed 4 - 12 phytoplankton
Sample speed >12 big stuff (low abundant)


Digitizing and PMT Events
The electronics of the CytoSense digitize the data from the PMT's this works as follows:

1. Event
We specify an event as one single triggered data scan (across all channels) which is normally 1 particle unless the concentration is too high or the trigger level is too low. One event varies between 100 and 100K bytes depending on the configuration of the machine. Note that you get a datapoint every 0.5um on every channel.Examples for a 10 channel machine:
A particle of 2000um = 4000 bytes * 12 = 48000 bytes (46KB).
A particle of&nbsp;&nbsp;&nbsp; 10um =&nbsp;&nbsp;&nbsp;&nbsp; 20 bytes * 12 =&nbsp; 240 bytes.

2. Triggering
The trigger level and the trigger channel (PMT) can be set in software. The electronics will monitor the selected trigger channel and if the PMT output level is higher then the set trigger, the electronics will start to capture and digitize all channels (PMT's).&nbsp; The electronics capture the data at 4MHz, combined with the speed of the particles shooting through the laser (2m/s) this results in a datapoint for all channels every 0.5um.
Once the trigger level drops below the set trigger level, the electronics stop capturing and will consider that event as 1 particle.

3. Limits
The electronics can capture and process 5000 particles/second (small particles and a standard 3 detector system). If you have extra PMT's in your configuration, you generate more data with your machine and this number will be a bit less. However, we are currently working on new and quicker electronics\! The electronic limit of 5K events/sec is not the only limitation of the system. Because of how our triggering system works, there needs to be a "gap" between particles. The electronics need to detect the end of 1 particles before it can detect the beginning of the next particle. If you pump to many particles/second into the machine, the system will eventually not be able to process all the particles because they are so packed together that the system will interpret it as one big particle.

4. Conclusion
The maximum amount of partciles (PMT events) the system can process is 5000 events/second.

SUB Power consumption
The amount of power varies depending on the configuration of your instrument (how many pmt's,how many lasers, high power laser, imaging in flow etc etc. To give you a general idea, if you have a full option machine during a measurement the instrument will peak at \+/\- 60W. When the system is powered but idle, the system will draw \+/\- 20W. Between measurements the system can entered a preprogrammed deep sleep, during this phase the system will draw \+/\- 2W.

I ]]></property>
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<property name="body"><![CDATA[[Technology presentation|http://www.fluidimaging.com/imaging-particle-analysis-explained.htm] from Fluid Imaging

Note that Jim Bellingham has some connection at Fluid Imaging, may be able to borrow an instrument for Fall 2013 CANON provided there is MBARI science interest.
\\

[Submersible FlowCam page at FluidImaging.com|http://www.fluidimaging.com/products-submersible.htm]\\]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging) \\ || LISST 100X \\ || [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | nephelometer | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron (SeaFLow) \\
2-20 micron (SeaLabel) \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| Fluor/scatter excitation \\ | 635 nm laser \\ | 457 nm laser \\ | various lasers\\ | 532 nm laser \\ | 670 nm laser \\ | 670 nm laser\\ | | N.A. |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | | |
| | | | | | | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\
50 fps 512x512 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | | |
| realtime data processing \\ | | yes | | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | | |
| Notes | | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[Developed by Heidi Sosik and Robert Olson at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr = 4.17 x 10^-3 ml/sec. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "At 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | 2400 s \\ | 1200 s \\ | 240 s \\ |
| p=10^3 cell/ml \\ | 240 s \\ | 120 s \\ | 24 s \\ |
| p=10^4 cell/ml \\ | \\ | | |
| p=10^5 cell/ml \\ | \\ | | |
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<property name="body"><![CDATA[O'Reilly's notes:

Attendees: Jac Fought, Harry Nelson, Francisco Chavez, Denis Klimov, Tom O'Reilly

Action items
1. Chavez - compare Harry's FlowCam result to microscope analysis, sample 14213CO3
2. Nelson - work to get a FlowCam, training to MBARI for CANON (cruises on Sept 16-19, Sept 30, October 6)

Harry has done some analysis of samples provided by Francisco. Used 100x magnification - 25-30 micron image resolution. 100 micron pre-filter. Analyzed with Visual Spread Sheet.
Pseudo-nitzschia predominates.
Some image processing problems, due to "pilot error" by new technician.

Chavez processes a 25 ml sample thusly:
Fix, freeze sample
Operator counts cells under microscope - takes several hours
Operator enters data - takes about 2 hours
FlowCam processed Chavez 25 ml sample as follows:
Acquire images at 25 frames per second - actually images 3.189 ml of the total sample
About 1 hour to process 20 ml sample - automated aspect ratio computation
Can process large size fractions faster, about 1 minute per ml

How could analysis be done autonomously, e.g. on AUV?
Trigger imaging on fluorescence signal (chlorphyll or phycoerythrin), which is useful in oligotrophic water (too much signal in coastal water)
Will get one image frame per trigger
Note that laser excites entire camera fov

FC: We are thinking about a good MBARI FlowCam application
Replace microscope counts
Integrate with LRAUV for in situ analysis
Attach FlowCam to ship water intake, or Pennington's pumped profiler - autonomously id/count Pseudo N
Trigger ESP sample with FlowCam

Realtime image filtering
HN: Difficult to automatically ID all organisms; filtering helps. Alexandrium is difficult; small, spherical. Pseudo N is easier.
HN: Submersible FlowCam is designed for remote operation. Have run on cable for 56 days, \~10 minutes/hour duty cycle during dayl
JF: Submersible FlowCam memory is expandable. Expect to use 150 MByte per hour


Notes added by Klimov:

\- 100um Nitex Mesh was used for pre-filtering
\- Pseudo-nitzschia chains may stuck on filter and it explains why they were not visible in FlowCam data
\- "Segmentation Threshold" (to discriminate between "dark" and "bright" pixels) was apparently set too high, this chops up long cells into separate images
\- Fluorescence trigger mode, every frame is unique, 20 FPS
\- Stats for 1H run:
&nbsp;&nbsp;&nbsp; 150 Mb file&nbsp;&nbsp;&nbsp;
&nbsp;&nbsp;&nbsp; 93k frames total, 3.6k frames used.
&nbsp;&nbsp;&nbsp; 1.64 parts/ image.
&nbsp;&nbsp;&nbsp; 19.97 FPS
&nbsp;&nbsp;&nbsp; Intensity Mean: 179.90
&nbsp;&nbsp;&nbsp; Intensity Min: 161.77
&nbsp;&nbsp;&nbsp; Intensity Max: 183.05

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*O'Reilly's notes on 10 am meeting.*

Attendees: Heidi Sosik, Denis Klimov, Tom O'Reilly

Questions:
Plans for small/low-power instrument?
Can FCB/IFCB be deployed without power/data cable-to-shore?
HS: Working on "low-relief" IFCBT for deployment on Wave Glider, AUV, other platform
Current IFCB takes 30W power

Particle size range overlap of FCB and IFCB?
HS: Difficult; IFCB laser is optimized for microplankton - picoplankton requires higher-power laser. FCB is still original prototype (large) - no funding or plans to refine. CytoBuoy claims pico-micro capability.

Could you replace sheath fluid with virtual core technology, ala SeaFlow (Need to add position-sensitive detector(s))?
HS: Would be concerned about flow-cell cleanliness - core fluid keeps particles moving through flow cell. Very occassionally get dirt in cell - would this be a greater problem with SeaFlow/SeaLabel?

Processing:
HS: Several stages; detect particles (reject particle-free images regions). Edge detection, etc. Classification
Now using "random forest" approach instead of SVM (2007):
\- rf requires less tuning than svm
\- svm requires complete characterized dataset for error characterization; rf doesn't
\- both methods yield comparable accuracy

How long did the image-processing/classification procedures take per image? On what hardware?
HS: particle detection/empty-image rejection executes in situ on instrument's "Atom" processor. Shore-side workflow in realtime, posted on MVCO website ([http://ifcb-data.whoi.edu/])
HS: Image processing is more computationally intensive than classification
\\

*Klimov's notes from 10:00, 12:00, 16:00 meetings*

Principles of operation:
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; FlowCytobot / Imaging FlowCytobot sample path arranged in such a way as sample goes "down hill" due to plankton sinking.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Newer Imaging FlowCytobot (licensed to Mclane) is developed entirely at WHOI. McLane did some adaptations to simplify production. 8 inch diameter tube, 40 inch long. First unit built in August 2013.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5ml sip, then 20 minutes analyzing. This time can be reduced by sipping less, say 1ml then 4 min analyzing, but the period can not be much shorter due to time overhead (pump start/ stop etc) and required statistics.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; this design has emphasis on accurate statistics so flow and volume need to be precise, so syringe pump is used with defined volume.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Emphasis on "binning" to get particle statistics per "shot" and not as continuous measurement; so "binning" is ok here.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Also, accurate flow rate is required, due to separation of "trigger volume" and image acquisition volume within a sample cuvette, and fixed time delay between trigger and acquisition of the image. Image is acquired with 1 us light pulse from Xenon lamp.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid is preventing the contact between sample water and walls of the cuvette, minimizes chance of contamination and particles attachment to cuvette walls, very important feature.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid is recirculated by filtering sample + sheath by volumetric Fisher filter. Excess water is dumped into environment before filter. Filter lasts 6-8 month deployment easy.
&nbsp;
Use of Imaging FlowCytobot on a mobile platform:
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Configuration of the sample path dictates "vertical" position of the instrument so it operation in horizontal orientation could be problematic.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; For glider use, perhaps the Imaging FlowCytobot can be split into set of housings and then arrange them horizontally.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Suggestion: keep volume of those compartments relatively small (under several hundred mL) to avoid vehicle loss in case of flooding one compartment.
&nbsp;
&nbsp;
Difference between FlowCytobot and Imaging FlowCytobot:
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Particle ranges: FlowCytobot 1-15 um, Imaging FlowCytobot 5-200um
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Cuvettes have different geometries: FlowCytobot has smaller cylindrical flow cavity for tighter light collimation of laser, and Imaging FlowCytobot has "50 um sheet" of fluid optimized for imaging and larger laser beam for triggering
\-&nbsp;&nbsp;&nbsp; Light sources are optimized differently for smaller circular path, or wider flat path
&nbsp;]]></property>
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<property name="body"><![CDATA[Attendees: Johnson, Massion, Klimov, O'Reilly

KJ: Want to keep cost cheap, less than $5K; want low power, suitable for profiling float deployment



No moving parts
Micro-electrode array exposed to external flow
Could have programmable electrode spacing to vary sensitivity
Probably don't need concurrent CTD
Shape of electric field is complex

TO: Would standard calibration beads with known size distribution help?
How about adaptively driving which electrodes are paired as particle moves across surface?

Hope for 5-200 um range - size spectrum
Impedance spectroscopy]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
\\]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an overview of her Imaging Cytobot instrument. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of her Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ |  cells/particles > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of her Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the [2010 CANON sampling workshop??|^CANON Sampling Workshop Report.20Apr10.pdf], attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of her Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the [2010 CANON sampling workshop??|^CANON Sampling Workshop Report.20Apr10.pdf] ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], engineering report), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of her Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the [2010 CANON sampling workshop??|^CANON Sampling Workshop Report.20Apr10.pdf] ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of her Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument, applied to HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application to HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
\\]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf],\\
Sosik Cytobot presentation) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf][Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf][Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf][Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheetâ??|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf][Thyssen et al (2008)â|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheetâ??|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

[TEST link to external attachment: ASTEP_2011_v8.pdf]\\

[TEST link to this page's attachment|^FlowCAM_Spec_Sheet_200ppi-1.pdf]:&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf][Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

[TEST link to external attachment: ASTEP_2011_v8.pdf]\\

[TEST link to this page's attachment|^FlowCAM_Spec_Sheet_200ppi-1.pdf]:&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted)\\ \\ \\ \\]]></property>
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<property name="body"><![CDATA[[Submersible FlowCam page at fluidimaging.com|http://www.fluidimaging.com/products-submersible.htm]\\]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf][Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

[TEST link to external attachment: ASTEP_2011_v8.pdf]\\

[TEST link to this page's attachment|^FlowCAM_Spec_Sheet_200ppi-1.pdf]:&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [McLane-IFCB-Datasheet.pdf]\\ | [ASTEP_2011_v8.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | [specification sheet] \\ | [specification sheet]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [McLane-IFCB-Datasheet.pdf]\\ | [ASTEP_2011_v8.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | [specification sheet] \\ | [specification sheet]\\ |
\\

[ASTEP_2011_v8.pdf]\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [McLane-IFCB-Datasheet.pdf]\\ | [ASTEP_2011_v8.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | [specification sheet] \\ | [specification sheet]\\ |
\\

[TEST link to external attachment: ASTEP_2011_v8.pdf]\\

[TEST link to this page's attachment|^FlowCAM_Spec_Sheet_200ppi-1.pdf]:&nbsp;


h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet \\ | [ASTEP_2011_v8.pdf]\\ | specification sheet \\ | specification sheet \\ | specification sheet \\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

LISST Holo


[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet \\ | [ASTEP_2011_v8.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | specification sheet \\ | specification sheet \\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet \\ | [ASTEP_2011_v8.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | specification sheet \\ | [specification sheet]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [McLane-IFCB-Datasheet.pdf]\\ | [ASTEP_2011_v8.pdf]\\ | [Thyssen et al (2008)|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | specification sheet \\ | [specification sheet]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis. \\

Thyssen et al describe...\\]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ |  pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging \\
(includes chl, phyco fluor channesl) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging \\
(includes chl, phyco fluor channesl) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging \\
(includes chl, phyco fluor channesl) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [Submersible FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging \\
(includes chl, phyco fluor channesl) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging (includes chl fluor channel)\\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | imaging | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, flow \\ | flow \\ | imaging, flow \\ | | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[[Technology presentation|http://www.fluidimaging.com/imaging-particle-analysis-explained.htm] from Fluid Imaging


Note that Jim Bellingham has connection at FluidImaging, may be able to borrow an instrument for Fall 2013 CANON.
\\

[Submersible FlowCam page at FluidImaging.com|http://www.fluidimaging.com/products-submersible.htm]\\]]></property>
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<property name="body"><![CDATA[Note that Jim Bellingham has connection at FluidImaging, may be able to borrow an instrument for Fall 2013 CANON.\\

[Submersible FlowCam page at FluidImaging.com|http://www.fluidimaging.com/products-submersible.htm]\\]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging flow cytometer\\ | flow cytometer\\ | imaging flow cytometer\\ | | imaging cytometer\\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [specification sheet|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing (except LISST Holo) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | organisms > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | \\ | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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<property name="body"><![CDATA[[Digital holographic microscopy at Wikipedia|http://en.wikipedia.org/wiki/Digital_holographic_microscopy]

The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]; describes lightweight 2 kg version for arctic app. A version of this instrument is sold by [Resolution Optics|http://resolutionoptics.com/].
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-? \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm\\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg\\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-? \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 10 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru optical path \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru optical path \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru optical path \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[[Digital holographic microscopy at Wikipedia|http://en.wikipedia.org/wiki/Digital_holographic_microscopy]

The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]. A version of this instrument is sold by [Resolution Optics|http://resolutionoptics.com/].\\]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Adaptability || Status || Adaptability \\ ||
| \\ \\
Flowcytometry in a flow with optical detection\\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC)\\
&nbsp;&nbsp; - Optical Absorption\\
&nbsp;&nbsp; - Fluorescence\\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD)\\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter. SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence&nbsp; \\ | "traditional" flowcytometry and most common for bench top instruments. | |
| Imaging flow cytometry \\
o&nbsp;&nbsp;&nbsp;&nbsp; Configuration of the channel: round or flat \\
o&nbsp;&nbsp;&nbsp;&nbsp; Primary imaging system, vs. "image on trigger". \\
o&nbsp;&nbsp;&nbsp;&nbsp; Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | | |
| Bulk optical properties \\
o&nbsp;&nbsp;&nbsp;&nbsp; Size-dependent diffraction \\
o&nbsp;&nbsp;&nbsp;&nbsp; Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | | | |
| Electric impedance detection. \\
o&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry. Proxy to membrane properties, mobility, cells size \\
o&nbsp;&nbsp;&nbsp;&nbsp; Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Adaptability || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter. \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence&nbsp; \\ | "traditional" flowcytometry and most common for bench top instruments. | |
| Imaging flow cytometry \\
o&nbsp;&nbsp;&nbsp;&nbsp; Configuration of the channel: round or flat \\
o&nbsp;&nbsp;&nbsp;&nbsp; Primary imaging system, vs. "image on trigger". \\
o&nbsp;&nbsp;&nbsp;&nbsp; Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | | |
| Bulk optical properties \\
o&nbsp;&nbsp;&nbsp;&nbsp; Size-dependent diffraction \\
o&nbsp;&nbsp;&nbsp;&nbsp; Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | | | |
| Electric impedance detection. \\
o&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry. Proxy to membrane properties, mobility, cells size \\
o&nbsp;&nbsp;&nbsp;&nbsp; Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)

fluorescent labeling

isotope labeling]]></property>
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<property name="body"><![CDATA[Categories, methods\\
|| Method || Adaptability || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection\\
o&nbsp;&nbsp;&nbsp;&nbsp; Optical Forward Scatter or (FSC). \\
 \\
o&nbsp;&nbsp;&nbsp;&nbsp; Optical Side Scatter or (SSC)\\
o&nbsp;&nbsp;&nbsp;&nbsp; Optical Absorption\\
o&nbsp;&nbsp;&nbsp;&nbsp; Fluorescence\\
o&nbsp;&nbsp;&nbsp;&nbsp; Multispectral with single detector: color-space-time coding (UCSD) | FSC seems to be most efficient for optical power utilization and most common "signature" parameter. \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret.\\
Fluorescence&nbsp; \\ | "traditional" flowcytometry and most common for bench top instruments. | |
| Imaging flow cytometry\\
o&nbsp;&nbsp;&nbsp;&nbsp; Configuration of the channel: round or flat\\
o&nbsp;&nbsp;&nbsp;&nbsp; Primary imaging system, vs. "image on trigger". \\
o&nbsp;&nbsp;&nbsp;&nbsp; Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | | |
| Bulk optical properties\\
o&nbsp;&nbsp;&nbsp;&nbsp; Size-dependent diffraction\\
o&nbsp;&nbsp;&nbsp;&nbsp; Holographic reconstruction | | | |
| Mass-spectrometry cytometry\\ | | | |
| Microfluidic cytometry | | | |
| Electric impedance detection. \\
o&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry. Proxy to membrane properties, mobility, cells size\\
o&nbsp;&nbsp;&nbsp;&nbsp; Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros: \\
 \\
Cons: \\
\- usually bulky and complex instruments requiring multiple detectors and alignment \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes\\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | | |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | Cons: how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\]]></property>
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros: \\
\\
Cons: \\
\- usually bulky and complex instruments requiring multiple detectors and alignment \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\ | Pros: relatively wide detection size range\\
Cons:&nbsp; \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence\\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | Cons: how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\]]></property>
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | |
| Imaging flow cytometry\\
&nbsp;&nbsp; - Configuration of the channel: round or flat\\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | | |
| Bulk optical properties\\
Size-dependent diffraction\\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | | | |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size\\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\]]></property>
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | | |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | Cons: how to maintain/replace microfluidic component\\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, less housing? \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | 8.3 mm^3/s | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s)\\
 WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s)\\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer\\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\
&nbsp;&nbsp;&nbsp; - Holographic reconstruction | | Pros: \\
\- optically, this is fast acquisition method \\ \\
Cons:&nbsp;\\
\- can be computationally intensive\\
\- bulk optical properties measured as oppose to individual cells\\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | |
| realtime data processing \\ | | yes | | | not implemented | |
| cost | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. | Pros: \\
\- wider dynamic range\\
\- better resolves larger cells with complex morphology\\ \\
Cons:&nbsp;\\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um\\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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\\
|| Method || Notes || Status || Value/ Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros: \\
\- established method\\
\- seems to be best for taxonomy (with fluorescence) \\
\\
Cons: \\
\- usually bulky and complex instruments requiring multiple detectors and alignment \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance\\
\\
Cons:&nbsp; \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | Cons: how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Status || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros: \\
\\
Cons: \\
\- usually bulky and complex instruments requiring multiple detectors and alignment \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\ | Pros: \\
\- relatively wide detection size range\\
\- relatively simple fluid handling \\
Cons:&nbsp; \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | Cons: how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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\\
|| Method || Notes || Status || Applicability\\ ||  Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros:\\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
&nbsp;\\ | Pros: \\
\\
Cons: \\
\- usually bulky and complex instruments requiring multiple detectors and alignment \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\ | | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons:\\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | | |
| Mass-spectrometry cytometry \\ | | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | | |
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Status || Value/ Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\\
Cons: \\
\- usually bulky and complex instruments requiring multiple detectors and alignment \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons:&nbsp; \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
 \\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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\\
|| Method || Notes || Status || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\ | "Traditional" flowcytometry and most common for bench top instruments. | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\\
\- down to sub um size range \\ \\
Cons:&nbsp;\\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes&nbsp; \\
 \\ | Pros: \\
\\
Cons: \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\ | | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | | |
| Mass-spectrometry cytometry \\ | | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\ | Emerging technology; attempt to reduce size, cost of traditional flow cytometer; and also to simplify maintenance or confine the fluid handle for toxic/ biohazardous specimens \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | | |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range\\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. | | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes\\
\- hard to interpret data for larger cells (> 50um) with complex morphology\\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow)\\
\- CytoSub can propable be integrated to Dorado \\
 \\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. | | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Bulk optical properties \\
Size-dependent diffraction \\
Holographic reconstruction | | | |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | >100 micron\\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | 10^6 particles/m^3 = 10^3 particles/liter\\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview and comparizon]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]


Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | >100 micron \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | 10^6 particles/m^3 = 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | http://www.brooke-ocean.com/lopc.html | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging\\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ???\\ | Pros:&nbsp;\\
\- LISST-HOLO adapted to Dorado\\
 \\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado\\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging \\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ??? \\ | Pros:&nbsp; \\
\- LISST-HOLO adapted to Dorado \\
\\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado \\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://iod.ucsd.edu/gatekeeper/documents/herman_et_al_04_lopc_jpr.pdf?]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging \\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ??? \\ | Pros:&nbsp; \\
\- LISST-HOLO adapted to Dorado \\
\\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado \\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\

Challenges

Limited dynamic range vs. unpredictable wide range population composition

Trade-off between size range, concentration range, and throughput is really optimized for \*narrow range\* of those parameters

If detection volume is set to be able to resolve pulses from small particles, then statistics on larger cells with low concentration is becoming unacceptably slow

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | Herman et al (2008)\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [iod.ucsd.edu/gatekeeper/documents/herman_et_al_04_lopc_jpr.pdf?]\\
[http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|iod.ucsd.edu/gatekeeper/documents/herman_et_al_04_lopc_jpr.pdf?] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm\\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse\\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | >100 micron \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | >100 micron \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg\\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W\\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meters\\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | >100 micron \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV\\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging \\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ??? \\ | Pros:&nbsp; \\
\- LISST-HOLO adapted to Dorado \\
\\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado \\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\

Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | | | |
| Physical volume vs. detectable volume ("virtual core") | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | | | |
| Physical volume vs. detectable volume ("virtual core")\\
Sheath fluid, vs. undiluted sample | | | |
| Calibration: \\
&nbsp;\- fluorescent and calibration bits. \\ | | | |
| Ability to re-process primary data. | | | |
| Cell sorting, actively separate and isolate particles having specified properties. 2011, up to 6-way sorting. \\
Mechanical sorting into "catcher tube". Enclosed path, one population.\\
Electrostatic deflection | | | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow\\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling\\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| | | | |
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | | | |
| Physical volume vs. detectable volume ("virtual core") | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
\\]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging \\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ??? \\ | Pros:&nbsp; \\
\- LISST-HOLO adapted to Dorado \\
\\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado \\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\

Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | | | |
| Physical volume vs. detectable volume ("virtual core") | | | |
| | | | |
| | | | |
| | | | |
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview and comparizon - 1]&nbsp;

[Technologies overview - 2]

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview and comparizon - 1]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]


Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Categories, methods
\\
|| Method || Notes || Applicability \\ || Adaptability \\ ||
| Flowcytometry in a flow with optical detection \\
&nbsp;&nbsp; - Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization. \\
&nbsp;&nbsp; - Optical Side Scatter or (SSC) \\
&nbsp;&nbsp; - Optical Absorption \\
&nbsp;&nbsp; - Fluorescence \\
&nbsp;&nbsp; - Multispectral with single detector: color-space-time coding (UCSD) \\ | FSC seems to be most efficient for optical power utilization and most common "signature" parameter, proxy to the organism biomass \\
SSC is quite dependent on the size and configuration of the scattering organism and if collected at one angle only, can be hard to interpret. \\
Fluorescence is common for taxonomy; signal levels are much lower, and usually require calibration with fluorescent bits. \\
"Traditional" flowcytometry and most common for bench top instruments.&nbsp; \\ | Pros: \\
\- established method \\
\- seems to be best for taxonomy (with fluorescence) \\
\- resolution and ID size range down to sub um \\  \\
Cons:&nbsp; \\
\- size range is relatively narrow \\
\- method of counting cells is optimized for relatively narrow range of target organism sizes \\
\- hard to interpret data for larger cells (> 50um) with complex morphology \\ | Pros: \\
\- probably can be adapted in a reasonable size / power configuration (miniaturization of a Seaflow) \\
\- CytoSub can propable be integrated to Dorado \\
\\
\\
Cons: \\
\- high cost \\
\- usually bulky and complex instruments \\
\- requiring multiple detectors and alignment \\
\- miniaturized Seaflow must compromise on power and sensitivity, and would have even narrower dynamic range \\ |
| Imaging flow cytometry \\
&nbsp;&nbsp; - Configuration of the channel: round or flat \\
&nbsp;&nbsp; - Primary imaging system, vs. "image on trigger". \\
&nbsp;&nbsp; - Combination with adherent cytometry: Celico (Cyntelect, purchased by Brooks Automation) | Commercial imaging flow cytometers seems to be oriented for oceanographic/ environmental markets. \\
"Image on trigger" helps to identify larger cells with complex morphology as add-on to "traditional" cytometer \\ | Pros: \\
\- wider dynamic range \\
\- better resolves larger cells with complex morphology \\  \\
Cons:&nbsp; \\
\- fundamental limit on low side of dynamic range; optical resolution > 1-2 um, ID limit is > 5-10 um \\ | Pros: \\
\- relatively wide detection size range \\
\- relatively simple fluid handling/ maintenance \\
\\
Cons: \\
\- require processing power; \\
\- training/ image database; \\
\- harder to implement fluorescence \\ |
| Holographic Imaging \\ | SHM, Submersible Holographic Microscope (Resolution Optics) \\ | Pros: ??? \\ | Pros:&nbsp; \\
\- LISST-HOLO adapted to Dorado \\
\\ |
| Bulk optical properties \\
&nbsp;&nbsp;&nbsp; - Size-dependent diffraction \\ | | Pros: \\
\- optically, this is fast acquisition method \\  \\
Cons:&nbsp; \\
\- can be computationally intensive \\
\- bulk optical properties measured as oppose to individual cells \\
\- set of assumption on optical properties/ shapes of cells&nbsp; \\ | Pros: \\
\-&nbsp; and LISST-100 adapted to Dorado \\ |
| Mass-spectrometry cytometry \\ | | | |
| Microfluidic cytometry | Traditional flow cytometry with cell counting/, with the exception that sample handling is performed in a microfluidic structure usually made of silicone rubber. \\
Emerging technology; attempt to reduce size, cost of traditional flow  cytometer; and also to simplify maintenance or confine the fluid handle  for toxic/ biohazardous specimens&nbsp; \\ | | Pros: \\
\- confined fluid path \\
\- simplified integration of solid-state detectors and light sources \\
\\
Cons: \\
\- how to maintain/replace microfluidic component \\ |
| Adherent cell cytometry. \\
&nbsp;&nbsp; - Proxy to membrane properties, mobility, cells size \\
&nbsp;&nbsp; - Resistance in a micro channel. Coulter counter, and proxy to cell volume | | | |
\\

Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic)\\
&nbsp;\- Micro fluidics, microchip. Fishman-R | | | |
| Physical volume vs. detectable volume ("virtual core") | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
| | | | |
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | >100 micron \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [http://www.brooke-ocean.com/lopc.html] | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement \\
\\  \\
Catastrophic failure (flooding) \\
&nbsp;\- flow path needs to be enclosed&nbsp; \\
\\ |
| Physical volume vs. detectable volume ("virtual core") - SeaFlow, Sealable \\ | Ability to re-process primary data. | \\ | Pros: \\
&nbsp;\- Allows processing of undiluted sample \\
&nbsp;\- no need for sheath fluid \\
\\
Cons:&nbsp; \\
&nbsp;\- virtual core is harder to characterize then physical volume \\ |
| Sheath fluid, vs. undiluted sample | | | |
| fluorescent and calibration bits. \\ | Used for calibration on some (most) benchtop flowcytometers | | Cons: \\
&nbsp;\- hard to implement in "in situ" instrument \\ |
| Cell sorting: \\
&nbsp; - Mechanical sorting into "catcher tube". Enclosed path, one population. \\
\\
&nbsp;\- Electrostatic deflection | actively separate and isolate particles having specified properties. | seem to be complex to implement and currently does not required \\ | |
| Focusing: \\
&nbsp; - Hydrodynamic focusing: coaxial laminar flow \\
&nbsp;\- Acoustic focusing (Ward) | This is physical sample focusing\\ | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement \\
\\  \\
Catastrophic failure (flooding) \\
&nbsp;\- flow path needs to be enclosed&nbsp; \\
\\ |
| Physical volume vs. detectable volume ("virtual core") - SeaFlow, Sealable \\ | Ability to re-process primary data. | \\ | Pros: \\
&nbsp;\- Allows processing of undiluted sample \\
&nbsp;\- no need for sheath fluid \\
\\
Cons:&nbsp; \\
&nbsp;\- virtual core is harder to characterize then physical volume \\ |
| Sheath fluid, vs. undiluted sample | | | |
| fluorescent and calibration bits. \\ | Used for calibration on some (most) benchtop flowcytometers | | Cons: \\
&nbsp;\- hard to implement in "in situ" instrument \\ |
| Cell sorting: \\
&nbsp; - Mechanical sorting into "catcher tube". Enclosed path, one population. \\
\\
&nbsp;\- Electrostatic deflection | actively separate and isolate particles having specified properties. | seem to be complex to implement and currently does not required\\ | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow \\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement \\
\\  \\
Catastrophic failure (flooding) \\
&nbsp;\- flow path needs to be enclosed&nbsp; \\
\\ |
| Physical volume vs. detectable volume ("virtual core") - SeaFlow, Sealable \\ | Ability to re-process primary data. | \\ | Pros: \\
&nbsp;\- Allows processing of undiluted sample \\
&nbsp;\- no need for sheath fluid \\
\\
Cons:&nbsp; \\
&nbsp;\- virtual core is harder to characterize then physical volume \\ |
| Sheath fluid, vs. undiluted sample | | | |
| fluorescent and calibration bits. \\ | Used for calibration on some (most) benchtop flowcytometers | | Cons: \\
&nbsp;\- hard to implement in "in situ" instrument \\ |
| Cell sorting: \\
&nbsp; - Mechanical sorting into "catcher tube". Enclosed path, one population. \\
\\
&nbsp;\- Electrostatic deflection | actively separate and isolate particles having specified properties. | seem to be complex to implement and currently does not required \\ | |
| Focusing: \\
\\
&nbsp;\- Hydrodynamic focusing: coaxial laminar flow \\
&nbsp;\- Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement \\
\\  \\
Catastrophic failure (flooding) \\
&nbsp;\- flow path needs to be enclosed&nbsp; \\
\\ |
| Physical volume vs. detectable volume ("virtual core") - SeaFlow, Sealable \\ | Ability to re-process primary data. | \\ | Pros: \\
Allows processing of undiluted sample\\ |
| Sheath fluid, vs. undiluted sample | | | |
| Calibration: \\
&nbsp;\- fluorescent and calibration bits. \\ | | | |
| Ability to re-process primary data. | | | |
| Cell sorting, actively separate and isolate particles having specified properties. 2011, up to 6-way sorting. \\
Mechanical sorting into "catcher tube". Enclosed path, one population. \\
Electrostatic deflection | | | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow \\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement \\
\\  \\
Catastrophic failure (flooding) \\
&nbsp;\- flow path needs to be enclosed&nbsp; \\
\\ |
| Physical volume vs. detectable volume ("virtual core") - SeaFlow, Sealable \\ | Ability to re-process primary data. | \\ | Pros: \\
&nbsp;\- Allows processing of undiluted sample\\
&nbsp;\- no need for sheath fluid \\
 \\
Cons:&nbsp; \\
&nbsp;\- virtual core is harder to characterize then physical volume \\ |
| Sheath fluid, vs. undiluted sample | | | |
|  fluorescent and calibration bits. \\ | Used for calibration on some (most) benchtop flowcytometers | | Cons:\\
&nbsp;\- hard to implement in "in situ" instrument\\ |
| Cell sorting, actively separate and isolate particles having specified properties. 2011, up to 6-way sorting. \\
Mechanical sorting into "catcher tube". Enclosed path, one population. \\
Electrostatic deflection | | | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow \\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | No\\ | Maintenance: \\ |
| Physical volume vs. detectable volume ("virtual core") \\
Sheath fluid, vs. undiluted sample | | | |
| Calibration: \\
&nbsp;\- fluorescent and calibration bits. \\ | | | |
| Ability to re-process primary data. | | | |
| Cell sorting, actively separate and isolate particles having specified properties. 2011, up to 6-way sorting. \\
Mechanical sorting into "catcher tube". Enclosed path, one population. \\
Electrostatic deflection | | | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow \\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | Most bench top flowcytometers use open space path. Flowcytometers for toxic and hazardous substances, and oceanographic use typically enclosed path. \\ | Design of flow path may affect optical performance, sensitivity \\ | Maintenance: \\
&nbsp;\- flow path needs to be easily accessible for cleaning or replacement\\
 \\ \\
Catastrophic failure (flooding) \\
&nbsp;\- flow path needs to be enclosed&nbsp; \\
 \\ |
| Physical volume vs. detectable volume ("virtual core") \\
Sheath fluid, vs. undiluted sample | | | |
| Calibration: \\
&nbsp;\- fluorescent and calibration bits. \\ | | | |
| Ability to re-process primary data. | | | |
| Cell sorting, actively separate and isolate particles having specified properties. 2011, up to 6-way sorting. \\
Mechanical sorting into "catcher tube". Enclosed path, one population. \\
Electrostatic deflection | | | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow \\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software \\
&nbsp;\- Gating and analyzing software \\
&nbsp;\- Population identification using computational methods (rare and hidden populations) \\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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<property name="body"><![CDATA[Options, features
|| Method \\ || Notes \\ || Applicability \\ || Adaptability ||
| Flow path: \\
&nbsp;\- Open space \\
&nbsp;\- flow cell (quartz, plastic) \\
&nbsp;\- Micro fluidics, microchip. Fishman-R | | | |
| Physical volume vs. detectable volume ("virtual core") \\
Sheath fluid, vs. undiluted sample | | | |
| Calibration: \\
&nbsp;\- fluorescent and calibration bits. \\ | | | |
| Ability to re-process primary data. | | | |
| Cell sorting, actively separate and isolate particles having specified properties. 2011, up to 6-way sorting. \\
Mechanical sorting into "catcher tube". Enclosed path, one population. \\
Electrostatic deflection | | | |
| Focusing: \\
Hydrodynamic focusing: coaxial laminar flow \\
Acoustic focusing (Ward) | | | |
| Real time or post processing, or both | | | |
| Fluorescent labeling \\
Staining (Worden - bacterial communities)Isotope labeling | | | |
| Processing and software\\
&nbsp;\- Gating and analyzing software\\
&nbsp;\- Population identification using computational methods (rare and hidden populations)\\
&nbsp;\- Population identification (Worden): trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach | | | |
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | records shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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|| Parameter \\ || Notes \\ || Range \\ || ||
| Cell size range, um\\
&nbsp;\- detectable&nbsp;\\
&nbsp;\- filtration \\ | | | |
| Concentration range, cells/mL | | | |
| Detection volume, uL, mL | | | |
| Flow rate, mL/min, uL/min\\
&nbsp;\- per channel cross section\\
 \\
&nbsp;\- per detection cross-section\\ | | | |
| Throughput range, counts/sec. 2E5 (LLNL) | | | |
| Overall energy efficiency; J/count | | | |
| Statistics and acceptable errors | | | |
| | | | |
| | | | |
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth.
\\]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]


[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado


Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth.
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The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with 5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf].
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The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters is described by [Bochdansky et al|^DeepDIHM.pdf].
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The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf].
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The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]\\]]></property>
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The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns)\\]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado\\ | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ | pulse \\ | |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-? \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter\\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging\\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-?\\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-? \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | ~5 W\\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

Discussion with Jared Swalwell
\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-? \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration\\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-? \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC\\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet \\ | CytoAUV proposal \\ | specification sheet \\ | specification sheet \\ | specification sheet \\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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\\
\\
|| || Imaging Flow Cytobot \\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Microscope \\ ||
| Responsible person\\ | O'Reilly | Swalwell | Hamilton | Ryan | Klimov |
| Sample integration time \\ | | continuous\\ | | | continuous |
| | | | | | |
| | | | | | |
| | | | | | |
| | | | | | |
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<property name="body"><![CDATA[\\ \\ \\
|| || Imaging Flow Cytobot\\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Holographic Microscope \\ ||
| Sample integration time\\ | | | | | |
| | | | | | |
| | | | | | |
| | | | | | |
| | | | | | |
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\\
\\
|| || Imaging Flow Cytobot \\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Microscope \\ ||
| Responsible person \\ | O'Reilly | Swalwell | Hamilton | Ryan | Klimov |
| Sampling interval \\ | One 5 ml sample per 20 min. \\ | continuous \\ | | | continuous |
| Pump rate \\ | 0.25 ml/min \\ | 15 ml/min\\ | | | N/A? |
| | | | | | |
| | | | | | |
| | | | | | |
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\\
\\
|| || Imaging Flow Cytobot \\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Microscope \\ ||
| Responsible person \\ | O'Reilly | Swalwell | Hamilton | Ryan | Klimov |
| Sample rate \\ | 5 ml sample per 20 min.\\ | continuous \\ | | | continuous |
| Pump rate\\ | 0.25 ml/min\\ | | | | |
| | | | | | |
| | | | | | |
| | | | | | |
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\\
\\
|| || Imaging Flow Cytobot \\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Microscope \\ ||
| Responsible person \\ | O'Reilly | Swalwell | Hamilton | Ryan | Klimov |
| Sampling interval \\ | One 5 ml sample per 20 min. \\ | continuous \\ | | | continuous |
| Sample intake\\ | syringe pump\\ | gear pump\\ | | | open sample volume\\ |
| Pump rate \\ | 0.25 ml/min \\ | 15 ml/min \\ | | | N/A? |
| | | | | | |
| | | | | | |
| | | | | | |
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\\
\\
|| || Imaging Flow Cytobot \\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Microscope \\ ||
| Responsible person \\ | O'Reilly | Swalwell | Hamilton | Ryan | Klimov |
| Sampling interval \\ | One 5 ml sample per 20 min. \\ | continuous \\ | | | continuous |
| Sample intake \\ | syringe pump, 0.25 ml/min \\ | gear pump, 15 ml/min \\ | | | open sample volume \\ |
| | | | | | |
| | | | | | |
| | | | | | |
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<property name="body"><![CDATA[\\
\\
\\
|| || Imaging Flow Cytobot \\ || Seaflow \\ || Flowcam \\ || LISST Holo \\ || Submersible Microscope \\ ||
| Responsible person \\ | O'Reilly | Swalwell | Hamilton | Ryan | Klimov |
| Sampling interval \\ | One 5 ml sample per 20 min. \\ | continuous \\ | | | continuous |
| Sample intake \\ | syringe pump, 0.25 ml/min \\ | gear pump, 15 ml/min \\ | | | open sample volume \\ |
| Calibration | | | | | |
| | | | | | |
| | | | | | |
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<property name="body"><![CDATA[Please see https://docs.google.com/document/d/1OBrgAMAs3Zy2SfnxJySLtFnk3qF2xgU6pdAt2H8u4WM/edit
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<property name="body"><![CDATA[Categories, methods
* Flowcytometry in a flow with optical detection

** Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization.
** Optical Side Scatter or (SSC)
** Optical Absorption
* Fluorescence
* Imaging flow cytometry
* Mass-spectrometry cytometry
* Microfluidic cytometry
* Adherent cell cytometry]]></property>
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<property name="body"><![CDATA[\\

A flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers "high-throughput" (for a large number of cells) automated quantification of set parameters\\

Categories, methods

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Flowcytometry in a flow with optical detection

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization.

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Side Scatter or (SSC)

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Absorption

o&nbsp;&nbsp;&nbsp;&nbsp; Fluorescence

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imaging flow cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mass-spectrometry cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Microfluidic cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry\\

Specifications and performance

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Detection size range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Concentration range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Throughput\\

Options

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid, vs. undiluted sample

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Real time or post processing, or both

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Fluorescent labeling

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Isotope labeling \\

Processing and software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Gating and analyzing software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Population identification using computational methods (rare and hidden populations)\\

Trends:

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Continue to decrease in size and energy consumption

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Increase in detection and precision measurements

Lower cost especially for medical and biosciences
\\]]></property>
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<property name="body"><![CDATA[\\

A flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers "high-throughput" (for a large number of cells) automated quantification of set parameters
\\

Categories, methods

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Flowcytometry in a flow with optical detectiono&nbsp;&nbsp;&nbsp;&nbsp; Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization.o&nbsp;&nbsp;&nbsp;&nbsp; Optical Side Scatter or (SSC)

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Absorption

o&nbsp;&nbsp;&nbsp;&nbsp; Fluorescence
\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imaging flow cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mass-spectrometry cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Microfluidic cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry
\\

Specifications and performance

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Detection size range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Concentration range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Throughput
\\

Options

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid, vs. undiluted sample

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Real time or post processing, or both

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Fluorescent labeling

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Isotope labeling
\\

Processing and software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Gating and analyzing software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Population identification using computational methods (rare and hidden populations)
\\

Trends:

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Continue to decrease in size and energy consumption

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Increase in detection and precision measurements

Lower cost especially for medical and biosciences
\\]]></property>
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<property name="body"><![CDATA[A flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers "high-throughput" (for a large number of cells) automated quantification of set parameters\\

Categories, methods

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Flowcytometry in a flow with optical detection

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization.

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Side Scatter or (SSC)

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Absorption

o&nbsp;&nbsp;&nbsp;&nbsp; Fluorescence

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imaging flow cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mass-spectrometry cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Microfluidic cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry\\

Specifications and performance

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Detection size range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Concentration range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Throughput\\

Options

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid, vs. undiluted sample

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Real time or post processing, or both

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Fluorescent labeling

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Isotope labeling \\

Processing and software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Gating and analyzing software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Population identification using computational methods (rare and hidden populations)\\

Trends:

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Continue to decrease in size and energy consumption

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Increase in detection and precision measurements

Lower cost especially for medical and biosciences
\\]]></property>
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<property name="body"><![CDATA[A flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers "high-throughput" (for a large number of cells) automated quantification of set parameters\\

Categories, methods
* Flowcytometry in a flow with optical detection
* Optical Forward Scatter or (FSC). Seems to be most efficient for optical power utilization.
* Optical Side Scatter or (SSC)

o&nbsp;&nbsp;&nbsp;&nbsp; Optical Absorption

o&nbsp;&nbsp;&nbsp;&nbsp; Fluorescence

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imaging flow cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mass-spectrometry cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Microfluidic cytometry

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Adherent cell cytometry\\

Specifications and performance

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Detection size range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Concentration range

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Throughput\\

Options

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid, vs. undiluted sample

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Real time or post processing, or both

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Fluorescent labeling

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Isotope labeling \\

Processing and software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Gating and analyzing software

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Population identification using computational methods (rare and hidden populations)\\

Trends:

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Continue to decrease in size and energy consumption

\- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Increase in detection and precision measurements

Lower cost especially for medical and biosciences
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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)

fluorescent labeling

isotope labeling

\\
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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)

fluorescent labeling

isotope labeling]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron (SeaFLow)\\
2-20 micron (SeaLabel) \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\
50 fps 512x512 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview and comparizon]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h3.

*{+}Bellingham's notes{+}*

Notes from telecon with the FlowCAM folks:

Francisco:

160-170 codes for organisms quantified in 'standard' water analysis.&nbsp; larger by microscopy, smaller by flow cytometry, some \~um size in both.

Samples 250 ml in size.

Preserve material with glutaraldehyde, filter 25 ml of fluid.
\- microscopy done from filter
\- some fluid frozen w liquid N2 for cytometer (sent to U of Hawaii)

Catalog organisms to 200 um in size

Lots of small stuff - use staining to see bacteria, etc.

For the microscopy - use different magnifications and look over different areas

Harry:

We would probably use 10x objective for 100x magnification over 100um couvette (?) w lower limit of about 10um critter.

4x objective has lower effective size resolution of 40um.

Can use 20x objective w 50um couvette but 'takes a while'

Harry will send us all some sample images of organisms at the various resolutions.

User builds their own library, does not come with library.&nbsp; Library is used for classification.&nbsp; Have taxonomic photos, but not a library.

How many entries does it need?&nbsp; Depends.

Three step process - build a library, build a filter, build a template from the filters.&nbsp; Is dynamic - can add and subtract from them.&nbsp; Use the filter iteratively (first pass for organism 1, then for organism 2, etc.).

Could build some libraries ahead of time.

Chavez:

Can we also get size distribution of what is in sample?

Harry:

Yes, that just comes from pixels.&nbsp; Easily done.&nbsp; Can also use fluorescence, but if the sample is really concentrated then several organisms might be in field of view.

1/4 ml/min volumetric flow rate for 100 um couvette.

Outcome of&nbsp; the meeting is that Francisco sent them some preserved material.&nbsp; They are running it this week.&nbsp; We are going to get a copy of their software and work on developing a library for the resulting images, and use it to develop a classifier for the remainder of the data....

*{+}Additional notes from Klimov:+*

10x objective, 100x magnification, 10-20um resolved microorganisms, 100um flow cell. This is a most common configuration.
4x objective, 40x magnification, 25-30um resolved microorganisms, 200um flow cell.
25x objective, 250x magnification, 50um flow cell. For highest resolution but also slowest pumping rate.

It was not clear what is the actual optical resolution of the system with say 10x objective. It should be higher then specified resolved microorganism size, perhaps 1-2 um.
Harry said "10 um" is "many pixels", as can be seen in "sample pictures".

&nbsp;
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<property name="body"><![CDATA[h3.


h3. Bellingham's notes

Notes from telecon with the FlowCAM folks:

Francisco:

160-170 codes for organisms quantified in 'standard' water analysis.&nbsp; larger by microscopy, smaller by flow cytometry, some \~um size in both.

Samples 250 ml in size.

Preserve material with glutaraldehyde, filter 25 ml of fluid.
\- microscopy done from filter
\- some fluid frozen w liquid N2 for cytometer (sent to U of Hawaii)

Catalog organisms to 200 um in size

Lots of small stuff - use staining to see bacteria, etc.

For the microscopy - use different magnifications and look over different areas

Harry:

We would probably use 10x objective for 100x magnification over 100um couvette (?) w lower limit of about 10um critter.

4x objective has lower effective size resolution of 40um.

Can use 20x objective w 50um couvette but 'takes a while'

Harry will send us all some sample images of organisms at the various resolutions.

User builds their own library, does not come with library.&nbsp; Library is used for classification.&nbsp; Have taxonomic photos, but not a library.

How many entries does it need?&nbsp; Depends.

Three step process - build a library, build a filter, build a template from the filters.&nbsp; Is dynamic - can add and subtract from them.&nbsp; Use the filter iteratively (first pass for organism 1, then for organism 2, etc.).

Could build some libraries ahead of time.

Chavez:

Can we also get size distribution of what is in sample?

Harry:

Yes, that just comes from pixels.&nbsp; Easily done.&nbsp; Can also use fluorescence, but if the sample is really concentrated then several organisms might be in field of view.

1/4 ml/min volumetric flow rate for 100 um couvette.

Outcome of&nbsp; the meeting is that Francisco sent them some preserved material.&nbsp; They are running it this week.&nbsp; We are going to get a copy of their software and work on developing a library for the resulting images, and use it to develop a classifier for the remainder of the data....

*{+}Additional notes from Klimov:+*

10x objective, 100x magnification, 10-20um resolved microorganisms, 100um flow cell. This is a most common configuration.
4x objective, 40x magnification, 25-30um resolved microorganisms, 200um flow cell.
25x objective, 250x magnification, 50um flow cell. For highest resolution but also slowest pumping rate.

It was not clear what is the actual optical resolution of the system with say 10x objective. It should be higher then specified resolved microorganism size, perhaps 1-2 um.
Harry said "10 um" is "many pixels", as can be seen in "sample pictures".

&nbsp;
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*{+}Bellingham's notes{+}*

Notes from telecon with the FlowCAM folks:

Attendees: Bellingham, Chavez, Klimov, Jac Fought, Harry (Fluid Imaging)\\

Francisco:

160-170 codes for organisms quantified in 'standard' water analysis.&nbsp; larger by microscopy, smaller by flow cytometry, some \~um size in both.

Samples 250 ml in size.

Preserve material with glutaraldehyde, filter 25 ml of fluid.
\- microscopy done from filter
\- some fluid frozen w liquid N2 for cytometer (sent to U of Hawaii)

Catalog organisms to 200 um in size

Lots of small stuff - use staining to see bacteria, etc.

For the microscopy - use different magnifications and look over different areas

Harry:

We would probably use 10x objective for 100x magnification over 100um couvette (?) w lower limit of about 10um critter.

4x objective has lower effective size resolution of 40um.

Can use 20x objective w 50um couvette but 'takes a while'

Harry will send us all some sample images of organisms at the various resolutions.

User builds their own library, does not come with library.&nbsp; Library is used for classification.&nbsp; Have taxonomic photos, but not a library.

How many entries does it need?&nbsp; Depends.

Three step process - build a library, build a filter, build a template from the filters.&nbsp; Is dynamic - can add and subtract from them.&nbsp; Use the filter iteratively (first pass for organism 1, then for organism 2, etc.).

Could build some libraries ahead of time.

Chavez:

Can we also get size distribution of what is in sample?

Harry:

Yes, that just comes from pixels.&nbsp; Easily done.&nbsp; Can also use fluorescence, but if the sample is really concentrated then several organisms might be in field of view.

1/4 ml/min volumetric flow rate for 100 um couvette.

Outcome of&nbsp; the meeting is that Francisco sent them some preserved material.&nbsp; They are running it this week.&nbsp; We are going to get a copy of their software and work on developing a library for the resulting images, and use it to develop a classifier for the remainder of the data....

*{+}Additional notes from Klimov:+*

10x objective, 100x magnification, 10-20um resolved microorganisms, 100um flow cell. This is a most common configuration.
4x objective, 40x magnification, 25-30um resolved microorganisms, 200um flow cell.
25x objective, 250x magnification, 50um flow cell. For highest resolution but also slowest pumping rate.

It was not clear what is the actual optical resolution of the system with say 10x objective. It should be higher then specified resolved microorganism size, perhaps 1-2 um.
Harry said "10 um" is "many pixels", as can be seen in "sample pictures".

&nbsp;
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview and comparizon]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

Telecon with FlowCam folks

Discussion with Jared Swalwell\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|http://cseweb.ucsd.edu/~kastner/papers/fpl13-cytometry.pdf]&nbsp; (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|http://cseweb.ucsd.edu/~kastner/papers/fpl13-cytometry.pdf]&nbsp; (Katner et al, 2012)


h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|https://www.beckmancoulter.com/wsrportal/wsrportal.portal?_nfpb=true&_windowLabel=UCM_RENDERER&_urlType=render&wlpUCM_RENDERER_path=%2Fwsr%2Fresearch-and-discovery%2Fproducts-and-services%2Fflow-cytometry%2Fpractical-flow-cytometry%2Findex.htm] (H. Shapiro - the standard text. Fill out form to download the book for free...)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

Cellular Astronomy: a Foreseeable Future in Cytometry (H. Shapiro, _Cytometry_, 2004)

&nbsp;


h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

Practical Flow Cytometry (H. Shapiro - the standard text)


[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Developed by Zhu, et al \[2011\]: _[_Optofluorescent imaging cytometry on a cell phone_|^Zhu Flow Cytometry on a Cell Phone ACHEM2011.pdf]_, ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647 (technology being marketed by [Holomic LLC|http://holomic.com])

Zhu et al [2013], Cost-effective and rapid blood analysis on a cell-phone


Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\
\\

[Cytometer movie|http://pubs.acs.org/doi/suppl/10.1021/ac201587a/suppl_file/ac201587a_si_001.avi]]]></property>
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<property name="body"><![CDATA[Developed by Zhu, et al \[2011\]: _[_Optofluorescent imaging cytometry on a cell phone_|^Zhu Flow Cytometry on a Cell Phone ACHEM2011.pdf]_, ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647 (technology being marketed by [Holomic LLC|http://holomic.com])

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\
\\

[Cytometer movie|http://pubs.acs.org/doi/suppl/10.1021/ac201587a/suppl_file/ac201587a_si_001.avi]]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging) \\ || [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron (SeaFLow) \\
2-20 micron (SeaLabel) \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\
50 fps 512x512 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging) \\ || LISST 100X\\ || [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | nephelometer | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron (SeaFLow) \\
2-20 micron (SeaLabel) \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| Fluor/scatter excitation\\ | 635 nm laser\\ | 457 nm laser\\ | | 532 nm laser\\ | 670 nm laser\\ | | | N.A. |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | | |
| | | | | | | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\
50 fps 512x512 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | | |
| realtime data processing \\ | | yes | | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | | |
| Notes | | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Vehicle payload constraints
|| || LRAUV \\ || Wave Glider \\ || Dorado \\ ||
| Power \\ | 50 W \\ | | |
| Volume | 12" x 36" (?) cylinder \\ | | |
| Weight | | | |
| Endurance | 10-20 days \\ | 60 days \\ | 1 day \\ |
| | | | |
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<property name="body"><![CDATA[Vehicle payload constraints
|| || LRAUV \\ || Wave Glider \\ || Dorado \\ ||
| Power \\ | < 50 W \\ | | |
| Volume | 12" x 36" (?)
cylinder \\ | | |
| Weight | | | |
| Vehicle endurance | 30 days \\ | 60 days \\ | 1 day \\ |
| Payload endurance\\ | | | |
\\ !LRAUV-range-vs-speed.png!]]></property>
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<property name="body"><![CDATA[Vehicle payload constraints

|| || LRAUV\\ || Wave Glider\\ || Dorado \\ ||
| Power \\ | 50 W\\ | | |
| Volume | 12" x 36" cylinder\\ | | |
| Weight | | | |
| Endurance | 10-20 days\\ | | |
| | | | |
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<property name="body"><![CDATA[Vehicle payload constraints
|| || LRAUV \\ || Wave Glider \\ || Dorado \\ ||
| Power \\ | 50 W \\ | | |
| Volume | 12" x 36" cylinder \\ | | |
| Weight | | | |
| Endurance | 10-20 days \\ | 60 days\\ | 1 day\\ |
| | | | |
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;&nbsp;

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Oceanographic cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

Some non-oceanographic instruments


h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

[Visit by Peter Lopez, 9/10/2014|CytometerTech:Visit by Peter Lopez 9-10-2014]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Howard Shapiro's web page|http://www.shapirolab.com/]

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Autonomous platforms

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;
\\
\\

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

[Visit by Peter Lopez, 9/10/2014|CytometerTech:Visit by Peter Lopez 9-10-2014]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Autonomous platforms

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;
\\
\\

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

Visit by Peter Lopez


h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;&nbsp;

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

[Visit by Peter Lopez, 9/10/2014|CytometerTech:Visit by Peter Lopez 9-10-2014]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Howard Shapiro's web page|http://www.shapirolab.com/]

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

Potential platforms&nbsp;&nbsp;


h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

[Visit by Peter Lopez, 9/10/2014|CytometerTech:Visit by Peter Lopez 9-10-2014]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Howard Shapiro's web page|http://www.shapirolab.com/]

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Autonomous platforms

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;
\\
\\

h1. Meeting notes

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

[Visit by Peter Lopez, 9/10/2014|CytometerTech:Visit by Peter Lopez 9-10-2014]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Howard Shapiro's web page|http://www.shapirolab.com/]


[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Autonomous platforms

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;\\

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. Autonomous platforms

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;\\

[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]


h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Lopez, O'Reilly, Klimov

Centrifugal elutriation - pre-sort particles

Sampling statistics problem

Partec - flow microscope

Denis - showed SM data
PL: Could you acoustically control concentration in SM measurement volume, to prevent excessive particles?

Round table:

Influx sorting discussion with Camille

Scholin: interested in particle-field distribution, to guide adaptive sampling
CS: Which is more amenable to real-time sampling: scatter/fluor vs morphological?
PL: Need to decide size range. Answer is not always flow cytometry. Look at Shapiro's battery-powered microscope, for remote diagnostics


JB: How small can a flow cytometer be?
PL: lasers are really small now... a lot of cytometers had to be flexible - now more specialized, smaller versions available. HIV/AIDS applications in developing world are driving size/power downward.
CS: What are prospects for in situ cell sorting?
PL: Will show some slides... chip-based, not electrostatic, but mechanical. Working with Livermore guys

FC: Do you sort live material?
PL: Yes - sorting effects on living samples are largely unknown - work to be done . Typically pressurized to 60 psi

PL: Centrifuging technique seems pretty gentle. Acoustic tech hasn't made it into sorting applications yet.

FC: Anyone thought of breaking up cells and analyzing organelles?
PL: Done with e.g. tumor cells. Also lyse cells to extract chromosomes, then run through cytometer

PL: Can get fluorescent beads that bind to specific target - then measure beads in cytometer. Can get that fluoresce in different colors

SS: Can cells be sorted on basis of morphology?

CP: Could we sort environmental DNA?
PL: Need some kind of particle basis for cytometry
TO: Could this be a mass-spec application?
PL: Maybe]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h1. Autonomous platforms

[Potential platforms|CytometerTech:Potential platforms and constraints]&nbsp;
\\ \\

h1. Meeting notes


[Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]

[Visit by Jarred Swalwell, seminar speaker on 2/5/2014|CytometerTech:Visit by Jarred Swalwell, Feb 5 2014]

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || LISST Holo (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[[Digital holographic microscopy at Wikipedia|http://en.wikipedia.org/wiki/Digital_holographic_microscopy]

The [LISST Holo|http://www.sequoiasci.com/products/fam_LISST_HOLO.cmsx] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]; describes lightweight 2 kg version for arctic app. A version of this instrument is sold by [Resolution Optics|http://resolutionoptics.com/].
* Simplicity: microscopy without lenses; laser + pinhole + CCD camera
* Maximum information: single hologram contains all 3D structural information
* Maximum resolution: "optimal" resolution "easily" attainable - down to level of bacteria
* Speed kinetics of motion/reactions can be followed at video rate in 3D
* &nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[h2. Questions for Resolution Optics

What exactly is output of realtime processing? Predetermined stack of images? Configurable?
Automated image depth determination?

Realtime particle classification?
How does spatial resolution vary with image plane depth?

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?)

What about embedded processing system?

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption
\- image storage (memory) capacity and total number of images possible
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?\\]]></property>
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<property name="body"><![CDATA[Questions for Resolution Optics

What exactly is output of realtime processing? Predetermined stack of images? Configurable?
Automated image depth determination?

Realtime particle classification?
How does spatial resolution vary with image plane depth?

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?)


What about embedded processing system?

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption
\- image storage (memory) capacity and total number of images possible
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?

&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[h2. Questions for Resolution Optics

What exactly is output of realtime processing? Predetermined stack of images? Configurable?
Automated image depth determination?

Realtime particle classification?
How does spatial resolution vary with image plane depth?

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?)

What about embedded processing system?

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption
\- image storage (memory) capacity and total number of images possible
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\]]></property>
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<property name="body"><![CDATA[h2. Questions for Resolution Optics
\\

What is maximum recommended particle concentration? User manual says&nbsp;In order to achieve accurate images, inline holography requires that a reasonable amount of the reference wave (unscattered light) reaches the camera sensor. Too many objects between the PS and the camera can reduce the amount of reference wave reaching the camera and will therefore result in poor reconstructions.\\ \\

What exactly is output of realtime processing? Predetermined stack of images? Configurable?
Automated image depth determination?

Realtime particle classification?
How does spatial resolution vary with image plane depth?

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?)

What about embedded processing system?

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption
\- image storage (memory) capacity and total number of images possible
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\]]></property>
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<property name="body"><![CDATA[[Digital holographic microscopy at Wikipedia|http://en.wikipedia.org/wiki/Digital_holographic_microscopy]

The [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]; describes lightweight 2 kg version for arctic app. A version of this instrument is sold by [Resolution Optics|http://resolutionoptics.com/].
* Simplicity: microscopy without lenses; laser + pinhole + CCD camera
* Maximum information: single hologram contains all 3D structural information
* Maximum resolution: "optimal" resolution "easily" attainable - down to level of bacteria
* Speed kinetics of motion/reactions can be followed at video rate in 3D
* &nbsp;]]></property>
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<property name="body"><![CDATA[[Digital holographic microscopy at Wikipedia|http://en.wikipedia.org/wiki/Digital_holographic_microscopy]

The [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]; describes lightweight 2 kg version for arctic app. A version of this instrument is sold by [Resolution Optics|http://resolutionoptics.com/].
* Simplicity: microscopy without lenses; laser + pinhole + CCD camera
* Maximum information: single hologram contains all 3D structural information
* Maximum resolution: "optimal" resolution "easily" attainable - down to level of bacteria
* Speed kinetics of motion/reactions can be followed at video rate in 3D



Resolution Optics may lend us a Submersible Microscope for evaluation.]]></property>
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<property name="body"><![CDATA[h2. Questions for Resolution Optics

\\

What is maximum recommended particle concentration? User manual says "In order to achieve accurate images, inline holography requires that a reasonable amount of the reference wave (unscattered light) reaches the camera sensor. Too many objects between the PS and the camera can reduce the amount of reference wave reaching the camera and will therefore result in poor reconstructions."
\\
\\

What exactly is output of realtime processing? Predetermined stack of images? Configurable?
Automated image depth determination?

Realtime particle classification?
How does spatial resolution vary with image plane depth?

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?)

What about embedded processing system?

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption
\- image storage (memory) capacity and total number of images possible
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\]]></property>
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<property name="body"><![CDATA[h2. Questions for Resolution Optics

\\

What is maximum recommended particle concentration? User manual says "In order to achieve accurate images, inline holography requires that a reasonable amount of the reference wave (unscattered light) reaches the camera sensor. Too many objects between the PS and the camera can reduce the amount of reference wave reaching the camera and will therefore result in poor reconstructions." {color:#ff0000}RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.{color}


What exactly is output of realtime processing? Predetermined stack of images? Configurable? {color:#ff0000}Can select single image depth for realtime processing. Can save other depths for later offline processing.{color}

Automated image depth determination? {color:#ff3300}This capability will be provided by RO's "Stingray" software, now in development{color}


Realtime particle classification?&nbsp; {color:#ff0000}Realtime particle size distribution, other statistics in one image plane provided by "Swordfish" software{color}


How does spatial resolution vary with image plane depth? {color:#ff0000}Highest resolution (1 micron) when target is against source window. Lowest resolution (4 microns) when target against camera window{color}


How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?) {color:#ff0000}Smooth sapphire windows may discourage biofouling, but likely to be an issue. Particles stuck to window can be eliminated through software.{color}


What about embedded processing system? {color:#ff0000}RO is working on an embedded battery-powered version; maybe available September 2014?{color}


Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption {color:#ff0000}5 Watts{color}
\- image storage (memory) capacity and total number of images possible {color:#ff0000}Depends on laptop drive capacity{color}
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\

ain outcome - MBARI can borrow a Submersible Microscope (older version) for 1.5 months maximum, starting "in April". Sergey or John might be able to visit MBARI to help us get started. Instrument is rated to 2000 meters, but currently has a 10 meter gigabit ethernet cable (R.O. might have a longer cable to loan us). Sample spacer is adjustable on this model.


Here are my actual notes of the meeting - please feel free to comment or correct.

Attendees:
Stephen Jones, Sergey Missan, George McMurtry, John Sampson
John Ryan, Brett Hobson, Francisco Chavez, Steve Haddock, Julio Harvey, Danelle Cline, Hans Thomas, Thom Maughan, Tom O'Reilly

Loaner SM instrument has same optical characteristics as newest version.

Spatial resolution varies with source-to-target distance. Best resolution is about 1 micron when close to source, 4 microns when close to camera.

Imaged volume is about 12 microliters: 2 x 2 mm FOV, 3 mm depth
Sampling rate is 16 fps, 190 microliters/sec
Single plane image transformation at 16 fps, i.e. can keep up in real time. Other planes can be processed later.

Check out the SM gallery

Software packages

Octopus: "manual" processing (hologram-to-image transform, measure size, etc)

Swordfish: High-speed real-time particle characterization (16 fps), historgrams, statistics

Stingray (in development): Automatic target tracking across image planes, morphological features, classifier. Problematic to track when targets overlap.

Particle concentration: if too many particles, there's not enough light for good reconstruction. But RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.

Sample spacer - adjustable in older model (the model we'd borrow), fixed at 8 mm in latest model.

Instrument has been deployed for up to 1 day at least.
Sapphire windows are smooth, but biofouling likely an issue for longer deployments.

To process, need reference holograms(s) - to options:
1. Collect clear-water reference at start of deployment, or
2. Alternate between reference and sample images during deployment (not sure how this works operationally - Tom)

Processing requires Windows laptop with Invidia gpu; raw data and images stored to laptop drive.

Instrument requires 12 V power, gigabit ethernet connection to laptop.

R.O. is working on an embedded, battery-powered data logger - maybe available in August or September 2014?

Camera: 2048 x 2048 pixel, 8 bits monochrome, 16 fps, up to 50 fps in binned mode
Holograms and images stored as png, tiff (other formats?)

Data can be analyzed with LabView, other software thanks to standard image formats.

Loaner instrument is rated to 2000 meters, but has 10 meter cable (R.O. might be able to loan us a longer one).

Loaner sample spacer can be adjusted.
Sergey or John Sampson may be able to come to MBARI to help set up and use the instrument.

Sergey will send document that describes method limitations.

Sergey has not seen any processing bottlenecks running at 16 fps for 24 hours.]]></property>
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\\

Submersible Microscope version 1.0.0 user guide


Conventional and holographic microscopy compared


Submersible microscope limitations
\\

h2. Questions for Resolution Optics

\\

What is maximum recommended particle concentration? User manual says "In order to achieve accurate images, inline holography requires that a reasonable amount of the reference wave (unscattered light) reaches the camera sensor. Too many objects between the PS and the camera can reduce the amount of reference wave reaching the camera and will therefore result in poor reconstructions." {color:#ff0000}RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.{color}

What exactly is output of realtime processing? Predetermined stack of images? Configurable? {color:#ff0000}Can select single image depth for realtime processing. Can save other depths for later offline processing.{color}

Automated image depth determination? {color:#ff3300}This capability will be provided by RO's "Stingray" software, now in development{color}

Realtime particle classification?&nbsp; {color:#ff0000}Realtime particle size distribution, other statistics in one image plane provided by "Swordfish" software{color}

How does spatial resolution vary with image plane depth? {color:#ff0000}Highest resolution (1 micron) when target is against source window. Lowest resolution (4 microns) when target against camera window{color}

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?) {color:#ff0000}Smooth sapphire windows may discourage biofouling, but likely to be an issue. Particles stuck to window can be eliminated through software.{color}

What about embedded processing system? {color:#ff0000}RO is working on an embedded battery-powered version; maybe available September 2014?{color}

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption {color:#ff0000}5 Watts{color}
\- image storage (memory) capacity and total number of images possible {color:#ff0000}Depends on laptop drive capacity{color}
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\

ain outcome - MBARI can borrow a Submersible Microscope (older version) for 1.5 months maximum, starting "in April". Sergey or John might be able to visit MBARI to help us get started. Instrument is rated to 2000 meters, but currently has a 10 meter gigabit ethernet cable (R.O. might have a longer cable to loan us). Sample spacer is adjustable on this model.

h3. Notes from the telecon

Here are my actual notes of the meeting - please feel free to comment or correct.

Attendees:
Stephen Jones, Sergey Missan, George McMurtry, John Sampson
John Ryan, Brett Hobson, Francisco Chavez, Steve Haddock, Julio Harvey, Danelle Cline, Hans Thomas, Thom Maughan, Tom O'Reilly

Loaner SM instrument has same optical characteristics as newest version.

Spatial resolution varies with source-to-target distance. Best resolution is about 1 micron when close to source, 4 microns when close to camera.

Imaged volume is about 12 microliters: 2 x 2 mm FOV, 3 mm depth
Sampling rate is 16 fps, 190 microliters/sec
Single plane image transformation at 16 fps, i.e. can keep up in real time. Other planes can be processed later.

Check out the SM gallery

Software packages

Octopus: "manual" processing (hologram-to-image transform, measure size, etc)

Swordfish: High-speed real-time particle characterization (16 fps), historgrams, statistics

Stingray (in development): Automatic target tracking across image planes, morphological features, classifier. Problematic to track when targets overlap.

Particle concentration: if too many particles, there's not enough light for good reconstruction. But RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.

Sample spacer - adjustable in older model (the model we'd borrow), fixed at 8 mm in latest model.

Instrument has been deployed for up to 1 day at least.
Sapphire windows are smooth, but biofouling likely an issue for longer deployments.

To process, need reference holograms(s) - to options:
1. Collect clear-water reference at start of deployment, or
2. Alternate between reference and sample images during deployment (not sure how this works operationally - Tom)

Processing requires Windows laptop with Invidia gpu; raw data and images stored to laptop drive.

Instrument requires 12 V power, gigabit ethernet connection to laptop.

R.O. is working on an embedded, battery-powered data logger - maybe available in August or September 2014?

Camera: 2048 x 2048 pixel, 8 bits monochrome, 16 fps, up to 50 fps in binned mode
Holograms and images stored as png, tiff (other formats?)

Data can be analyzed with LabView, other software thanks to standard image formats.

Loaner instrument is rated to 2000 meters, but has 10 meter cable (R.O. might be able to loan us a longer one).

Loaner sample spacer can be adjusted.
Sergey or John Sampson may be able to come to MBARI to help set up and use the instrument.

Sergey will send document that describes method limitations.

Sergey has not seen any processing bottlenecks running at 16 fps for 24 hours.]]></property>
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<property name="body"><![CDATA[h2. Questions for Resolution Optics

\\

What is maximum recommended particle concentration? User manual says "In order to achieve accurate images, inline holography requires that a reasonable amount of the reference wave (unscattered light) reaches the camera sensor. Too many objects between the PS and the camera can reduce the amount of reference wave reaching the camera and will therefore result in poor reconstructions." {color:#ff0000}RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.{color}

What exactly is output of realtime processing? Predetermined stack of images? Configurable? {color:#ff0000}Can select single image depth for realtime processing. Can save other depths for later offline processing.{color}

Automated image depth determination? {color:#ff3300}This capability will be provided by RO's "Stingray" software, now in development{color}

Realtime particle classification?&nbsp; {color:#ff0000}Realtime particle size distribution, other statistics in one image plane provided by "Swordfish" software{color}

How does spatial resolution vary with image plane depth? {color:#ff0000}Highest resolution (1 micron) when target is against source window. Lowest resolution (4 microns) when target against camera window{color}

How to discrimate between "old" and "new" particles in each image? (not pumped?)
If not a fresh volume every time, how to discriminate shift direction, etc? How to get adequate volumetric statistics?

How to integrate instrument with mobile platform, e.g. flow cell with pump, vs "passive" flow based on vehicle motion? Turbulent vs laminar flow, etc?

Instrument fouling issues? What if particle stuck to window? (e.g. can processing eliminate specific image planes, like against the window?) {color:#ff0000}Smooth sapphire windows may discourage biofouling, but likely to be an issue. Particles stuck to window can be eliminated through software.{color}

What about embedded processing system? {color:#ff0000}RO is working on an embedded battery-powered version; maybe available September 2014?{color}

Julio's questions:
\- instrument flow rate
\- resolution range (size range of organisms the instrument can image)
\- percentage of flow-through volume imaged by the instrument's "eye"
\- power consumption {color:#ff0000}5 Watts{color}
\- image storage (memory) capacity and total number of images possible {color:#ff0000}Depends on laptop drive capacity{color}
\- options for variable sampling --- burst mode versus continuous sampling over a deployment.&nbsp; Possible for the AUV to trigger sampling in an adaptive manner?
\\

ain outcome - MBARI can borrow a Submersible Microscope (older version) for 1.5 months maximum, starting "in April". Sergey or John might be able to visit MBARI to help us get started. Instrument is rated to 2000 meters, but currently has a 10 meter gigabit ethernet cable (R.O. might have a longer cable to loan us). Sample spacer is adjustable on this model.

h3. Notes from the telecon


Here are my actual notes of the meeting - please feel free to comment or correct.

Attendees:
Stephen Jones, Sergey Missan, George McMurtry, John Sampson
John Ryan, Brett Hobson, Francisco Chavez, Steve Haddock, Julio Harvey, Danelle Cline, Hans Thomas, Thom Maughan, Tom O'Reilly

Loaner SM instrument has same optical characteristics as newest version.

Spatial resolution varies with source-to-target distance. Best resolution is about 1 micron when close to source, 4 microns when close to camera.

Imaged volume is about 12 microliters: 2 x 2 mm FOV, 3 mm depth
Sampling rate is 16 fps, 190 microliters/sec
Single plane image transformation at 16 fps, i.e. can keep up in real time. Other planes can be processed later.

Check out the SM gallery

Software packages

Octopus: "manual" processing (hologram-to-image transform, measure size, etc)

Swordfish: High-speed real-time particle characterization (16 fps), historgrams, statistics

Stingray (in development): Automatic target tracking across image planes, morphological features, classifier. Problematic to track when targets overlap.

Particle concentration: if too many particles, there's not enough light for good reconstruction. But RO looked at 5-10 micron plankton at 5x106 cells/liter with no trouble.

Sample spacer - adjustable in older model (the model we'd borrow), fixed at 8 mm in latest model.

Instrument has been deployed for up to 1 day at least.
Sapphire windows are smooth, but biofouling likely an issue for longer deployments.

To process, need reference holograms(s) - to options:
1. Collect clear-water reference at start of deployment, or
2. Alternate between reference and sample images during deployment (not sure how this works operationally - Tom)

Processing requires Windows laptop with Invidia gpu; raw data and images stored to laptop drive.

Instrument requires 12 V power, gigabit ethernet connection to laptop.

R.O. is working on an embedded, battery-powered data logger - maybe available in August or September 2014?

Camera: 2048 x 2048 pixel, 8 bits monochrome, 16 fps, up to 50 fps in binned mode
Holograms and images stored as png, tiff (other formats?)

Data can be analyzed with LabView, other software thanks to standard image formats.

Loaner instrument is rated to 2000 meters, but has 10 meter cable (R.O. might be able to loan us a longer one).

Loaner sample spacer can be adjusted.
Sergey or John Sampson may be able to come to MBARI to help set up and use the instrument.

Sergey will send document that describes method limitations.

Sergey has not seen any processing bottlenecks running at 16 fps for 24 hours.]]></property>
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<property name="body"><![CDATA[\\

Submersible Microscope version 1.0.0 user guide

Conventional and holographic microscopy compared

Limitations

[Telecon with Resolution Optics, 1/31/2014|CytometerTech:Submersible Microscope telecon January 31, 2014]\\]]></property>
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\\

[Telecon with Resolution Optics, 1/31/2014|CytometerTech:Submersible Microscope telecon January 31, 2014]\\

h3. Further information provided by Resolution Optics (John Samson, 2/1/2014)

\\

[Submersible Microscope version 1.0.0 user guide|^Submersible-User-Guide-v1.0.0.pdf] (original version of the Submersible Microscope, which MBARI might borrow)

[Conventional and holographic microscopy compared|^ED-DIHMConventionalMicroscopyComparison.pdf]

[Limitations|^ED-Limitations.pdf]\\]]></property>
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<property name="body"><![CDATA[\\

[Submersible Microscope version 1.0.0 user guide|^Submersible-User-Guide-v1.0.0.pdf] (original version of the Submersible Microscope, which MBARI might borrow)

[Conventional and holographic microscopy compared|^ED-DIHMConventionalMicroscopyComparison.pdf]

[Limitations|^ED-Limitations.pdf]

[Telecon with Resolution Optics, 1/31/2014|CytometerTech:Submersible Microscope telecon January 31, 2014]\\]]></property>
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<property name="body"><![CDATA[\\ \\

Telecon with Resolution Optics, 1/31/2014\\

h3. Further information provided by Resolution Optics (John Samson, 2/1/2014)
\\

[Submersible Microscope version 1.0.0 user guide|^Submersible-User-Guide-v1.0.0.pdf] (original version of the Submersible Microscope, which MBARI might borrow)

[Conventional and holographic microscopy compared|^ED-DIHMConventionalMicroscopyComparison.pdf]

[Limitations|^ED-Limitations.pdf]\\]]></property>
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<property name="body"><![CDATA[[Digital holographic microscopy at Wikipedia|http://en.wikipedia.org/wiki/Digital_holographic_microscopy]

The [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] has been integrated with Dorado

Jericho et al describe a [submersible digital inline holographic microscope|^SubmersibleHolographicMicroscope.pdf] (SDIHM), with \~2 micron spatial resolution and subsecond temporal resolution. Rated to 20 meters depth. A deep version rated to 6000 meters, with \~5 micron resolution is described by [Bochdansky et al|^DeepDIHM.pdf]. Spatial resolution is considerably higher than [LISST Holo|http://www.sequoiasci.com/products/LISSTHOLOspecs.cmsx] (~25 microns). [Video presentation|https://www.youtube.com/watch?v=q4-y77SrFiA]; describes lightweight 2 kg version for arctic app. A version of this instrument is sold by [Resolution Optics|http://resolutionoptics.com/].
* Simplicity: microscopy without lenses; laser + pinhole + CCD camera
* Maximum information: single hologram contains all 3D structural information
* Maximum resolution: "optimal" resolution "easily" attainable - down to level of bacteria
* Speed kinetics of motion/reactions can be followed at video rate in 3D

Resolution Optics [may lend us a Submersible Microscope for evaluation|CytometerTech:Submersible Microscope telecon January 31, 2014].]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot] (Heidi Sosik, McLane Research) \\ || [SeaLabel] (Jarred Swalwell, UW) \\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://www.sequoiasci.com/product/lisst-holo/] (Sequoia Scientific) \\ || LOPC || Submersible holographic microscope (Resolution Optics) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | holographic imaging \\ | pulse \\ | holographic imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ | 100 micron - 3.5 mm \\ | 1 micron-2 mm (depends on particle opacity, optical setup) \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | | < 10^3 particles/liter \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 76.7 x 13.3 cm | | 30 x 10 cm \\ |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ | 11.4/6.0 kg \\ | 1.81/1.39 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ | < 20 W \\ | \~5 W (not incl. computer) \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ | 660, 3400, 6000 meter \\ | 100, 6000 meter \\ |
| flow rate thru measurement volume \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | | | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | | | CCD |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ | | 16 fps 2048x2048 \\
50 fps 512x512 \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | | | |
| realtime data processing \\ | | yes | | | not implemented | yes | requires human operator, windows PC \\ |
| cost | | | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | | Size histogram for particles 100-1500 micron; shape info for particles > 1.5 mm \\ | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ | [Herman et al (2008)|http://www.alexherman.com/recent_paper_001.php]\\
[Web page|http://www.brooke-ocean.com/lopc.html]\\
[specifications, integration guide|http://www.brooke-ocean.com/document/TD-0141-04-01A.pdf]\\ | [specification sheet|http://resolutionoptics.com/products/submersible]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | | | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1400 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | | | |
| Notes | | | | | Has been integrated with Dorado \\ | Has been integrated with Dorado AUV \\ | Hobson investigating for possible AUV integration \\ |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013|CytometerTech:Johnson Lab Coulter Counter]

[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Practical Flow Cytometry|http://onlinelibrary.wiley.com/book/10.1002/0471722731] (H. Shapiro - the standard text.)

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

[Cellular Astronomy: a Foreseeable Future in Cytometry|^CelluluarAstronomy-Shapiro.pdf] (H. Shapiro, _Cytometry_, 2004)

[A Hardware-accelerated Approach for Imaging Flow Cytometry|^HardwareAcceleratedImagingFlowCytometry.pdf] (Lee, Meng, et al, 2013 International Conference on Field Programmable Logic and Applications)

[MIT 3D Optical Systems Group|http://3doptics.mit.edu/website/publications]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.


In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles based on electrical properties, and does not rely on optical sources or sensors.The particles flow through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap.&nbsp;

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf]have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species
* &nbsp;]]></property>
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The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.
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The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species
* &nbsp;]]></property>
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The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species]]></property>
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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles suspended in an electrolyte fluid, based on changing electrical properties. The technique does not rely on optical sources or sensors.The particles are pumped through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap.&nbsp;

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species]]></property>
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The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.
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The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.\\]]></property>
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h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.


In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

\\]]></property>
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h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted a [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

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h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted a [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

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[Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted a [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

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h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies.


MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

\\]]></property>
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h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm].

MBARI collaborated with UW to submit a NASA ASTEP proposal in 2011. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we su an internal MBARI proposal that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm].

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

\\]]></property>
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h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's&nbsp; SeaFlow cytometer with LRAUV.


MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell would participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h1. Technologies


h3. Coulter Counter
\\]]></property>
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h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

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<property name="body"><![CDATA[The Coulter Counter counts and sizes particles based on electrical properties, and does not rely on optical sources or sensors.

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.\\ \\]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| 10^5 cells/ml \\
Time to measure 1000 cells \\ | 2.4 sec \\
84 joule \\ | 0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec \\ | 40 sec \\ | 333 sec \\ | 200 - 800 sec \\ | |
| 10^5 cells/ml\\
Time to measure 1000 cells \\ | 2.4 sec\\ | 0.04 sec\\ | 0.3 sec\\ | 0.2 - 0.8 sec\\ | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| 10^5 cells/ml \\
Time to measure 1000 cells \\ | 2.4 sec \\ | 0.04 sec \\ | 0.3 sec \\ | 0.2 - 0.8 sec \\ | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec \\ | 40 sec \\ | 333 sec\\ | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec \\ | 40 sec \\ | 333 sec \\ | 200 - 800 sec\\ | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml\\
Time to measure 1000 cells \\ | | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec \\ | 40 sec\\ | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| 100 cells/ml \\
Time to measure 1000 cells \\ | 2400 sec\\ | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).
\\

The prototype CytoSub instrument was integrated with AutoSub by Alex Cunningham's team at the Environmental Optics Lab in Glasgow, in 2002 ([presentation|^Cunningham-CytoSub-slides.ppt], [paper1|^CytoSub-AutoSub.pdf], [paper2|^CytoSub-AutoSub-2.pdf]). The prototype has since been refined to today's commercial CytoSub, with smaller size, better performance, and imaging capability. But CytoSub hasn't been deployed on another AUV since AutoSub (according to CytoSense CEO George Dubelaar).&nbsp; ]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | ? pulse/sec \\
&nbsp; 1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options)\\
idle: 20 W \\
sleep: 2 W \\
 \\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ |  5000 pulse/sec \\
&nbsp; 1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs\\ | | 3-10 PMTs\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements\\

Gating and analyzing software


\\
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;


Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\
\\

\\
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<property name="body"><![CDATA[Categories:&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

1. Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

2. Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters


Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\ \\

(Forward Scatter or FSC)

(Side Scatter or SSC)\\ \\]]></property>
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<property name="body"><![CDATA[Categories:&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

1. Cell sorter vs. Cell Analyzer

2. Sheath fluid, vs. undiluted sample

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
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<property name="body"><![CDATA[Categories:&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

1. Cell sorter vs. Cell Analyzer

2. Sheath fluid, vs. undiluted sample

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
 \\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
 \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[Categories:&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;


1. Cell sorter vs. Cell Analyzer

2. Sheath fluid, vs. undiluted sample


Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements\\]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec\\
40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec\\
0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec\\
333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec\\
 \\
0.33 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
 \\
2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 2.4 sec \\
84 joule \\ | 0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Time, energy to measure 1000 cells (100 cells/ml)\* \\ | 2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 2.4 sec \\
84 joule \\ | 0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Time*, energy to measure 1000 cells (100 cells/ml) \\ | 2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Time*, energy to measure 1000 cells \\
(10^5 cells/ml) \\ | 2.4 sec \\
84 joule \\ | 0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate:
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Time, energy to measure 1000 cells (100 cells/ml) \\ | 2400 sec \\
84000 joule \\ | 40 sec \\
1400 joule \\ | 333 sec \\
19980 joule \\ | 200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Time, energy to measure 1000 cells \\
(10^5 cells/ml) \\ | 2.4 sec \\
84 joule \\ | 0.04 sec \\
1.4 joule \\ | 0.3 sec \\
20 joule \\ | 0.2 - 0.8 sec \\
12 - 48 joule \\ | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulses/sec \\
167 images/min \\ | 24,000 pulses/sec \\ | ? pulses/sec \\
&nbsp; 1500 images/min \\ | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulses/sec \\
\\
167 images/min \\ | 24,000 pulses/sec \\ | ? pulses/sec\\
25 images/sec \\ | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour \\ | 900 ml/hour \\ | 108 ml/hour \\ | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour \\ | 900 ml/hour \\ | 108 ml/hour \\ | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| max throughput | ? pulses/sec \\
 \\
167 images/min \\ | 24,000 pulses/sec \\ | ? pulses/sec\\ | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range\\ | | | 10^3-10^9 cells/liter\\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | 900 ml/hour (continuous) \\ | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour \\ | 900 ml/hour \\ | 108 ml/hour\\ | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | 15 ml/minute (continuous)\\ | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ |  900 ml/hour (continuous) \\ | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaFlow and SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ |  0.4-700 micron \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | 900 ml/hour (continuous) \\ | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 pulses/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | \\ | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden (ref) \\ |
| Coastal population dynamics \\ | \\ | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Washington coast 1998 _Pseudo-nitzschia_ bloom, 18000 cell/ml ([Ref|http://www.coexploration.org/habs/ppt/HAB_online99/sld007.htm]) \\
Washington coast 1997 Pseudo-nitzschia bloom, 13000 cell/ml ([Trainer et al 1998|http://www.ncbi.nlm.nih.gov/pubmed/10223627]) \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | From [Li et al (2009)|http://www.sciencemag.org/content/326/5952/539.full]:\\
Nanophytoplankton\\
Picophytoplankton \\
Bacterioplankton:&nbsp; \\ | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet \\ | [CytoAUV proposal|^emergence-of-automated-high-frequency-flow-cytometry.pdf] \\ | specification sheet \\ | specification sheet \\ | specification sheet \\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet \\ | CytoAUV proposal \\ | specification sheet \\ | specification sheet \\ | specification sheet \\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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Summary from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/ : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis. ]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Washington coast 1998 _Pseudo-nitzschia_ bloom, 18000 cell/ml ([Ref|http://www.coexploration.org/habs/ppt/HAB_online99/sld007.htm]) \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Washington coast 1998 _Pseudo-nitzschia_ bloom, 18000 cell/ml ([Ref|http://www.coexploration.org/habs/ppt/HAB_online99/sld007.htm]) \\
Washington coast 1997 Pseudo-nitzschia bloom, 13000 cell/ml ([Trainer et al 1998|http://www.ncbi.nlm.nih.gov/pubmed/10223627]) \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Washington coast 1998 _Pseudo-nitzschia_ bloom, 18000 cell/ml ([Ref|http://www.coexploration.org/habs/ppt/HAB_online99/sld007.htm]) \\
Washington coast 1997 Pseudo-nitzschia bloom, 13000 cell/ml ([Trainer et al 1998|http://www.ncbi.nlm.nih.gov/pubmed/10223627]) \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico Karenia bloom: \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico _Karenia_ bloom: \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | pseudo-nitzschia; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico Karenia bloom: \~700 cell/ml (Sosik)\\ | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico _Karenia_ bloom: 20-40 um, \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\
Gulf of Mexico _Dinophysis_ bloom: 20-40 um,&nbsp; \~300 cell/ml (Sosik IFCB presentation)\\
Gulf of Maine _Alexandrium_ bloom: 40-50 um, \~5 cell/ml  (Sosik IFCB presentation) | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | _prochlorococcus_; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
_syncechococcus_; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([Binder et al 1996|^Binder et al_DSR_1996.pdf], [CANON ocean eddies group|^OpenOceanEddiesGroup.pdf]) \\ |
| Coastal population dynamics \\ | cells/particles > 2 um (Chavez) \\
\~10^5 phytoplankton cell/ml ([Li and Dickie (2001)  Nova Scotia|http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010701%2944:3%3C236::AID-CYTO1116%3E3.0.CO;2-5/full])&nbsp; \\ | Ryan, Scholin \\
Chavez \\ |
| HAB detection and survey \\ | _Pseudo-nitzschia_; Width = 2-8um, Length =   40-175um \\
Gulf of Mexico _Karenia_ bloom: \~700 cell/ml ([Sosik IFCB presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ | Ryan, Scholin ([CANON HAB working group|^HABWorkingGroupCANONSampling.pdf], \\
[Sosik Imaging Flow Cytobot presentation|^Sosik_HAB_cases_CANON_2010_Workshop.ppt]) \\ |
| Polar survey \\ | | Worden, Bellingham ([NASA ASTEP proposal|CytometerTech:Home^ASTEP_2011_v8.pdf]) \\
Smith? \\ |
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<id name="id">20120163</id>
<property name="body"><![CDATA[Polychromator for Flow Cytometry, 6 channel,&nbsp; sequential filtering (high efficiency), PMT + optical filter, high throughput

[http://www.asahi-spectra.com/]&nbsp;\\

Confocal Fluorescence sensor, 1 channel, a photodiode

FL-SD-xxxx

[www.ese-gmbh.de]&nbsp;\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


[Coulter Counter|CytometerTech:Coulter Counter]


[Cell phone cytometer|CytometerTech:Cell phone cytometer]


[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


Optical Detectors

\\

h1.


h3. \\

\\

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

\\

h1.


h3. \\

\\

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]



h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]



[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]


h3. [Meeting notes|CytometerTech:Meeting notes]




h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[The emergence of automated high-frequency flow cytometry|http://plankt.oxfordjournals.org/content/30/3/333.full] (Journal of Plankton Research, 2008)&nbsp;


h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[The emergence of automated high-frequency flow cytometry|http://plankt.oxfordjournals.org/content/30/3/333.full] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden (ref) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden (ref) \\ |
| Coastal population dynamics \\ | pseudonitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
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h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 um, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 um, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 um, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden (ref) \\ |
| Coastal population dynamics \\ | \\ | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | pseudonitzschia; Width = 2-8um, Length =   40-175um | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | 32 kg\\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm\\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | 32 kg \\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | 32 kg \\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min\\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | 32 kg \\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | 32 kg \\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| flow rate\\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case\\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter\\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| spec link \\ | | | | | [here|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| spec link\\ | | | | | [here|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | specification sheet\\ | CytoAUV proposal\\ | specification sheet\\ | specification sheet\\ | specification sheet\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || [FlowCam|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass \\ | 32 kg \\ | | | | 7.2 kg + 8.2 kg batt-case \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|Comparisons between cytometers, comparison to other methods^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam


h3. [Comparisons|Comparisons between cytometers, comparison to other methods]


\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam


h3. [Comparisons|CytometerTech:Applications, comparisons between cytometers, comparison to other methods]


\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[LISST Holo|CytometerTech:LISST Holo]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Useful links

[Flow Cytometry - a Basic Introduction|http://flowbook-wiki.denovosoftware.com/]


[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | | | | no |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method\\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam


h3.

Cytometers compared with one another and to other methods

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]


h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam


h3.

Cytometers compared with one another and to other methods

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam


h3.

Cytometers compared with one another and to other methods

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

h1. FlowCam


h3.

Cytometers compared with one another and to other methods

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design...
* Optical background (Br)
* Particle size range
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam


h3.

Cytometers compared with one another and to other methods

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120145</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

Flow cytometry: retrospective, fundamentals, and recent instrumentation&nbsp; - includes discussion of emerging cytometry technologies

h3. Imaging versus flow cytometers (Webinar)
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range
* Detector sensitivity (Qr)
* Optical background (Br)
* Particle size range
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. Imaging versus flow cytometers (Webinar)

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hour (continuous) \\ | | 8.3 mm^3/s | With 4X Objective and 300µm Flow Cell: Up to 3mL/min (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 0.75mL/min(12.5 mm^3/s) \\ | |
| throughput | 167 images/min \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\ \\

h1.


h1. Cytometer performance

\\

Detector sensitivity (Qr)

Particle size range\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120150</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. Imaging versus flow cytometers (Webinar)

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087395</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120148</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. Imaging versus flow cytometers (Webinar)

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. Imaging versus flow cytometers (Webinar)

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\

h2. 3/7/2013 - telecon with Holomic LLC

&nbsp;Pre-call:

Denis - the cell phone cytometer is not prssure-tolerant.
Holomic achieves high optical efficiency; can we achieve that?

Ketaki Sood (marketing) , Nevan Karlovac (CEO), Ozcan (scientist)
O'Reilly, Bellingham, Klimov

JGB: Gave MBARI background. Autonomy. Increasing emphasis on microbiology. Physical sampling.
Mentioned summer intern program.

Ozcan: what about broad-field microscopy?
JGB: tricky in situ. Contextual sensors for water samples

JGB: What are max flow rates that prototype can sustain?
Holomic: Low so far, Microliters per minute...

Holomic: Current software gives particle counts, not size
Also wide-field fluorescent microscope

DK: Unattended operation is key. Low power, size

Holomic hasn't focused on low power
Holomic: would require significant funding to build instrument for MBARI
JGB: MBARI engineering is capable of significant contribution
Holomic: formulate your requirments, parameters, etc. Holomic sells products. Cell phone cytometer is not yet a product.
JGB: Oceanographic market is quite small.
How important is continuous sampling?
Holomic: Will keep MBARI in mind as they develop the cytometers

Post call:
Need to develop requirements
\- particle densities (concentration)
\- organism
\- flow rates, integration time
\- sensitivity, chlorophyll concentration
\- excitation/fluorescent wavelengths

Compare to BD, Seaflow
Need to talk with Alex, Scholin, about the above
Example: want to resolve organisms that generate signal detected by EcoPuck; want equivalent sensitivity
Send them a thank-you email, invite them to visit

For next Tuesday:
Target organisms and sizes
How to detect (fluorescence, polarization..)
Characteristics
Natural concentrations

JGB: John Ryan is a good resource for the above
Meet again in 1.5 weeks - March 19
Ask Dorota what organisms BOGS tracks; she's compiling a table

Ask Ryan and Chavez; what organisms would you look for with flow cytometer?

Denis and Tom to interview\\

h2. 2/26/2013

&nbsp;Action items for next meeting

Contact Zhu about cell phone cytometer; latest developments, availability of device - Tom
Look at Zhu et al paper to determine feasibility of reproducing device - Denis
Consider potential embedded imaging intern project - Tom
Review capabilities of Sosik's Imaging Flow Cytobot - Jim


Note: Post-doc candidate Eric Rehm will visit MBARI on March 18-19

Let's explore possible Becton-Dickinson tour when Alex returns (she has several contacts there).


JGB: Cell phones for robotics are very interesting and promising - high capability, low-cost sensors, computing power
Post-doc Eric Rehm will visit on March 18-19

DK: Note that theoretical imaging limit is about 1 micron
DK: Variable bandpass filter via electronic control/piezo-electric control
JGB: Could pulse multiple frequencies on a given particle to measure multiple parameters

Could flow channel be designed to segregate/orient particles based on pressure gradient?

Flow "panel" rather than "stream"?

Investigate flow cytobot - what have they achieved?

Look at citations of Zhu et al:
Microfluidic diagnostics for the developing world:
http://pubs.rsc.org/en/Content/ArticleLanding/2012/LC/C2LC90022J

Millipore Scepter: $3.5K - gives similar data as LISST, which is much more expensive

Approaches:
Coulter
Imaging
Flow cytometer

Ask Zhu et al if device is available

Think about intern project

Denis will look into reproducing cell phone camera

Review flow cytobot work

Becton-Dickinson tour/contact?




h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120151</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120158</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\
\\

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\
\\

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087402</id>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\
\\

h3. [|CytometerTech:Meeting notes][Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. &nbsp;Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

h3.

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]
\\ \\

h3. Meeting notes


h2.
\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. Optical Detectors

\\

h1.


h3. \\

\\

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. &nbsp;


h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

h3.

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3.


h3.


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3. Optical Detectors

\\

h1.


h3. \\

\\

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.

\\

h1. Useful links

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
ukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria 10^5-10^6 cells/ml \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<id name="id">20120104</id>
<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria 10^5-10^6 cells/ml \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria 10^5-10^6 cells/ml \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter\\ |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 1.4x10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 4.7x10^3 cells/ml \\
\\
ukaryotic ultraphytoplankton; 2-20 microns, 4.7x10^3 cells/ml \\
\\
heterotrophic bacteria \\
\\ | Worden |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 1.4x10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 4.7x10^3 cells/ml \\
\\
ukaryotic ultraphytoplankton; 2-20 microns, 4.7x10^3 cells/ml \\
\\
heterotrophic bacteria \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf])\\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Measured properties
\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal)\\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | | | | no |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ || LISST Holo\\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | |
| instrument mass \\ | | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ | |
| flow rate \\ | 5 ml/20 min \\ | | | | |
| sheath fluid? \\ | yes | no \\ | yes | no | |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | | | | |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[|^taxa-kolber.docx]


[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]


[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [FlowCam|CytometerTech:FlowCam]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| instrument mass\\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| flow rate \\ | 5 ml/20 min \\ | | | |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| flow rate\\ | 5 ml/20 min\\ | | | |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1. Measured properties

\\

h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 10^4-10^5 cells/ml \\
\\
syncechococcus; 0.8-1.5 microns, 10^3-10^4 cells/ml \\
\\
eukaryotic ultraphytoplankton; 2-20 microns, 10^3-10^4 cells/ml \\
\\
heterotrophic bacteria; (size?), 10^5-10^6 cells/ml; Hoechst/DNA stain, blue fluorescence, scatter properties \\
\\ | Worden ([ref|^Binder et al_DSR_1996.pdf]) \\ |
| Coastal population dynamics \\ | | Ryan, Scholin \\
Chavez? \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\
Smith? \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| instrument mass \\ | | | | |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| flow rate \\ | 5 ml/20 min \\ | | | |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
| realtime data processing\\ | | | | |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements


[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam

\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Useful links

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<id name="id">20120124</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications


[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam

\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087368</id>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120123</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam
\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120126</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications

[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam

\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1.


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]
\\

h1. Useful links
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications

[^taxa-kolber.docx]

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. &nbsp;Existing instruments


h3. SeaFlow, SeaLabel


h3.


h3. CytoSense, CytoBuoy, CytoSub


h3. Imaging Flow Cytobot


h3. FlowCam

\\

h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h1. Useful links


h3.


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087369</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. FlowCam


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. FlowCam


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087318</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120072</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. FlowCam



h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<id name="id">20120069</id>
<property name="body"><![CDATA[h1. Edit AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer - Worden (oligotrophic)

Harmful Algal Bloom survey - Ryan, Scholin

Polar surveys - Worden, Bellingham (NASA ASTEP proposal)\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot\\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1. Potential AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer - Worden (oligotrophic)

Harmful Algal Bloom survey - Ryan, Scholin

Polar surveys - Worden, Bellingham (NASA ASTEP proposal)
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons among cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. FlowCam



h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Edit AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer - Worden (oligotrophic)


Harmful Algal Bloom survey - Ryan, Scholin

Polar surveys - Worden, Bellingham (NASA ASTEP proposal)

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

The below characteristic values are found in various sources, including peer-reviewed publications and manufacturers marketing literature (e.g. specification sheets)
|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared with one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [FlowCam|CytometerTech:FlowCam]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. Potential AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer - Worden (oligotrophic)

Harmful Algal Bloom survey - Ryan, Scholin

Polar surveys - Worden, Bellingham (NASA ASTEP proposal)
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W\\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons between cytometers, comparison to other methods]

h1. &nbsp;


h1. Technologies

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; - includes discussion of emerging cytometry technologies

h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [FlowCam|CytometerTech:FlowCam]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\]]></property>
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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size, concentration \\ || investigator ||
| Oligotrophic population dynamics \\ | prochlorococcus; 0.5-0.8 microns, 1.4x10^5 cells/ml\\
 \\
syncechococcus; 0.8-1.5 microns, 4.7x10^3 cells/ml\\
 \\
ukaryotic ultraphytoplankton; 4.7x10^3 cells/ml\\
 \\
heterotrophic bacteria \\
 \\ | Worden |
| Coastal population dynamics \\ | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | Ryan, Scholin \\ |
| Polar survey \\ | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size \\ || target cell concentration\\ || investigator ||
| Oligotrophic population dynamics \\ | | | Worden |
| Coastal population dynamics \\ | | | Ryan, Scholin \\ |
| HAB detection and survey \\ | | | Ryan, Scholin \\ |
| Polar survey \\ | | | Worden, Bellingham (NASA ASTEP proposal) \\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1. Potential AUV applications

|| Application \\ || target cells, size \\ || investigator ||
| Oligotrophic population dynamics \\ | | Worden |
| Coastal population dynamics\\ | | Ryan, Scholin\\ |
| HAB detection and survey\\ | | Ryan, Scholin\\ |
| Polar survey\\ | | Worden, Bellingham (NASA ASTEP proposal)\\ |
\\

h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | 67 - 96 W \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |
\\

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[h2. 5/25/2013

&nbsp;Met with Alex Worden to discuss her cytometry applications, approaches

Attendees: Alex, Jim, Denis, Tom


h3.
Tom's notes

Jarred is willing to give a talk when he visits Alex' lab in May.&nbsp; Will keep us apprised of the schedule
Jarred has grant to develop staining capability for Seaflow/(Sealabel?) \-&nbsp; measure grazing by diatoms, dinoflagellates, reproductive rates

Very important to engage UW collaborators at high intellectual level (as opposed to "contract labor").
UW has very extensive expertise in oligotrophic cytometry - informatics and biological. Too expensive/daunting to attempt to replicate that...

Big science problems:
Oligotrophic ocean: what picoplankton organisms are out there? How are the populations changing on various spatial and time-scales? Why are they changing?
Only a few cytometers able to resolve picoplankton
Need 488 nm excitation for phyto pigments

Diurnal growth cycles can now be extracted from Seaflow data, based on new modeling approach.
AUV advantages
realtime survey capability to inform ship sampling plan
3D measurement capability
Long-duration measurements during extended missions
Vehicle sensor payload provides contextual data (e.g. nutrient measurements important\!)

AW would use Cyto-AUV to write papers that utilizes the above advantages
&nbsp;
Instrument features:
Need 488 nm excitation
Must resolve pico\- and nanoplankton (0.2 - 20 micron)
imaging probably not useful - can't discriminate between very small (< 3 micron) organisms, e.g. grazers
staining is useful (e.g. for fungi, bacteria, DNA measurement) but not necessary
in-situ calibration w/ beads is critical

Measurement approaches:
Need 10% sigma or better on counting. Note that large counting errors can be amplified when deriving other quantities (e.g. growth rates). Note that medical applications usually require 1% sigma or better (10,000 count)
Always add calibration beads to sample to verify alignment, detection, etc (except for DNA samples)
Usually able to use single configuration for given seawater sample (detectors have 4-decade dynamic range). May need to change configuration for different water mass (e.g. open-ocean vs eddy?)
Not sure how large cells affect Seaflow measurements
BD Influx measurements are typically 10 minutes (25 microliters/minute)
AW lab does not "gate" on fluorescence or scatter - keep all raw data (may not be practical for coastal waters)
Current focus on cells smaller than 5 micron in open ocean, but including larger cells may be important in some environments
Prochlorococcus and synechococcus are readily identifiable - eukaryotes more problematic

Major challenges:
Time consuming, expensive to collect sparse 3D datasets from CTD casts. Seaflow is vast improvement, but surface water only.
Data analysis (see below)

Data analysis challenges:
Cytometer signatures depend on many factors; diverse organism populations, nutrients, depth, etc...
Lots of human judgement, calibration, tweaking required to analyze data - difficult to automate (look at Ribalet et al PNAS paper on bio-diversity index)
UW team has enormous experience and knowledge - biological combined with informatic


Potential alternatives to cytometry - Raman is talked about, no one appears to have used it yet.



h3. Denis' notes


Application:
\-&nbsp;&nbsp;&nbsp; What groups of organisms are over there? Cytometer on AUV could provide a yo-yo capability, 3D and so on, this means presence.
\-&nbsp;&nbsp;&nbsp; Day-night dynamics.
\-&nbsp;&nbsp;&nbsp; Characterize food web is good information is microbiology

Observational challenges:
\-&nbsp;&nbsp;&nbsp; Total throughput from sampling to real data, is very low (presently), sometimes takes years if sample are analyzed in the lab.&nbsp; This also puts a limit on a numbers of samples.
\-&nbsp;&nbsp;&nbsp; Presence is very low (presently), limited number of ship cruises

Target organisms and mixed populations
\-&nbsp;&nbsp;&nbsp; Not really concerned with high dynamic range on sizes (<5um?).
\-&nbsp;&nbsp;&nbsp; Discriminate between groups of organisms, using optical methods, Ch A and accessory pigments.

Features:
\-&nbsp;&nbsp;&nbsp; Imaging. Value of imaging is limited, organisms below 5um appear as "blobs", can not distinguish. Low Value.
\-&nbsp;&nbsp;&nbsp; Real time processing. Normally cytometer is used during cruises by Worden group. On ship, adaptive sampling strategy is used, and decisions on cruise plan are made based on CTD and cytometer data, if it possible at all, and a team have enough bandwidth to do so. High Value.
\-&nbsp;&nbsp;&nbsp; Bacterial communities need staining.
\-&nbsp;&nbsp;&nbsp; Population identification. Gating is not used, instead, trigger on scattering signal is used, and then accumulate data with other parameters. This is "see everything" approach. This works well in "blue water". Coastal zones with much more silt etc.,&nbsp; is a different story.

Value of integration with mobile platform
\-&nbsp;&nbsp;&nbsp; adaptive behavior, contextual data; real-time data, reconnaissance, surviving;&nbsp; persistent presence, high-res. All High Value.

Procedure:
\-&nbsp;&nbsp;&nbsp; Typically, sample is split in 2, with calibration bids, and without, and both run thru cytometer.
\-&nbsp;&nbsp;&nbsp; Beads are needed to calibrate optics for sensitivity and alignment.
\-&nbsp;&nbsp;&nbsp; Typical sampling rage is 25uL/mil, so it takes 10 min to analyze 250 uL; ~ 1000 eukaryotes, number of cyano bacteria's ~ 100x higher.
\-&nbsp;&nbsp;&nbsp; Statistical errors: <10% is good.
\-&nbsp;&nbsp;&nbsp; As a "rule of thumb", about 10k cells needs to be accumulated in flow cytometry, in order to compute growth rate, which is difficult.
\-&nbsp;&nbsp;&nbsp; Gain control: manual, interactive. Use to need gain control adjustment before running some samples, or to resolve different species in the same sample. Now, with 4 orders of dynamic range, only occasional adjustment for regions of ocean are being made.&nbsp;

Data analysis.
\-&nbsp;&nbsp;&nbsp; Not a static process. Interactive process requiring involvement of skillful individual such as scientist.
\-&nbsp;&nbsp;&nbsp; Signatures of groups of organisms are not static, that is why very helpful to use calibration beads.
\-&nbsp;&nbsp;&nbsp; There is a lot of knowledge went into data processing in established groups, would be very hard to replicate that.
\-&nbsp;&nbsp;&nbsp; Interdisciplinary field between biology and computation => high value.

Trends:
\-&nbsp;&nbsp;&nbsp; Imaging cytometry
\-&nbsp;&nbsp;&nbsp; Smaller particles
\-&nbsp;&nbsp;&nbsp; Certain interest to Raman, but nobody did it yet.

&nbsp;\\

h2. 3/27/2013

Sorry these notes are delayed. Denis have I missed anything important?

Attendees: Denis, Tom

Note that Dorota's "Taxa" table is now online.

Reviewed instrument comparison tables on project Confluence page.
Consider LISST Holo to be an imaging cytometer; should be included with other existing cytometers
Condense some table rows into a single row, with more descriptive text in each cell

Good start on science applications/requirements page

DK: We are a month behind schedule specified in our proposal - hoped to have "literature search" complete by March 1.
DK: As we read articles and attach them, it is useful to markup the PDF file with notes

Alex is available next week - review nature of her lab's work beforehand

Action items:
Denis to review new technologies described in "perspectives" section of Cytotechnology article.
Tom to continue instrument comparison tables, filling out science applications/requirements page
All: prepare to interview Worden by reading her lab's publications and posters (e.g. this one)
&nbsp;
\\

h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\

h2. 3/7/2013 - telecon with Holomic LLC

&nbsp;Pre-call:

Denis - the cell phone cytometer is not prssure-tolerant.
Holomic achieves high optical efficiency; can we achieve that?

Ketaki Sood (marketing) , Nevan Karlovac (CEO), Ozcan (scientist)
O'Reilly, Bellingham, Klimov

JGB: Gave MBARI background. Autonomy. Increasing emphasis on microbiology. Physical sampling.
Mentioned summer intern program.

Ozcan: what about broad-field microscopy?
JGB: tricky in situ. Contextual sensors for water samples

JGB: What are max flow rates that prototype can sustain?
Holomic: Low so far, Microliters per minute...

Holomic: Current software gives particle counts, not size
Also wide-field fluorescent microscope

DK: Unattended operation is key. Low power, size

Holomic hasn't focused on low power
Holomic: would require significant funding to build instrument for MBARI
JGB: MBARI engineering is capable of significant contribution
Holomic: formulate your requirments, parameters, etc. Holomic sells products. Cell phone cytometer is not yet a product.
JGB: Oceanographic market is quite small.
How important is continuous sampling?
Holomic: Will keep MBARI in mind as they develop the cytometers

Post call:
Need to develop requirements
\- particle densities (concentration)
\- organism
\- flow rates, integration time
\- sensitivity, chlorophyll concentration
\- excitation/fluorescent wavelengths

Compare to BD, Seaflow
Need to talk with Alex, Scholin, about the above
Example: want to resolve organisms that generate signal detected by EcoPuck; want equivalent sensitivity
Send them a thank-you email, invite them to visit

For next Tuesday:
Target organisms and sizes
How to detect (fluorescence, polarization..)
Characteristics
Natural concentrations

JGB: John Ryan is a good resource for the above
Meet again in 1.5 weeks - March 19
Ask Dorota what organisms BOGS tracks; she's compiling a table

Ask Ryan and Chavez; what organisms would you look for with flow cytometer?

Denis and Tom to interview
\\

h2. 2/26/2013

&nbsp;Action items for next meeting

Contact Zhu about cell phone cytometer; latest developments, availability of device - Tom
Look at Zhu et al paper to determine feasibility of reproducing device - Denis
Consider potential embedded imaging intern project - Tom
Review capabilities of Sosik's Imaging Flow Cytobot - Jim

Note: Post-doc candidate Eric Rehm will visit MBARI on March 18-19

Let's explore possible Becton-Dickinson tour when Alex returns (she has several contacts there).

JGB: Cell phones for robotics are very interesting and promising - high capability, low-cost sensors, computing power
Post-doc Eric Rehm will visit on March 18-19

DK: Note that theoretical imaging limit is about 1 micron
DK: Variable bandpass filter via electronic control/piezo-electric control
JGB: Could pulse multiple frequencies on a given particle to measure multiple parameters

Could flow channel be designed to segregate/orient particles based on pressure gradient?

Flow "panel" rather than "stream"?

Investigate flow cytobot - what have they achieved?

Look at citations of Zhu et al:
Microfluidic diagnostics for the developing world:
[http://pubs.rsc.org/en/Content/ArticleLanding/2012/LC/C2LC90022J]

Millipore Scepter: $3.5K - gives similar data as LISST, which is much more expensive

Approaches:
Coulter
Imaging
Flow cytometer

Ask Zhu et al if device is available

Think about intern project

Denis will look into reproducing cell phone camera

Review flow cytobot work

Becton-Dickinson tour/contact?

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
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<property name="body"><![CDATA[h2. 3/27/2013

Sorry these notes are delayed. Denis have I missed anything important?

Attendees: Denis, Tom

Note that Dorota's "Taxa" table is now online.

Reviewed instrument comparison tables on project Confluence page.
Consider LISST Holo to be an imaging cytometer; should be included with other existing cytometers
Condense some table rows into a single row, with more descriptive text in each cell

Good start on science applications/requirements page

DK: We are a month behind schedule specified in our proposal - hoped to have "literature search" complete by March 1.
DK: As we read articles and attach them, it is useful to markup the PDF file with notes

Alex is available next week - review nature of her lab's work beforehand

Action items:
Denis to review new technologies described in "perspectives" section of Cytotechnology article.
Tom to continue instrument comparison tables, filling out science applications/requirements page
All: prepare to interview Worden by reading her lab's publications and posters (e.g. this one)
&nbsp;\\

h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\

h2. 3/7/2013 - telecon with Holomic LLC

&nbsp;Pre-call:

Denis - the cell phone cytometer is not prssure-tolerant.
Holomic achieves high optical efficiency; can we achieve that?

Ketaki Sood (marketing) , Nevan Karlovac (CEO), Ozcan (scientist)
O'Reilly, Bellingham, Klimov

JGB: Gave MBARI background. Autonomy. Increasing emphasis on microbiology. Physical sampling.
Mentioned summer intern program.

Ozcan: what about broad-field microscopy?
JGB: tricky in situ. Contextual sensors for water samples

JGB: What are max flow rates that prototype can sustain?
Holomic: Low so far, Microliters per minute...

Holomic: Current software gives particle counts, not size
Also wide-field fluorescent microscope

DK: Unattended operation is key. Low power, size

Holomic hasn't focused on low power
Holomic: would require significant funding to build instrument for MBARI
JGB: MBARI engineering is capable of significant contribution
Holomic: formulate your requirments, parameters, etc. Holomic sells products. Cell phone cytometer is not yet a product.
JGB: Oceanographic market is quite small.
How important is continuous sampling?
Holomic: Will keep MBARI in mind as they develop the cytometers

Post call:
Need to develop requirements
\- particle densities (concentration)
\- organism
\- flow rates, integration time
\- sensitivity, chlorophyll concentration
\- excitation/fluorescent wavelengths

Compare to BD, Seaflow
Need to talk with Alex, Scholin, about the above
Example: want to resolve organisms that generate signal detected by EcoPuck; want equivalent sensitivity
Send them a thank-you email, invite them to visit

For next Tuesday:
Target organisms and sizes
How to detect (fluorescence, polarization..)
Characteristics
Natural concentrations

JGB: John Ryan is a good resource for the above
Meet again in 1.5 weeks - March 19
Ask Dorota what organisms BOGS tracks; she's compiling a table

Ask Ryan and Chavez; what organisms would you look for with flow cytometer?

Denis and Tom to interview
\\

h2. 2/26/2013

&nbsp;Action items for next meeting

Contact Zhu about cell phone cytometer; latest developments, availability of device - Tom
Look at Zhu et al paper to determine feasibility of reproducing device - Denis
Consider potential embedded imaging intern project - Tom
Review capabilities of Sosik's Imaging Flow Cytobot - Jim

Note: Post-doc candidate Eric Rehm will visit MBARI on March 18-19

Let's explore possible Becton-Dickinson tour when Alex returns (she has several contacts there).

JGB: Cell phones for robotics are very interesting and promising - high capability, low-cost sensors, computing power
Post-doc Eric Rehm will visit on March 18-19

DK: Note that theoretical imaging limit is about 1 micron
DK: Variable bandpass filter via electronic control/piezo-electric control
JGB: Could pulse multiple frequencies on a given particle to measure multiple parameters

Could flow channel be designed to segregate/orient particles based on pressure gradient?

Flow "panel" rather than "stream"?

Investigate flow cytobot - what have they achieved?

Look at citations of Zhu et al:
Microfluidic diagnostics for the developing world:
[http://pubs.rsc.org/en/Content/ArticleLanding/2012/LC/C2LC90022J]

Millipore Scepter: $3.5K - gives similar data as LISST, which is much more expensive

Approaches:
Coulter
Imaging
Flow cytometer

Ask Zhu et al if device is available

Think about intern project

Denis will look into reproducing cell phone camera

Review flow cytobot work

Becton-Dickinson tour/contact?

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot](Heidi Sosik, McLane Research) \\ || [SeaLabel](Jarred Swalwell, UW)\\ || [CytoSub] (CytoBuoy BV) \\ || [FlowCam] (Fluid Imaging, Batelle) \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] (Sequoia Scientific) \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ .9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
40000 sec (OPP) \\
1400 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 40 sec (OPP) \\
&nbsp; 1.4 kJoule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, less housing? \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).
\\

The prototype CytoSub instrument was integrated with AutoSub by Alex Cunningham's team at the Environmental Optics Lab in Glasgow, in 2002. The prototype has since been refined to today's commercial CytoSub, with smaller size, better performance, and imaging capability. But CytoSub hasn't been deployed on another AUV since AutoSub (CytoSense marketing guy George Dubelaar).&nbsp; ]]></property>
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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).
\\

The prototype CytoSub instrument was integrated with AutoSub by Alex Cunningham's team at the Environmental Optics Lab in Glasgow, in 2002 ([presentation|^Cunningham-CytoSub-slides.ppt], [paper1|^CytoSub-AutoSub.pdf], [paper2|^CytoSub-AutoSub-2.pdf]). The prototype has since been refined to today's commercial CytoSub, with smaller size, better performance, and imaging capability. But CytoSub hasn't been deployed on another AUV since AutoSub (CytoSense marketing guy George Dubelaar).&nbsp; ]]></property>
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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).
\\ \\

CytoSense marketing guy George Dubelaar indicates that CytoSub has only been installed on one AUV - AutoSub - in 2002. The prototype instrument deployed on AutoSub in 2002 has been refined - smaller size, better performance, imaging. \\]]></property>
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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).
\\
\\

CytoSense marketing guy George Dubelaar indicates that CytoSub has only been installed on one AUV - AutoSub - in 2002. The prototype instrument deployed on AutoSub in 2002 has been refined - smaller size, better performance, imaging - but has not been deployed on another AUV.
\\]]></property>
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, less housing? \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | 4.5 W sampling?\\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample) \\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

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Summary from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/] : CytoBuoy b.v. is a dutch company which manufactures particle analysis  instruments and software for mainly aquatic and marine science. Since  2001, the bench top scanning flow cytometer CytoSense is designed for  pico\- , nano\- and micro-plankton studies. It combines classical flow  cytometry data with silico-images of the measured particles and targeted  video imaging. This instrument is equipped with 2 lasers (460 or 488 or  532 or 561&nbsp;nm and 445 or 635 or 640 or 660&nbsp;nm) and up to 10 detectors.  The CytoSense works with a hydrodynamic sheath fluid injection system  with external and recirculating mode, and an auto-adaptive speed  controlled from 0.2 to 20&nbsp;µL/s. The CytoSense may be extended with a  video imaging-in-flow at rates of up to 1,000 scans per second. The  CytoSub module "Shallow" allows a submerged use in shallow waters (depth  of 20 meter max.) and CytoSub module "Deep" transforms the CytoSense  flow cytometer into a CytoSub instrument for submerged operation down to  200 meters. The Buoy module transforms the CytoSense into a CytoBuoy  analyzer for moored operation, with 8 solar panels systems with  rechargeable batteries and flashlight, telemetry and Argos transponder.  CytoUSB software is used for instrument operation and storage of  measured data files (8 bits---3.5 decades). CytoClus software is used for  data analysis.
\\

[Thyssen et al|CytometerTech:Home^emergence-of-automated-high-frequency-flow-cytometry.pdf](2008) evaluated CytoSub performance in the Bay of Marseille and the southern Indian Ocean; they compared CytoSub data to data acquired by "conventional" cytometers. They note that limitations in instrument memory and sampled volume can lead to undersampling, but describe a workaround to overcome this. (This problem might not apply to present-day CytoSub instruments).\\]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, less housing?\\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal??|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, less housing? \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || Imaging Flow Cytobot \\ || SeaLabel || CytoSub \\ || Submersible FlowCam \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging, pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg, less housing? \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | 40-60 W continuous \\ | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 8-11 mm^3/sec \\ | | | | |
| throughput | \\ | 24,000 events/sec \\ | | 10,000 images/min = 167 images/sec \\ | 2 Hz (analysis post-sample)\\ |
| sampling cycle \\ | 5 ml/20 min \\ | continuous | 4cc/5 min \\ | | |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | no |
| cost | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet (applies to submersible?)|^FlowCAM_Spec_Sheet_200ppi-1.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1.]]></property>
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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)

fluorescent labeling

isotope labeling


\\
\\]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472 of their [recent paper|^Seaflow-Limnology-and-Oceanography.pdf]. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they are all detectable, and assume that each cell is individually detected (i.e. we don't see multiple cells counted as one).
\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) || N=100 (sigma=10%) \\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | 20000 s \\ | 4000 s \\ |
| p = 10^3 cell/ml \\ | 4000 s \\ | 2000 s \\ | 400 s \\ |
| p = 10^4 cell/ml \\ | 400 s \\ | 200 s \\ | 40 s \\ |
| p = 10^5 cell/ml \\ | 40 s \\ | 20 s \\ | 4 s \\ |
Note that the virtual core size (and hence OPP flow rate) is adjustable. The example value of \~15 uL/min corresponds to a virtual core diameter of \~6 microns (the physical stream diameter is \~200 microns). For a low number density, the virtual core diameter and OPP flow rate could be increased with only small risk of coincident counting, resulting in shorter counting times. Science likely wants to resolve several constituent populations with different number densities. ]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472 of their [recent paper|^Seaflow-Limnology-and-Oceanography.pdf]. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they are all detectable, and assume that each cell is individually detected (i.e. we don't see multiple cells counted as one).\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) || N=100 (sigma=10%) \\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | 20000 s \\ | 4000 s \\ |
| p = 10^3 cell/ml \\ | 4000 s \\ | 2000 s \\ | 400 s \\ |
| p = 10^4 cell/ml \\ | 400 s \\ | 200 s \\ | 40 s \\ |
| p = 10^5 cell/ml \\ | 40 s \\ | 20 s \\ | 4 s \\ |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472 of their [recent paper|^Seaflow-Limnology-and-Oceanography.pdf]. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)
\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) || N=100 (sigma=10%) \\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | 20000 s \\ | 4000 s \\ |
| p = 10^3 cell/ml \\ | 4000 s \\ | 2000 s \\ | 400 s \\ |
| p = 10^4 cell/ml \\ | 400 s \\ | 200 s \\ | 40 s \\ |
| p = 10^5 cell/ml \\ | 40 s \\ | 20 s \\ | 4 s \\ |]]></property>
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<property name="body"><![CDATA[1. If instrument of "Sea-flow class" would be available on AUV, how would you use it?

&nbsp;&nbsp;&nbsp; (application, coastal vs. open ocean, eddies, midwater vs. surface, spacial vs. temporal variability, etc.)

2.&nbsp; Range of target organisms?

&nbsp;&nbsp; (size range, concentration range, methods of discrimination, optical properties, fluorescent properties)

3.&nbsp; ]]></property>
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<property name="body"><![CDATA[1. If instrument of "Sea-flow class" would be available on AUV, how would you use it?

&nbsp;&nbsp;&nbsp; (application, coastal vs. open ocean, eddies, midwater vs. surface, etc.)

2.&nbsp; Range of target organisms?

&nbsp;&nbsp; (size range, concentration range, methods of discrimination, optical properties, fluorescent properties)
\\]]></property>
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<property name="body"><![CDATA[1. If instrument of "Sea-flow class" would be available on AUV, how would you use it? \\]]></property>
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<property name="body"><![CDATA[1. If instrument of "Sea-flow class" would be available on AUV, how would you use it?

&nbsp;&nbsp;&nbsp;&nbsp; - application

&nbsp;&nbsp;&nbsp;&nbsp; - coastal vs. open ocean

&nbsp;&nbsp;&nbsp;&nbsp; - eddies

&nbsp;&nbsp;&nbsp;&nbsp; - midwater vs. surface

&nbsp;&nbsp;&nbsp;&nbsp; - spacial vs. temporal variability

2.&nbsp; Range of target organisms?

&nbsp; &nbsp;&nbsp; - size range

&nbsp;&nbsp;&nbsp;&nbsp; - concentration range

&nbsp;&nbsp;&nbsp;&nbsp; - methods of discrimination

&nbsp;&nbsp;&nbsp;&nbsp; - optical properties (forward scatter, side scatter, absorption, polarization etc.)

&nbsp;&nbsp;&nbsp;&nbsp; - fluorescent properties

3. Which features are more or less important?

&nbsp;&nbsp;&nbsp;&nbsp; - value of imaging (on-demand, occasional, primary)

&nbsp;&nbsp;&nbsp;&nbsp; - value of physical sorting, pick-and-accumulate

&nbsp; &nbsp;&nbsp; - real time or post processing

&nbsp; &nbsp;&nbsp; - fluorescent labeling

&nbsp;&nbsp;&nbsp;&nbsp; - traditional gating vs. computational population ID (how to find rare and hidden populations)
\\
\\

4. Value of new features of integration on autonomous mobile platform?

&nbsp; &nbsp;&nbsp; - adaptive behavior, contextual sensors data

&nbsp; &nbsp;&nbsp; - real-time data for reconnaissance and surveying&nbsp;&nbsp;

&nbsp; &nbsp;&nbsp; - persistent presence, high-res
\\


5. Any new trends in cytometry, alternative approaches, etc or you aware of? ]]></property>
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<id name="id">21004629</id>
<property name="body"><![CDATA[1. If instrument of "Sea-flow class" would be available on AUV, how would you use it?

&nbsp;&nbsp;&nbsp;&nbsp; - application

&nbsp;&nbsp;&nbsp;&nbsp; - coastal vs. open ocean

&nbsp;&nbsp;&nbsp;&nbsp; - eddies

&nbsp;&nbsp;&nbsp;&nbsp; - midwater vs. surface

&nbsp;&nbsp;&nbsp;&nbsp; - spacial vs. temporal variability

2.&nbsp; Range of target organisms?

&nbsp; &nbsp;&nbsp; - size range

&nbsp;&nbsp;&nbsp;&nbsp; - concentration range

&nbsp;&nbsp;&nbsp;&nbsp; - methods of discrimination

&nbsp;&nbsp;&nbsp;&nbsp; - optical properties (forward scatter, side scatter, absorption, polarization etc.)


&nbsp;&nbsp;&nbsp;&nbsp; - fluorescent properties

3. Which features are more or less important?

&nbsp;&nbsp;&nbsp;&nbsp; - value of imaging (on-demand, occasional, primary)


&nbsp;&nbsp;&nbsp;&nbsp; - value of physical sorting, pick-and-accumulate

&nbsp; &nbsp;&nbsp; - real time or post processing

&nbsp; &nbsp;&nbsp; - fluorescent labeling

&nbsp;&nbsp;&nbsp;&nbsp; - traditional gating vs. computational population ID (how to find rare and hidden populations)
\\ \\

4. Value of new features of integration on autonomous mobile platform?


&nbsp; &nbsp;&nbsp; - adaptive behavior, contextual sensors data


&nbsp; &nbsp;&nbsp; - real-time data for reconnaissance and surveying&nbsp;&nbsp;


&nbsp; &nbsp;&nbsp; - persistent presence, high-res
\\

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of  producing an image of the cell, flow cytometry  offers  "high-throughput" (for a large number of cells) automated quantification  of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)

fluorescent labeling

isotope labeling
\\
\\]]></property>
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<id name="id">21004627</id>
<property name="body"><![CDATA[1. If instrument of "Sea-flow class" would be available on AUV, how would you use it?

&nbsp;&nbsp;&nbsp;&nbsp; - application?

&nbsp;&nbsp;&nbsp;&nbsp; - coastal vs. open ocean

&nbsp;&nbsp;&nbsp;&nbsp; - eddies?

&nbsp;&nbsp;&nbsp;&nbsp; - midwater vs. surface

&nbsp;&nbsp;&nbsp;&nbsp; - spacial vs. temporal variability

2.&nbsp; Range of target organisms?

&nbsp;&nbsp; (size range, concentration range, methods of discrimination, optical properties, fluorescent properties)

3. Which features are more or less important?

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - imaging?&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp; - sorting vs. analyzer?

&nbsp; &nbsp; - real time or post processing?&nbsp;

&nbsp; &nbsp;&nbsp; - fluorescent labeling?&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp; - traditional gating vs. computational population ID (rare and hidden populations)\\

Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of  producing an image of the cell, flow cytometry  offers  "high-throughput" (for a large number of cells) automated quantification  of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)

fluorescent labeling

isotope labeling\\
\\]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004641</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971878</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004642</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\

h2. Performance notes

&nbsp;Following PMT pulse, camera/LED may be triggered based on pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). \\]]></property>
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<id name="id">21004639</id>
<property name="body"><![CDATA[0. What is the big science question(s) that you want to solve? How does cytometry help you solve it? What observational challenges do you face?\\

1. If instrument of "Sea-flow" class would be available on AUV, how would you use it?

&nbsp; &nbsp;&nbsp; - what science question would you address? What paper would you write?


&nbsp;&nbsp;&nbsp;&nbsp; - coastal zones vs. open ocean, eddies, midwater vs. surface

&nbsp;&nbsp;&nbsp;&nbsp; - spacial vs. temporal variability

2.&nbsp; Range of target organisms in mixed populations?

&nbsp; &nbsp;&nbsp; - size range

&nbsp;&nbsp;&nbsp;&nbsp; - concentration range

&nbsp;&nbsp;&nbsp;&nbsp; - methods of discrimination

&nbsp;&nbsp;&nbsp;&nbsp; - optical properties (forward scatter, side scatter, absorption, polarization etc.)

&nbsp;&nbsp;&nbsp;&nbsp; - fluorescent properties

3. Which features are more or less important?

&nbsp;&nbsp;&nbsp;&nbsp; - value of imaging (on-demand, occasional, primary)

&nbsp;&nbsp;&nbsp;&nbsp; - value of physical sorting, pick-and-accumulate

&nbsp; &nbsp;&nbsp; - real time or post processing

&nbsp; &nbsp;&nbsp; - fluorescent labeling

&nbsp;&nbsp;&nbsp;&nbsp; - traditional gating vs. computational population ID (how to find rare and hidden populations)

4. Value of new features of integration on autonomous mobile platform?

&nbsp; &nbsp;&nbsp; - adaptive behavior, contextual sensors data

&nbsp; &nbsp;&nbsp; - real-time data for reconnaissance and surveying&nbsp;&nbsp;

&nbsp; &nbsp;&nbsp; - persistent presence, high-res
\\

5. Any new trends in cytometry, alternative approaches, etc or you aware of? ]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004637</id>
<property name="body"><![CDATA[1. If instrument of "Sea-flow" class would be available on AUV, how would you use it?

&nbsp;&nbsp;&nbsp;&nbsp; - application

&nbsp;&nbsp;&nbsp;&nbsp; - coastal zones vs. open ocean

&nbsp;&nbsp;&nbsp;&nbsp; - eddies

&nbsp;&nbsp;&nbsp;&nbsp; - midwater vs. surface

&nbsp;&nbsp;&nbsp;&nbsp; - spacial vs. temporal variability

2.&nbsp; Range of target organisms in mixed populations?

&nbsp; &nbsp;&nbsp; - size range

&nbsp;&nbsp;&nbsp;&nbsp; - concentration range

&nbsp;&nbsp;&nbsp;&nbsp; - methods of discrimination

&nbsp;&nbsp;&nbsp;&nbsp; - optical properties (forward scatter, side scatter, absorption, polarization etc.)

&nbsp;&nbsp;&nbsp;&nbsp; - fluorescent properties

3. Which features are more or less important?

&nbsp;&nbsp;&nbsp;&nbsp; - value of imaging (on-demand, occasional, primary)

&nbsp;&nbsp;&nbsp;&nbsp; - value of physical sorting, pick-and-accumulate

&nbsp; &nbsp;&nbsp; - real time or post processing

&nbsp; &nbsp;&nbsp; - fluorescent labeling

&nbsp;&nbsp;&nbsp;&nbsp; - traditional gating vs. computational population ID (how to find rare and hidden populations)

4. Value of new features of integration on autonomous mobile platform?

&nbsp; &nbsp;&nbsp; - adaptive behavior, contextual sensors data

&nbsp; &nbsp;&nbsp; - real-time data for reconnaissance and surveying&nbsp;&nbsp;

&nbsp; &nbsp;&nbsp; - persistent presence, high-res
\\

5. Any new trends in cytometry, alternative approaches, etc or you aware of? ]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971874</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004647</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\ \\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971884</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004650</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).


h2. Performance notes

Core consists of seawater flowing at 15 ml/hr. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\
\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | | | |
| p=10^3 cell/ml \\ | | | |
| p=10^4 cell/ml \\ | | | |
| p=10^5 cell/ml \\ | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971887</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004649</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\  \\
|| || N=1000 (sigma=3.1%)\\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%)\\ ||
| p=10^2 cell/ml \\ | | | |
| p=10^3 cell/ml\\ | | | |
| p=10^4 cell/ml\\ | | | |
| p=10^5 cell/ml\\ | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971886</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004643</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\

h2. Performance notes

&nbsp;Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]).
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971880</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004645</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\

h2. Performance notes

&nbsp;Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]).
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971882</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004655</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr = 4.12 x 10^-3 ml/sec. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | 2400 s \\ | 1200 s\\ | 240 s\\ |
| p=10^3 cell/ml \\ | 240 s\\ | 120 s\\ | 24 s \\ |
| p=10^4 cell/ml \\ | \\ | | |
| p=10^5 cell/ml \\ | \\ | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971892</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004652</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr = 4.12 x 10^-3 ml/sec. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | | | |
| p=10^3 cell/ml \\ | | | |
| p=10^4 cell/ml \\ | | | |
| p=10^5 cell/ml \\ | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971889</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004651</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | | | |
| p=10^3 cell/ml \\ | | | |
| p=10^4 cell/ml \\ | | | |
| p=10^5 cell/ml \\ | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20971888</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004654</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr = 4.12 x 10^-3 ml/sec. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | 2400 sec\\ | | |
| p=10^3 cell/ml \\ | | | |
| p=10^4 cell/ml \\ | | | |
| p=10^5 cell/ml \\ | | | |
\\]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">21004659</id>
<property name="body"><![CDATA[Developed by Heidi Sosik and Robert Olson at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr = 4.12 x 10^-3 ml/sec. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | 2400 s \\ | 1200 s \\ | 240 s \\ |
| p=10^3 cell/ml \\ | 240 s \\ | 120 s \\ | 24 s \\ |
| p=10^4 cell/ml \\ | \\ | | |
| p=10^5 cell/ml \\ | \\ | | |
\\]]></property>
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</property>
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<id name="id">21004549</id>
<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs:\\
CHL (680),\\
SSC (635) \\ | 5 PMTs: \\
Position sensitive detectors (2), CHL1, CHL2, Phyco-erythrin \\ | 3-10 PMTs \\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs \\ | 5 PMTs:\\
Position sensitive detectors (2), CHL1, CHL2, Phyco-erythrin \\ | 3-10 PMTs \\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely"\\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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<property name="body"><![CDATA[Categories:&nbsp;

Forward Scatter or (FSC), Side Scatter or (SSC),&nbsp;Absorption, fluorescence,&nbsp;

Imaging flow cytometry

Mass-spectrometry cytometry

Microfluidic cytometry

Adherent cell cytometry

Options:&nbsp;

Cell sorter vs. Cell Analyzer can actively separate and isolate particles having specified properties

Sheath fluid, vs. undiluted sample

Real time or post processing
\\

A flow cytometer is similar to a microscope,  except that, instead of producing an image of the cell, flow cytometry  offers "high-throughput" (for a large number of cells) automated quantification of set parameters

Trends: continue to decrease in size and energy consumption and to increase in detection and precision measurements
\\

Gating and analyzing software,

Population identification using computational methods (rare and hidden populations)\\

\\
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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect\\
 \\
CHL1\\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
Position sensitive detectors (2), CHL1, CHL2, Phyco-erythrin \\ | FSC Photodiode\\
SSC PMT\\
CHL PMT\\
(up to 7 add. channels) \\
 \\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | ? | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olsen and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 108 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olsen and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus-level identification of nano\- and micro-plankton.\\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSense, CytoBuoy, CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ |  0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | 3 pulse/sec \\
333 sec \\
19980 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | 3000 pulse/sec \\
0.33 sec \\
20 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33333 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | f=64.8 ml/hr:\\
1.8 pulse/sec \\
 \\
555 sec\\
33333 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr\\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33333 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 25 pulse/sec \\
40 sec \\
1400 joule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33333 joule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | f=64.8 ml/hr:\\
1800 pulse/sec\\
0.55 sec\\
33.3 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 0.25 pulse/sec \\
4000 sec \\
140 KJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 KJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 250 pulse/sec \\
&nbsp; 4 sec \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84000 joule \\ | 0.25 pulse/sec\\
4000 sec\\
140 KJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 KJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12000 - 48000 joule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 joule \\ | 25000 pulse/sec \\
0.04 sec \\
1.4 joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 0.25 pulse/sec \\
4000 sec \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 250 pulse/sec \\
&nbsp; 4 sec \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJ \\ | 0.25 pulse/sec \\
4000 sec \\
140 kJ \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJ \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJ (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 J \\ | 250 pulse/sec \\
&nbsp; 4 sec \\
&nbsp; 140 J \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 J \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 J \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 02.5 pulse/sec (detected) \\
4000 sec (OPP) \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 4 sec (OPP) \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp; If n = 1000, coefficient of variation = 3.1%\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 02.5 pulse/sec (detected) \\
4000 sec (OPP) \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 4 sec (OPP) \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp;

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
4000 sec (OPP) \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 4 sec (OPP) \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure n cells, where C is concentration and f is flow rate through measurement volume ("core"):
!equation.jpg|width=128,height=32!
&nbsp; If n = 1000, coefficient of variation = 3.1%
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
4000 sec (OPP) \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 4 sec (OPP) \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.
\\

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

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h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
4000 sec (OPP) \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 4 sec (OPP) \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 particles/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)


h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.


[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
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<property name="body"><![CDATA[h1.


h1. Comparison between existing oceanographic cytometers

The below characteristic values are found in various sources,  including peer-reviewed publications and manufacturers marketing  literature (e.g. specification sheets)
|| || [Imaging Flow CytoBot]\\ || [SeaLabel] || [CytoSub] \\ || [FlowCam] \\ || [LISST Holo|http://sequoiasci.com/products/LISSTHOLOspecs.cmsx] \\ ||
| type | imaging, pulse \\ | pulse \\ | imaging (optional), pulse \\ | imaging \\
(includes chl, phyco fluor channels) \\ | imaging \\ |
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 0.4-700 micron ("pico" option) \\ | 10 - 600 micron \\ | 25 micron-2.5 mm \\ |
| cell concentration range \\ | | | 10^3-10^9 cells/liter \\ | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm | 13.3 cm × 76.7 cm |
| instrument mass (air/water) \\ | 32 kg \\ | | 65 kg \\ | 18 kg (without housing?) \\ | 9.5/3.6 kg \\ |
| power \\ | 35 W \\ | 35 W \\ | sampling: 60 W (full options) \\
idle: 20 W \\
sleep: 2 W \\
\\ | 40-60 W continuous \\ | 4.5 W sampling? \\ |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | 200 meter \\ | 300 meter \\ |
| flow rate \\ | 15 ml/hr \\ | 900 ml/hr \\
f(vcore) ~ 90 ml/hr \\
f(OPP) ~ 9 ml/hr \\ | 0.25-64.8 ml/hr \\ | With 4X Objective and 300µm Flow Cell: Up to 180 ml/hour (50 mm^3/s) \\
WIth 10X Objective and 80µm Flow Cell: Up to 45 ml/hour (12.5 mm^3/s) \\ | |
| Detectors | 2 PMTs: \\
CHL (680), \\
SSC (635) \\ | 5 PMTs: \\
2 position sensitive detect \\
\\
CHL1 \\
CHL2 \\
Phyco-erythrin \\ | FSC Photodiode \\
SSC PMT \\
CHL PMT \\
(up to 7 add. channels) \\
\\ | | |
| max throughput | ? pulse/sec \\
167 images/min \\ | 24,000 pulse/sec \\ | 5000 pulse/sec \\
1500 images/min \\ | 10,000 images/min \\ | 2 Hz (analysis post-sample) \\ |
| sheath fluid? \\ | yes | no \\ | yes | no | no |
| unattended duration \\ | 6 months "routinely" \\ | ? | ? | ? | |
| realtime data processing \\ | | yes | | | not implemented |
| cost | | | | | |
| Notes on measurement method \\ | [Olson and Sosik|http://www.whoi.edu/cms/files/IFCB_33704.pdf] claim scatter/fluorescence is usually not sufficient for genus/species-level identification of nano\- and micro-plankton. \\ | | | | |
| References | [specification sheet|^McLane-IFCB-Datasheet.pdf]\\
[Olson et al (2003)|^FlowCytobot-Olson_et_al_DSR2003_8932.pdf]\\
[Olson and Sosik (2007)|http://www.whoi.edu/cms/files/IFCB_33704.pdf]\\ | [CytoAUV 2013 proposal|^CytoAUV_proposal_2013-v3.pdf]\\ | [Thyssen et al (2008)|^J. Plankton Res.-2008-Thyssen-333-43.pdf]\\
[specification sheet|^CytosenseSpecifications.pdf]\\ | [Web page|http://www.fluidimaging.com/products-submersible.htm]\\
[specification sheet|^Submersible_Spec_Sheet_200ppi-3.pdf] \\ | [specification sheet|^LISST-HOLO.pdf]\\ |
| Event rate, time, energy to measure 1000 cells (100 cells/ml)\* \\ | 0.417 pulse/sec \\
2400 sec \\
84 kJoule \\ | 2.5 pulse/sec (detected) \\
4000 sec (OPP) \\
140 kJoule \\ | f=64.8 ml/hr: \\
1.8 pulse/sec \\
555 sec \\
33 kJoule \\ | 5 - 20 particles/sec \\
\\
200 - 800 sec \\
12 - 48 kJoule (60 W) \\ | |
| Event rate, time, energy to measure 1000 cells \\
(10^5 cells/ml)\* \\ | 417 pulse/sec \\
2.4 sec \\
84 Joule \\ | 2500 pulse/sec (detected) \\
&nbsp; 4 sec (OPP) \\
&nbsp; 140 Joule \\ | f=64.8 ml/hr: \\
1800 pulse/sec \\
0.55 sec \\
33.3 Joule \\ | 5000-20000 pulse/sec \\
0.2 - 0.8 sec \\
12 - 48 Joule \\ | |
&nbsp;\* Time to measure N cells, where p is cell number density (i.e.&nbsp; concentration) and f is flow rate through measurement volume:
!equation.jpg|width=128,height=32!
&nbsp; If N = 1000, coefficient of variation = 3.1% and SNR = 32.

(See Bellingham's [notes on cytometer performance|^IM 230-Flow Cytometer Performance for AUV Operations.docx].)

h1. Comparison to other autonomous methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing of pulse signals (image analysis more complex) \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. Indirect cluster-based species ID for non-imaging cytometers \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | Based on statistical clustering of light scatter/fluorescence correlation \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\
\\

h1.


h1. Cytometer performance

\\
* Linear range (signal : number of photons)
* Detector efficiency (Qr) - determined by laser power, optical design, PMT sensitivity... photoelectrons detected per equivalent fluorochrome molecule
* Optical background (Br)
* Particle size range&nbsp;
* Signal processing speed (pulses/sec, images/sec)

h1.]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min
|| || N=1000 || N=500 || N=100 ||
| 10^2 cell/ml\\ | | | |
| 10^3 cell/ml\\ | | | |
| 10^4 cell/ml\\ | | | |
| 10^5 cell/ml \\ | | | |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)\\
|| || N=1000 || N=500 || N=100 ||
| p = 10^2 cell/ml \\ | | | |
| p = 10^3 cell/ml \\ | | | |
| p = 10^4 cell/ml \\ | | | |
| p = 10^5 cell/ml \\ | | | |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)
\\
|| || N=1000 || N=500 || N=100 ||
| p = 10^2 cell/ml \\ | 40000 s\\ | | |
| p = 10^3 cell/ml \\ | 4000 s\\ | | |
| p = 10^4 cell/ml \\ | 400 s\\ | | |
| p = 10^5 cell/ml \\ | 40 s \\ | | |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)
\\
|| || N=1000 (sigma=3.1%)\\ || N=500 (sigma=4.4%) || N=100 (sigma=10%)\\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | | |
| p = 10^3 cell/ml \\ | 4000 s \\ | | |
| p = 10^4 cell/ml \\ | 400 s \\ | | |
| p = 10^5 cell/ml \\ | 40 s \\ | | |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)
\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) || N=100 (sigma=10%) \\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | 20000 s\\ | 4000 s\\ |
| p = 10^3 cell/ml \\ | 4000 s \\ | 2000 s\\ | 400 s\\ |
| p = 10^4 cell/ml \\ | 400 s \\ | 200 s\\ | 40 s\\ |
| p = 10^5 cell/ml \\ | 40 s \\ | 20 s\\ | 4 s\\ |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. Swalwell is developing the next generation SeaFlow, called SeaLabel. SeaLabel significantly reduces instrument size and power usage.

[2011 NASA ASTEP proposal|^Seaflow-Limnology-and-Oceanography.pdf]

[2013 MBARI CytoAUV MBARI proposal|^CytoAUV_proposal_2013-v3.pdf] (not finally submitted; includes SeaLabel description \[CONFIDENTIAL\])
\\
\\
\\
\\

h2. Performance notes

&nbsp;Measurement time, event rate, power - Swalwell et al describe seawater flow rates on page 472 of their [recent paper|^Seaflow-Limnology-and-Oceanography.pdf]. Seawater is pumped into the the instrument at a "nominal" rate of 15 ml/min. Only particles in the inner part of the stream are detectable, and only a fraction of those particles are in focus. Only the in-focus "optically-positioned particles" (OPP) can be analyzed. The flow rate of detectable particles is \~1/10 the flow rate of the stream while the flow rate of OPP is \~1/100 the flow rate of the detectable particles. Thus the flow rate of the OPP is \~15 uL/min.

the flow rate of the detectable particles is \~1/10 of the flow rate of the stream while the flow rate of OPP particles within the virtual\- core is \~1/100 of the flow rate of the detectable particles. Therefore, the flow rate of the virtual-core is \~15 µL per min = 2.5 x 10^-4 ml/sec.

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)
\\
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) || N=100 (sigma=10%) \\ ||
| p = 10^2 cell/ml \\ | 40000 s \\ | 20000 s \\ | 4000 s \\ |
| p = 10^3 cell/ml \\ | 4000 s \\ | 2000 s \\ | 400 s \\ |
| p = 10^4 cell/ml \\ | 400 s \\ | 200 s \\ | 40 s \\ |
| p = 10^5 cell/ml \\ | 40 s \\ | 20 s \\ | 4 s \\ |]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\

h2. 3/7/2013 - telecon with Holomic LLC

&nbsp;Pre-call:

Denis - the cell phone cytometer is not prssure-tolerant.
Holomic achieves high optical efficiency; can we achieve that?

Ketaki Sood (marketing) , Nevan Karlovac (CEO), Ozcan (scientist)
O'Reilly, Bellingham, Klimov

JGB: Gave MBARI background. Autonomy. Increasing emphasis on microbiology. Physical sampling.
Mentioned summer intern program.

Ozcan: what about broad-field microscopy?
JGB: tricky in situ. Contextual sensors for water samples

JGB: What are max flow rates that prototype can sustain?
Holomic: Low so far, Microliters per minute...

Holomic: Current software gives particle counts, not size
Also wide-field fluorescent microscope

DK: Unattended operation is key. Low power, size

Holomic hasn't focused on low power
Holomic: would require significant funding to build instrument for MBARI
JGB: MBARI engineering is capable of significant contribution
Holomic: formulate your requirments, parameters, etc. Holomic sells products. Cell phone cytometer is not yet a product.
JGB: Oceanographic market is quite small.
How important is continuous sampling?
Holomic: Will keep MBARI in mind as they develop the cytometers

Post call:
Need to develop requirements
\- particle densities (concentration)
\- organism
\- flow rates, integration time
\- sensitivity, chlorophyll concentration
\- excitation/fluorescent wavelengths

Compare to BD, Seaflow
Need to talk with Alex, Scholin, about the above
Example: want to resolve organisms that generate signal detected by EcoPuck; want equivalent sensitivity
Send them a thank-you email, invite them to visit

For next Tuesday:
Target organisms and sizes
How to detect (fluorescence, polarization..)
Characteristics
Natural concentrations

JGB: John Ryan is a good resource for the above
Meet again in 1.5 weeks - March 19
Ask Dorota what organisms BOGS tracks; she's compiling a table

Ask Ryan and Chavez; what organisms would you look for with flow cytometer?

Denis and Tom to interview
\\

h2. 2/26/2013

&nbsp;Action items for next meeting

Contact Zhu about cell phone cytometer; latest developments, availability of device - Tom
Look at Zhu et al paper to determine feasibility of reproducing device - Denis
Consider potential embedded imaging intern project - Tom
Review capabilities of Sosik's Imaging Flow Cytobot - Jim

Note: Post-doc candidate Eric Rehm will visit MBARI on March 18-19

Let's explore possible Becton-Dickinson tour when Alex returns (she has several contacts there).

JGB: Cell phones for robotics are very interesting and promising - high capability, low-cost sensors, computing power
Post-doc Eric Rehm will visit on March 18-19

DK: Note that theoretical imaging limit is about 1 micron
DK: Variable bandpass filter via electronic control/piezo-electric control
JGB: Could pulse multiple frequencies on a given particle to measure multiple parameters

Could flow channel be designed to segregate/orient particles based on pressure gradient?

Flow "panel" rather than "stream"?

Investigate flow cytobot - what have they achieved?

Look at citations of Zhu et al:
Microfluidic diagnostics for the developing world:
[http://pubs.rsc.org/en/Content/ArticleLanding/2012/LC/C2LC90022J]

Millipore Scepter: $3.5K - gives similar data as LISST, which is much more expensive

Approaches:
Coulter
Imaging
Flow cytometer

Ask Zhu et al if device is available

Think about intern project

Denis will look into reproducing cell phone camera

Review flow cytobot work

Becton-Dickinson tour/contact?

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
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<property name="body"><![CDATA[h2. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;]]></property>
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<property name="body"><![CDATA[h2. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access https://oceana.mbari.org/confluence/display/CytometerTech/Home

3. Update Confluence "Technologies" page with Polychromator reference - Denis



Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development


Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; http://www.google.com/patents/US20070026382
&nbsp; licensed to:
&nbsp; http://www.ciencia.com/

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437

&nbsp; http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; http://cronos.rutgers.edu/~diez/index_files/Page312.htm


&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.


Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at https://oceana.mbari.org/confluence/display/CytometerTech/Home

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter


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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles suspended in an electrolyte fluid, based on changing electrical properties. The technique does not rely on optical sources or sensors.The particles are pumped through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap. Variant techniques that utilize the Coulter principle include [Scanning ION Occlusion Sensing|http://en.wikipedia.org/wiki/Scanning_Ion_Occlusion_Sensing] and [CASY|http://en.wikipedia.org/wiki/CASY_cell_counting_technology].

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species

The [Millipore Scepter|http://www.millipore.com/catalogue/module/c85360] hand-held Coulter counter for medical applications is available for $3.5K. Here is a [blog|http://ucflow.blogspot.com/2011/10/counting-cells-with-emd-millipore.html] describing its use. (pointed out by Ken Johnson)]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. CytoBuoy, CytoBot, CytoSub
\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013\\ \\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

\**\*

link to the [test page|https://oceana.mbari.org/confluence/display/CytometerTech/test+page]


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. CytoBuoy, CytoBot, CytoSub

\\

\\]]></property>
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<property name="body"><![CDATA[Developed at UCLA by Zhu et al
\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. Cell phone cytometer



h3. CytoBuoy, CytoBot, CytoSub

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. CytoBuoy, CytoBot, CytoSub

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.
\\]]></property>
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<property name="body"><![CDATA[Developed at UCLA by Zhu et al

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: < 2 micron

Paper contains fairly detailed description of materials, design\\ \\
!figure.jpg|width=619,height=450!\\]]></property>
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<property name="body"><![CDATA[Developed at UCLA by Zhu et al

&nbsp;Imaging flow cytometer


Low-cost materials

Phone provides camera, potential image processing capability


Spatial resolution: < 2 micron\\]]></property>
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<property name="body"><![CDATA[Developed at UCLA by Zhu et al

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;


\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\]]></property>
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<property name="body"><![CDATA[Polychromator for Flow Cytometry, 6 channel,&nbsp; sequential filtering (high efficiency), PMT + optical filter, high throughput

[http://www.asahi-spectra.com/]&nbsp;\\ \\ \\]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119781</id>
<property name="body"><![CDATA[Developed at UCLA by Zhu et al

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\ !figure.jpg|width=619,height=450!\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]



h3. CytoBuoy, CytoBot, CytoSub


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.
\\]]></property>
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<property name="body"><![CDATA[Zhu, et al \[2011\]: "Optofluorescent imaging cytometry on a cell phone", ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647\\

Developed at UCLA by Zhu et al

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. CytoBuoy, CytoBot, CytoSub


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]


\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.
\\]]></property>
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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles suspended in an electrolyte fluid, based on changing electrical properties. The technique does not rely on optical sources or sensors.The particles are pumped through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap. Variant techniques that utilize the Coulter principle include [Scanning ION Occlusion Sensing|http://en.wikipedia.org/wiki/Scanning_Ion_Occlusion_Sensing] and [CASY|http://en.wikipedia.org/wiki/CASY_cell_counting_technology].

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species

The [Millipore Scepter|http://www.millipore.com/catalogue/module/c85360] hand-held Coulter counter for medical applications is available for $3.5K (pointed out by Ken Johnson)]]></property>
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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles suspended in an electrolyte fluid, based on changing electrical properties. The technique does not rely on optical sources or sensors.The particles are pumped through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap. Variant techniques that utilize the Coulter principle include [Scanning ION Occlusion Sensing|http://en.wikipedia.org/wiki/Scanning_Ion_Occlusion_Sensing] and [CASY|http://en.wikipedia.org/wiki/CASY_cell_counting_technology].

The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species
* Test]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.
\\

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. CytoBuoy, CytoBot, CytoSub
\\

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<property name="body"><![CDATA[A [Coulter Counter|http://en.wikipedia.org/wiki/Coulter_counter] counts and sizes particles suspended in an electrolyte fluid, based on changing electrical properties. The technique does not rely on optical sources or sensors.The particles are pumped through a narrow aperture separating two electrodes, between which a weak electric current flows. The voltage across the aperture is sensitive to changes in impedance, which is proportional to the volume of particles that pass through the gap. Variant techniques that utilize the Coulter principle include [Scanning ION Occlusion Sensing|http://en.wikipedia.org/wiki/Scanning_Ion_Occlusion_Sensing] and [CASY|http://en.wikipedia.org/wiki/CASY_cell_counting_technology].


The Ken Johnson lab is developing a small Coulter Counter for potential use on profiling floats, buoys, and other small platforms.

[WHOI developed an in-situ Coulter Counter|^InSituCoulterCounter.pdf] in the mid-1960s for use at-sea.

[Marie et al|Home^PhytoplanktonCountingByFlowCytometry.pdf] have pointed out some drawbacks to the Coulter technique:
* Difficult to quantify particles less than 1-2 microns (i.e. cannot be used for picoplankton)
* Cannot distinguish between cells and other detritus or air bubbles
* Cannot discriminate between similarly-sized microbe species]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST&nbsp;


h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Image generation is currently very time-consuming, performed post-mission.

JGB notes that image processing could be much more efficient - see work by MIT&nbsp;


h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Image generation is currently very time-consuming, performed post-mission.

JGB notes that image processing could be much more efficient - see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV


LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems. &nbsp;
\\ \\

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)


LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems. &nbsp;

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013\\ \\

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.


JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\
\\

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\
\\

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\
\\

h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
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Population dynamics: spatio-temporal variations over hours, days, longer

Harmful Algal Bloom survey
\\

Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
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Population dynamics: spatio-temporal variations over hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods


|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparison to other methods]


h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2. [|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [|CytometerTech:SeaFlow and SeaLabel]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3. [SeaFlow and SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparison to other methods]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
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<property name="body"><![CDATA[h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access https://oceana.mbari.org/confluence/display/CytometerTech/Home

3. Update Confluence "Technologies" page with Polychromator reference - Denis



Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.


Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at https://oceana.mbari.org/confluence/display/CytometerTech/Home

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter


&nbsp;\\ \\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;

2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Some&nbsp; cytometer on a chip references:
&nbsp; patent:
&nbsp; [http://www.google.com/patents/US20070026382]
&nbsp; licensed to:
&nbsp; [http://www.ciencia.com/]

&nbsp; a paper on the topic (lens on a chip?):
&nbsp; [http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4388437]

&nbsp; [http://static.sdu.dk/mediafiles//Files/Om_SDU/Centre/nanosyd/Flow%20Cytometry%20JH_CKO.pdf]

&nbsp; Rutgers fellow that work on electroosmotic flow in microchannels
&nbsp; [http://cronos.rutgers.edu/~diez/index_files/Page312.htm]

&nbsp;Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the target organisms

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]\\]]></property>
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz\\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow cytobot \\ || Seaflow || CytoSub \\ ||
| cell size range \\ | | | |
| | | | |
| dimensions | | | |
| power \\ | | | |
| reference | | | |]]></property>
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers
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<property name="body"><![CDATA[h2. 3/12/2013

Interview with John Ryan.

Ryan, Klimov, Bellingham, O'Reilly
\\

Ryan is interested in particle measurements, going back to MUSE-2000 experiment looking at coupling of phytoplankton with re-suspended&nbsp; sediment. Has never used cytometry. Lots of work with LISST-100x and LISST-Holo.

LISST-100x yields particle size distributions (volume concentration, NOT particle counts) and shape info. Groups sizes into 32 bins between 1-250 microns.

LISST-Holo has been integrated with Dorado. Images particles in 25-2500 micron range. Images are identifiable at least to genus level.&nbsp;

Acquires 1 image per 5 seconds. Image generation (30 sec per image?) is currently very time-consuming, performed post-mission.

JGB notes that LISST Holo image processing could be much more efficient - e.g. see work by [George Barbastathis|http://meche.mit.edu/people/index.html?id=9] of MIT&nbsp;

In situ Holo processing could enable HAB-seeking AUV

LIST 100x processing is also slow, non-realtime. No one has worked to make processing realtime.

Ryan, Maughan, Cline are working on processing algorithms (post-mission non-realtime for now) through CANON, contingency time

Must make several assumptions for LISST-100x processing; particle transparency, shape... there are also unexplained "blank" anomalies; must use "at sea" blank rather than "in lab" blank - why?&nbsp; (e.g. include dive to off-shelf deep clear water for "blank" sample)

LISST-Holo only costs $25K

JGB: LISST-100x is very difficult to work with, calibrate due to above problems.&nbsp; Cytometer approach is more direct, requires fewer assumptions.

JR: Imaging Flow Cytobot is very cool, not yet integrated with AUV though.

JGB: Check out [FlowCam|http://www.fluidimaging.com/products-particle-imaging-analyzer.htm] \- some early problems (e.g. with biofouling) but making progress. Might be able to borrow one for CANON Fall 2013
\\

h2. 3/7/2013 - telecon with Holomic LLC


&nbsp;Pre-call:

Denis - the cell phone cytometer is not prssure-tolerant.
Holomic achieves high optical efficiency; can we achieve that?

Ketaki Sood (marketing) , Nevan Karlovac (CEO), Ozcan (scientist)
O'Reilly, Bellingham, Klimov

JGB: Gave MBARI background. Autonomy. Increasing emphasis on microbiology. Physical sampling.
Mentioned summer intern program.

Ozcan: what about broad-field microscopy?
JGB: tricky in situ. Contextual sensors for water samples

JGB: What are max flow rates that prototype can sustain?
Holomic: Low so far, Microliters per minute...

Holomic: Current software gives particle counts, not size
Also wide-field fluorescent microscope

DK: Unattended operation is key. Low power, size

Holomic hasn't focused on low power
Holomic: would require significant funding to build instrument for MBARI
JGB: MBARI engineering is capable of significant contribution
Holomic: formulate your requirments, parameters, etc. Holomic sells products. Cell phone cytometer is not yet a product.
JGB: Oceanographic market is quite small.
How important is continuous sampling?
Holomic: Will keep MBARI in mind as they develop the cytometers

Post call:
Need to develop requirements
\- particle densities (concentration)
\- organism
\- flow rates, integration time
\- sensitivity, chlorophyll concentration
\- excitation/fluorescent wavelengths

Compare to BD, Seaflow
Need to talk with Alex, Scholin, about the above
Example: want to resolve organisms that generate signal detected by EcoPuck; want equivalent sensitivity
Send them a thank-you email, invite them to visit

For next Tuesday:
Target organisms and sizes
How to detect (fluorescence, polarization..)
Characteristics
Natural concentrations

JGB: John Ryan is a good resource for the above
Meet again in 1.5 weeks - March 19
Ask Dorota what organisms BOGS tracks; she's compiling a table

Ask Ryan and Chavez; what organisms would you look for with flow cytometer?

Denis and Tom to interview



h2. 2/5/2013

Action items for next meeting:

1. Look at cytometers-on-a-chip literature - Jim, Denis, Tom

2. Fix Confluence access - Tom
Done - please login into Confluence and verify that you can access [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

3. Update Confluence "Technologies" page with Polychromator reference - Denis

Agenda:
1. Discuss action item status from last meeting (see below)
2. Jim has some information from ONR meeting

Denis: American Society for Cell Biology Trade show
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

Denis: Polychromator for flow cytometry (Asahi Spectra) - simplified alignment (about 4x4")
ESE Fluo Sens SD - similar assembly for fluorometer

Jim: attended ONR meeting; saw presentation on Electro-osmosis
Accelerate fluid through a charged tube; potentially eliminate cytometer pump
Could you build cytometer-on-a-chip? Could run at ambient pressure
Try googling cytometer on a chip; multiple hits. Why can't we use one of these?

Denis: Miniature silicone rubber diaphragm pumps on MEMS chip is a common technique

Jim: Why are cytometers still pretty complicated and large?
Take another look at cell phone cytometer...
Check out "google scholar", patent database for "cytometer on a chip"
Several home medical devices in development

Jim: We should cold-call some of these researchers, ask them questions
What are target organisms?&nbsp;
Denis: what are minimum throughput requirements, size ranges?
Jim: talk with Chavez, Scholin, Worden

DAC workshop this week, with Scholin, Delong - we will attend, get an idea of the organism targets

Jim: Eric Reihm has been offered post-doc at MBARI, has not accepted yet.

Action items from last meeting:

1. Set up project library - Tom
Done - confluence page at [https://oceana.mbari.org/confluence/display/CytometerTech/Home]

2. Refine technology evaluation matrix - Denis
Denis will work on this

3. Check for local relevant trade shows - Denis
American Society for Cell Biology Trade show.
Photonics West - this week
Cytometery development workshop - every year at Asilomar. Shapiro has been co-chair

4. Ask Johnson for Coulter counter briefing - Tom Done
Done - Ken notes that project has been inactive for serveral months, hopes to restart soon (with Ginger Elrod as chief engineer). See [https://oceana.mbari.org/confluence/display/CytometerTech/Coulter+Counter]

&nbsp;
\\
\\

h3. 1/18/2013 - Kickoff meeting

Action items:

1. Set up project library - Tom
2. Refine technology evaluation matrix - Denis
3. Check for local relevant trade shows - Denis
4. Ask Johnson for Coulter counter briefing - Tom

Attendees: Jim, Denis, Tom

JGB is recuiting potential post-doc Eric Rehm from University of Washington; he's primarily interested in ocean optics, with extensive software expertise. (Note Rehm's 2007 cytometry publication with Swalwell and Armbrust.)

Would be good to arrange Rehm visit to MBARI, before post-doc decision in mid-February.
Perhaps he could participate in Jim's DAC workshop to be held Feb 6-7.
Jim will pursue travel funding options with George Matsumoto, other sources

How to engage MBARI scientists with cytometry?

CANON PIs: Worden, Scholin, Chavez. JGB notes that we shouldn't expect a lot of engagement from scientists at least during early phases of feasibility project.
Note that Jim is holding a CANON DAC workshop, Feb 6-7; he will see if we can give brief presentation describing our project.

Johnson lab is developing a Coulter counter. We should talk with them about details of their project. Note that Ken Johnson is thinking about how AUV skin surface might be used as Coulter counter detector. JGB notes that at minimum Johnson would be great advisor to our project, although he's not too engaged with CANON

Tom and Denis discussed meeting/lab-tour from Johnson group - Tom will ask Ken

Literature search of existing technologies; we should rank these in evaluation table (refined/codensed version of criteria we presented in proposal)
CytoBuoy
CytoBot
SeaFlow
Cell phone
Other technologies

Denis suggests we check biological, optical trade shows.

We should meet about every two weeks.
&nbsp;]]></property>
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow cytobot \\ || Seaflow || CytoSub \\ ||
| cell size range \\ | | | |
| | | | |
| dimensions | | | |
| power \\ | | | |
| reference | | | |]]></property>
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow cytobot \\ || Seaflow || CytoSub \\ ||
| cell size range \\ | | | |
| | | | |
| dimensions | | | |
| power \\ | | | |
| reference | | | |]]></property>
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Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow cytobot\\ || Seaflow || CytoSub \\ ||
| min cell size\\ | | | |
| | | | |
| dimensions | | | |
| power \\ | | | |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ |  \~hourly? \\ | \~1 Hz\\ | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow cytobot \\ || Seaflow || CytoSub \\ ||
| cell size range \\ | | | |
| | | | |
| dimensions | | | |
| power \\ | | | |
| reference | | | |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow cytobot \\ || Seaflow || CytoSub \\ ||
| cell size range \\ | | | |
| | | | |
| dimensions | | | |
| power \\ | | | |
| reference | http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot | | http://www.cytobuoy.com/products/submersible/ |]]></property>
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<property name="body"><![CDATA[The [SeaFlow cytometer|^Seaflow-Limnology-and-Oceanography.pdf] was invented by Jared Swalwell of the University of Washington Armbrust Lab. One major SeaFlow innovation is patented "[virtual core|http://www.ncbi.nlm.nih.gov/pubmed/19753629]" technology. Most cytometers form a single-file line or "core" of cells by injecting the cells into a stream of "sheath fluid" when then flows past the light excitation beam. Seaflow eliminates the need for an actual core and sheath fluid by utilizing three positional detectors and software to determine which cells are in proper position relative to the excitation beam, rejecting measurements that don't fall within the measurement region. \\]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow Cytobot \\ || SeaLabel || CytoSub \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| | | | |
| instrument dimensions | 26 x 102 cm\\ | 17 x 23 x 28 cm \\ | 37 x 75 cm\\ |
| power \\ | | 35 W\\ | |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow Cytobot \\ || SeaLabel || CytoSub \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| | | | |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ |
| power \\ | 35 W\\ | 35 W \\ | |
| max depth\\ | | shipboard | 20 meter\\ |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow Cytobot \\ || Seaflow || CytoSub \\ ||
| cell size range (micron) \\ | | 0.5-20 \\ | |
| | | | |
| dimensions | | | |
| power \\ | | | |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys


h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow Cytobot \\ || SeaLabel || CytoSub \\ ||
| cell size range \\ | 1-100 micron\\ | 0.5-20 micron \\ | 1 micron - 1 mm\\ |
| | | | |
| instrument dimensions | | 17 x 23 x 28 mm\\ | |
| power \\ | | | |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. FlowCam



h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | \\ |
| power \\ | 35 W \\ | 35 W \\ | ? | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | | 24,000 events/sec\\ | | 10,000 images/min\\ |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm\\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | |
| power \\ | 35 W \\ | 35 W \\ | ? | |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ |
| power \\ | 35 W \\ | 35 W \\ | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer - Worden


Harmful Algal Bloom survey - Ryan, Scholin


Polar surveys - Worden, Bellingham (NASA ASTEP proposal)


h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

The below characteristic values are found in various sources, including peer-reviewed publications and manufacturers marketing literature (e.g. specification sheets)
|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

The below characteristic values are found in various sources, including peer-reviewed publications and manufacturers marketing literature (e.g. specification sheets)

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| sheath fluid? \\ | yes | no \\ | yes | no |
| unattended duration \\ | ? | ? | ? | ? |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved) \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ || FlowCam \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ | 2 micron - 2 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ | 46 x 38 x 66 cm |
| power \\ | 35 W \\ | 35 W \\ | ? | ? |
| max depth \\ | 40 meter \\ | shipboard | 200 meter \\ | |
| throughput | 5ml sample/20 min \\ | 24,000 events/sec \\ | | 10,000 images/min \\ |
| unattended duration\\ | ? | ? | ? | ? |]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoSense, CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging Flow Cytobot \\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || CytoSub \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ |
| power \\ | 35 W \\ | 35 W \\ | ? |
| max depth \\ | 40 meter \\ | shipboard | 20 meter \\ |]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087280</id>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])
\\]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|Applications, comparisons]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || Imaging flow Cytobot \\ || SeaLabel || CytoSub \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ |
| power \\ | 35 W \\ | 35 W \\ | ? |
| max depth \\ | 40 meter\\ | shipboard | 20 meter \\ |]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087277</id>
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</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20120048</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometers compared one another and to other methods|Applications, comparisons]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h2.


h3.


h3. [Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]


h3.


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. [CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || LISST Holo\\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Long processing time (but could be improved)\\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | | KHz \\ |
| Processing | | simple \\ | complex | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes | yes |
| Samples per deployment \\ | 10's | | | | |
| | | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || [CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub] \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ |
| power \\ | 35 W \\ | 35 W \\ | ? |
| max depth \\ | 40 meter \\ | shipboard | 20 meter \\ |]]></property>
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<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over minutes, hours, days, longer

Harmful Algal Bloom survey

Polar surveys

h1. Comparison to other AUV-based methods

|| || ESP || Fluorometry \\ || LISST 100x \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID; straightforward data processing \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; complex data processing; must assume particle transmittance, shape; calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample rate \\ | \~hourly? \\ | \~1 Hz \\ | | KHz \\ |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\

h1. Comparison of existing oceanographic cytometers

|| || [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]\\ || [SeaLabel|CytometerTech:SeaFlow and SeaLabel] || CytoSub \\ ||
| cell size range \\ | 1-100 micron \\ | 0.5-20 micron \\ | 1 micron - 1 mm \\ |
| instrument dimensions | 26 x 102 cm \\ | 17 x 23 x 28 cm \\ | 37 x 75 cm \\ |
| power \\ | 35 W \\ | 35 W \\ | ? |
| max depth \\ | 40 meter \\ | shipboard | 20 meter \\ |]]></property>
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<property name="body"><![CDATA[Zhu, et al \[2011\]: _[_Optofluorescent imaging cytometry on a cell phone_|^Zhu Flow Cytometry on a Cell Phone ACHEM2011.pdf]_, ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647

Developed at UCLA by Zhu et al

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119868</id>
<property name="body"><![CDATA[Developed by Zhu, et al \[2011\]: _[_Optofluorescent imaging cytometry on a cell phone_|^Zhu Flow Cytometry on a Cell Phone ACHEM2011.pdf]_, ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647 (technology being marketed by [Holomic LLC|holomic.com])


Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\
\\

[Cytometer movie|http://pubs.acs.org/doi/suppl/10.1021/ac201587a/suppl_file/ac201587a_si_001.avi]]]></property>
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<property name="body"><![CDATA[Zhu, et al \[2011\]: _[_Optofluorescent imaging cytometry on a cell phone_|^Zhu Flow Cytometry on a Cell Phone ACHEM2011.pdf]_, ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647

Developed at UCLA by Zhu et al

Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\ \\

[Cytometer movie|http://pubs.acs.org/doi/suppl/10.1021/ac201587a/suppl_file/ac201587a_si_001.avi]]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoBot, CytoSub


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements


h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoBot, CytoSub


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<id name="id">20119938</id>
<property name="body"><![CDATA[h1. AUV applications

Population dynamics: spatio-temporal variations over hours, days, longer


Harmful Algal Bloom survey
\\

Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

[Cytometry compared to other methods|CytometerTech:Cytometry compared to other methods]


h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[AUV applications


Population dynamics


Harmful Algal Bloom survey\\

Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\]]></property>
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</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Doesn't discriminate cells from other particles; Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087176</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119932</id>
<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| Processing | | simple \\ | complex | simple? \\ |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087174</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. [Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087172</id>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuous |
| | | | | |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\]]></property>
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</property>
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<object class="BodyContent" package="com.atlassian.confluence.core">
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<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | seconds; continuous | | seconds; continuos |
| | | | | |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment \\ | 10's | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087168</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119925</id>
<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID \\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment. \\ |
| Sample time \\ | hours; discrete \\ | second; continuous | | seconds; continuos |
| | | | | |
| Species ID? \\ | yes \\ | no | no | yes |
| Samples per deployment\\ | 10's | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087167</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119924</id>
<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast sampling; bulk pigments \\ | | Species ID\\ |
| Drawbacks | Limited by onboard reagents; long sampling time \\ | Doesn't discriminate species \\ | Calibration problematic \\ | Complex optics, hydraulics; precise optical alignment req.\\ |
| Sample time \\ | hours \\ | seconds | | seconds |
| | | | | |
| Species ID? \\ | \\ | | | |
| Duration | | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087166</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119922</id>
<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || Cytometer \\ ||
| Advantages | Species ID \\ | Fast; bulk pigments \\ | | |
| Drawbacks | Limited by onboard reagents \\ | Doesn't discriminate species \\ | Calibration problematic \\ | |
| Sample time \\ | hours \\ | seconds | | |
| | | | | |
| Species ID? \\ | \\ | | | |
| Duration | | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087164</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119919</id>
<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || SeaFlow Cytometer \\ ||
| Sample time \\ | hours \\ | seconds | | |
| Species ID? \\ | \\ | | | |
| | | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087161</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119920</id>
<property name="body"><![CDATA[Cytometry can be compared to other methods used on AUVs
\\
|| || ESP || Fluorometry \\ || LISST \\ || SeaFlow Cytometer \\ ||
| Advantages | Species ID\\ | Fast; bulk pigments\\ | | |
| Drawbacks | Limited by onboard reagents\\ | Doesn't discriminate species\\ | Calibration problematic\\ | |
| Sample time \\ | hours \\ | seconds | | |
| | | | | |
| Species ID? \\ | \\ | | | |
| Duration | | | | |
| | | | | |
\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087162</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119915</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot](here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087157</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119913</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole

HAB and Imaging Flow Cytobot case studies, from the CANON Sampling Workshop (2010)\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot]\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087155</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119914</id>
<property name="body"><![CDATA[Developed by Heidi Sosik at Woods Hole

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot]\\]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087156</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119912</id>
<property name="body"><![CDATA[]]></property>
<property name="content" class="Page" package="com.atlassian.confluence.pages"><id name="id">20087154</id>
</property>
</object>
<object class="BodyContent" package="com.atlassian.confluence.core">
<id name="id">20119910</id>
<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]

h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoSub


h3. Imaging Flow Cytobot



h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3. [Meeting notes|CytometerTech:Meeting notes]


h2.


h1. Background

Scientific motivation for in-situ autonomous cytometry was described at the [2010 CANON sampling workshop|http://www.mbari.org/canon/workshop.htm], attended by scientists and engineers from multiple institutions. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science requirements

[List of commonly targeted organisms (D. Kolber)|^taxa-kolber.docx]


h1. &nbsp;


h1. Technologies


h3. [Coulter Counter|CytometerTech:Coulter Counter]


h3. [SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]


h3. [Cell phone cytometer|CytometerTech:Cell phone cytometer]


h3. [Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]


h3. CytoBuoy, CytoBot, CytoSub


h3. [Optical Detectors|https://oceana.mbari.org/confluence/display/CytometerTech/Optical+detectors+for+flow+cytometry]

\\

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Developed by Zhu, et al \[2011\]: _[_Optofluorescent imaging cytometry on a cell phone_|^Zhu Flow Cytometry on a Cell Phone ACHEM2011.pdf]_, ??Anal. Chem.??, 2011, 83 (17), pp 6641-6647 (technology being marketed by [Holomic LLC|http://holomic.com])

Zhu et al [2013], Cost-effective and rapid blood analysis on a cell-phone, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594636/


Imaging flow cytometer

Low-cost materials

Phone provides camera, potential image processing capability

Spatial resolution: \~2 micron

Paper contains fairly detailed description of materials, design

Select filters and LED for target cell type

Image processing performed on laptop computer when this paper was published, algorithms implemented in [OpenCV|http://code.opencv.org/projects/opencv/wiki]. Note that Android has OpenCV implementation.&nbsp;

\\
Throughput largely limited by camera frame rate. Frame rate of 120 fps could result in whole-blood imaging time of 20 seconds.

\\  !figure.jpg|width=619,height=450!\\
\\

[Cytometer movie|http://pubs.acs.org/doi/suppl/10.1021/ac201587a/suppl_file/ac201587a_si_001.avi]]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with FlowCam folks, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[Developed by Heidi Sosik and Robert Olson at Woods Hole.

[HAB and Imaging Flow Cytobot case studies|^Sosik_HAB_cases.ppt], Sosik's presentation from the CANON Sampling Workshop (2010)
\\

[Sold by McLane Reseach Labs|http://www.mclanelabs.com/master_page/product-type/samplers/imaging-flowcytobot] (here is the McLane [specification sheet|^McLane-IFCB-Datasheet.pdf])

Instrument emphasizes imaging - camera/flash-LED is triggered by CHL or SSC PMT pulse height (configurable threshold).

h2. Performance notes

Core consists of seawater flowing at 15 ml/hr = 4.17 x 10^-3 ml/sec. Following PMT pulse, camera/LED may be triggered based on CHL or SSC pulse height and threshold settings. If camera/LED is triggered, subsequent pulses are ignored for at least 80 msec until camera is done ([Olson and Sosik 2007|^IFCB_33704-1.pdf]). According to Mike Matthewson (McLane): "Att 1000 cell/ml \[...\] IFCB looks at nearly all the sample (i.e., 15 ml/hour \[sheath is not sample\]); at 5000 cell/ml it looks at \~half of the water passing through the instrument. Reliable concentrations can be obtained up to at least 15,000 cell/ml. Again, the volume of sample actually examined is kept track of and used to calculate cell concentrations."
\\

Compute time 'T' to measure N OPP cells at this flow rate 'f', for given values of number density 'p':

&nbsp;T = N / (f * p)

We assume that cells are not necessarily all the same size, but they  are all detectable, and assume that each cell is individually detected  (i.e. we don't see multiple cells counted as one).
|| || N=1000 (sigma=3.1%) \\ || N=500 (sigma=4.4%) \\ || N=100 (sigma=10%) \\ ||
| p=10^2 cell/ml \\ | 2400 s \\ | 1200 s \\ | 240 s \\ |
| p=10^3 cell/ml \\ | 240 s \\ | 120 s \\ | 24 s \\ |
| p=10^4 cell/ml \\ | \\ | | |
| p=10^5 cell/ml \\ | \\ | | |
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

Telecon with Fluid Imaging,&nbsp;


[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

Visit by Heidi Sosik, 9/11/2013


[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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<property name="body"><![CDATA[This is the home page for the [901303 Cytometer Technologies for Autonomous Platforms|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] space.

h3.


h1. Background

Scientific motivation for _in situ_ autonomous cytometry was described at the 2010 CANON sampling workshop ([web page|http://www.mbari.org/canon/workshop.htm], [final report|^CANON Sampling Workshop Report.20Apr10.pdf], [engineering report|^CANONSamplingWorkshopEngineeringReport.pdf]), attended by scientists and engineers from multiple institutions. Heidi Sosik from WHOI presented an [overview of the Imaging Cytobot|^Sosik_HAB_cases_CANON_2010_Workshop.ppt] instrument and its application for HAB detection. Several breakout groups worked to identify compelling science problems and potential technical approaches to address them. Autonomous cytometry was identified as a key technology by the following breakout groups: Harmful algal blooms and phytoplankton, Zooplankton, Thin layers, and Mesoscale eddies. As a result of this workshop, Worden, Bellingham, Swalwell (UW) and O'Reilly began discussing potential integration of Swalwell's [SeaFlow cytometer|http://armbrustlab.ocean.washington.edu/resources/seaflow/] with LRAUV.

MBARI collaborated with UW's Armbrust, Swalwell and others to submit a [NASA ASTEP proposal in 2011|^ASTEP_2011_v8.pdf]. We proposed to miniaturize SeaFlow, integrate it with LRAUV, and deploy the system in a Greenland fjord.&nbsp; NASA rated the proposal highly, but was unable to fund it.

In 2012, we submitted an internal [MBARI proposal|https://mww.mbari.org/resources/2013_Proposal_Process/Abstracts/901303_CytoAUV_2013_updated.doc] that would miniaturize SeaFlow, integrate it with LRAUV, and test the system in Monterey Bay. We proposed that SeaFlow inventor Swalwell participate in a consulting role, providing guidance on approaches to minimize instrument size and power consumption, improve shock protection, etc. Although rated as "likely to be approved" by MBARI management, we were unable to reach agreement with Swalwell on his technical and scientific role. In response we submitted an internal MBARI [feasibility study|https://mww.mbari.org/resources/2013_Proposal_Process/phase_I_pdfs/901303_FeasibilityStudyCytometerTechnologyForAutonomousPlatforms.pdf] to look at a broad range of commercial and research cytometers which could potentially be integrated with LRAUV and other MBARI autonomous platforms.

h1. Science applications and requirements

[Taxa tracked in MBARI BOG database (D. Kolber)|https://docs.google.com/document/d/1WdLq86y746JG-xvxvr8085kcTkOeig9y3M_GS4GtTTc/edit]

[Potential AUV applications|CytometerTech:Science applications and requirements]

h1. Existing instruments

[SeaFlow, SeaLabel|CytometerTech:SeaFlow and SeaLabel]

[CytoSense, CytoBuoy, CytoSub|CytometerTech:CytoSense, CytoBuoy, CytoSub]

[Imaging Flow Cytobot|CytometerTech:Imaging Flow CytoBot]

[FlowCam|CytometerTech:FlowCam]

[Digital Holographic Microscopes|CytometerTech:Digital holographic microscopy]

[Cytometers compared with one another and to other methods|CytometerTech:Comparisons between cytometers, comparison to other methods]

h1. Technologies

[Coulter Counter|CytometerTech:Coulter Counter]

[Cell phone cytometer|CytometerTech:Cell phone cytometer]

[Cell-substrate Impedance Sensing, Electroporation|https://oceana.mbari.org/confluence/display/CytometerTech/Cell-Substrate+Impedance+Sensing+Electroporation]

[Optical Detectors|CytometerTech:Optical detectors for flow cytometry]

[Technologies overview - 1]&nbsp;

[Technologies overview - 2]

[Technologies overview - 3 (Specifications and parameters))]&nbsp;

h3. [Meeting notes|CytometerTech:Meeting notes]

Ken Johnson and Gene Massion - Coulter Counter, 9/12/2013


[Visit by Heidi Sosik, 9/11/2013|CytometerTech:Visit by Heidi Sosik on 9-11-2013]

[Telecon with Fluid Imaging, 6/12/2013|CytometerTech:FlowCam telecon - June 12, 2013]

[Telecon with Fluid Imaging, 8/20/2013|CytometerTech:FlowCam telecon - August 20, 2013]

[Discussion with Jared Swalwell on 6/6/2013|^2013-06-06-MeetingNotes-Jarred Swalwell-by-DK.pdf]\\

h1. Useful links

[Flow Cytometry - A Basic Introduction|http://flowbook-wiki.denovosoftware.com/]

[Flow cytometry: retrospective, fundamentals, and recent instrumentation|http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279584/]&nbsp; (Cytotechnology, 2012); includes discussion of emerging cytometry technologies

[Imaging versus flow cytometers (Webinar)|http://webinar.sciencemag.org/webinar/archive/what-cytometry-can-do-you]

[http://plankt.oxfordjournals.org/content/30/3/333.full|http://plankt.oxfordjournals.org/content/30/3/333.full][The emergence of automated high-frequency flow cytometryâ??|^emergence-of-automated-high-frequency-flow-cytometry.pdf] (Journal of Plankton Research, 2008)&nbsp;

h1. Potentially relevant workshops, conferences, trade shows

[Cytometry Development Workshop|http://www.sanfordburnham.org/labs/Price/CDW2012/], Asilomar&nbsp; - Next workshop is October 23-27, 2013
\\
This is apparently a technology-oriented workshop for experts in the field - perhaps Alex Worden is the only one who would qualify.

+American Society for cell Biology+ , conference and expo, mid December annually.

[www.ascb.org]&nbsp;]]></property>
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*O'Reilly's notes on 10 am meeting.*

*Attendees: Heidi Sosik, Denis Klimov, Tom O'Reilly*

Questions:
Plans for small/low-power instrument?
Can FCB/IFCB be deployed without power/data cable-to-shore?
HS: Working on "low-relief" IFCBT for deployment on Wave Glider, AUV, other platform
Current IFCB takes 30W power

Particle size range overlap of FCB and IFCB?
HS: Difficult; IFCB laser is optimized for microplankton - picoplankton requires higher-power laser. FCB is still original prototype (large) - no funding or plans to refine. CytoBuoy claims pico-micro capability.

Could you replace sheath fluid with virtual core technology, ala SeaFlow (Need to add position-sensitive detector(s))?
HS: Would be concerned about flow-cell cleanliness - core fluid keeps particles moving through flow cell. Very occassionally get dirt in cell - would this be a greater problem with SeaFlow/SeaLabel?

Processing:
HS: Several stages; detect particles (reject particle-free images regions). Edge detection, etc. Classification
Now using "random forest" approach instead of SVM (2007):
\- rf requires less tuning than svm
\- svm requires complete characterized dataset for error characterization; rf doesn't
\- both methods yield comparable accuracy

How long did the image-processing/classification procedures take per image? On what hardware?
HS: particle detection/empty-image rejection executes in situ on instrument's "Atom" processor. Shore-side workflow in realtime, posted on MVCO website ([http://ifcb-data.whoi.edu/])
HS: Image processing is more computationally intensive than classification
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*O'Reilly's notes on 10 am meeting.*

*Attendees: Heidi Sosik, Denis Klimov, Tom O'Reilly*

Questions:
Plans for small/low-power instrument?
Can FCB/IFCB be deployed without power/data cable-to-shore?
HS: Working on "low-relief" IFCBT for deployment on Wave Glider, AUV, other platform
Current IFCB takes 30W power

Particle size range overlap of FCB and IFCB?
HS: Difficult; IFCB laser is optimized for microplankton - picoplankton requires higher-power laser. FCB is still original prototype (large) - no funding or plans to refine. CytoBuoy claims pico-micro capability.

Could you replace sheath fluid with virtual core technology, ala SeaFlow (Need to add position-sensitive detector(s))?
HS: Would be concerned about flow-cell cleanliness - core fluid keeps particles moving through flow cell. Very occassionally get dirt in cell - would this be a greater problem with SeaFlow/SeaLabel?

Processing:
HS: Several stages; detect particles (reject particle-free images regions). Edge detection, etc. Classification
Now using "random forest" approach instead of SVM (2007):
\- rf requires less tuning than svm
\- svm requires complete characterized dataset for error characterization; rf doesn't
\- both methods yield comparable accuracy

How long did the image-processing/classification procedures take per image? On what hardware?
HS: particle detection/empty-image rejection executes in situ on instrument's "Atom" processor. Shore-side workflow in realtime, posted on MVCO website ([http://ifcb-data.whoi.edu/])
HS: Image processing is more computationally intensive than classification\\

*Klimov's notes from 10:00, 12:00, 16:00 meetings*

Principles of operation:
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; FlowCytobot / Imaging FlowCytobot sample path arranged in such a way as sample goes "down hill" due to plankton sinking.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Newer Imaging FlowCytobot (licensed to Mclane) is developed entirely at WHOI. McLane did some adaptations to simplify production. 8 inch diameter tube, 40 inch long. First unit built in August 2013.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5ml sip, then 20 minutes analyzing. This time can be reduced by sipping less, say 1ml then 4 min analyzing, but the period can not be much shorter due to time overhead (pump start/ stop etc) and required statistics.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; this design has emphasis on accurate statistics so flow and volume need to be precise, so syringe pump is used with defined volume.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Emphasis on "binning" to get particle statistics per "shot" and not as continuous measurement; so "binning" is ok here.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Also, accurate flow rate is required, due to separation of "trigger volume" and image acquisition volume within a sample cuvette, and fixed time delay between trigger and acquisition of the image. Image is acquired with 1 us light pulse from Xenon lamp.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid is preventing the contact between sample water and walls of the cuvette, minimizes chance of contamination and particles attachment to cuvette walls, very important feature.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sheath fluid is recirculated by filtering sample + sheath by volumetric Fisher filter. Excess water is dumped into environment before filter. Filter lasts 6-8 month deployment easy.
&nbsp;
Use of Imaging FlowCytobot on a mobile platform:
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Configuration of the sample path dictates "vertical" position of the instrument so it operation in horizontal orientation could be problematic.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; For glider use, perhaps the Imaging FlowCytobot can be split into set of housings and then arrange them horizontally.
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Suggestion: keep volume of those compartments relatively small (under several hundred mL) to avoid vehicle loss in case of flooding one compartment.
&nbsp;
&nbsp;
Difference between FlowCytobot and Imaging FlowCytobot:
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Particle ranges: FlowCytobot 1-15 um, Imaging FlowCytobot 5-200um
\-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Cuvettes have different geometries: FlowCytobot has smaller cylindrical flow cavity for tighter light collimation of laser, and Imaging FlowCytobot has "50 um sheet" of fluid optimized for imaging and larger laser beam for triggering
\-&nbsp;&nbsp;&nbsp; Light sources are optimized differently for smaller circular path, or wider flat path
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