MONDAY: Standardized the navigation bar of the CPF MCS GUI. Started work on the individual CPF plots page. Experimented with the pre-release "tab" functionality of Dash.
TUESDAY: Had a 2.5 hr meeting with Gene about starting a new CPF depth controller project. Read Laughlin Barker's (2014 intern) report. Discussed the physics model of the CPF, previous MATLAB and Simulink models, the PID speed controller, and how the current cascaded-PID depth controller can be improved. Reviewed lead compensator design via the root locus and frequency response methods. Contemplated a lead-compensation vs. LQG approach.
WEDNESDAY: Intern BBQ. Continued to experiment with tab functionality. Installed MATLAB and Simulink on my work laptop. Started reviewing drag coefficient estimation for cylinders and plant linearization.
THURSDAY: Meeting with Mike Risi to discuss controls at MBARI. Supporting an outreach volunteer event at Sherwood Elementary in Salinas.

This week has been mostly working to get the final draft of my open house poster ready for printing. It was a but more difficult than expected because I only have experience making academic posters rather than a poster for the general public. But I finally got it done! I have also been working on my methods and am nearly at a final draft. This week has been all about the intern BBQ with shopping on Monday then prep Tuesday and Wednesday. During BBQ prep I ended up giving myself a nasty cut but thankfully Nina was there to save the day! In lieu of attending the BBQ I got to go to lunch with Nina Bednarsek, the seminar speaker. I really enjoyed her talk about ocean acidification as it is a topic I have recently become interested in. Today I will be going to speak to middle school kids about science with Alisa which is always fun. Hope everyone has a great weekend!

It has been a very busy week back after the holiday break! I started work on developing algorithms, specific to the Monterey Bay region, that will help predict carbonate system parameters from easier, more ubiquitous input measurements like temperature, salinity and oxygen. On Tuesday I was on the Rachel Carson for the monthly BOG cruise collecting water samples from three mooring sites in the bay. Myself and my lab's tech ran pH samples through the Agilent phSYS system simultaneously with the BCG SUMO system while on the boat. The BOG folks also collected samples for pH which I ran yesterday back at MBARI. So all three measurements will provide some really interesting comparison data. Today I'm going back out in Elkhorn Slough to do some more sampling, which will also mean more samples to run on the pHSYS system. Oh yah and also we cooked food for all of MBARI - great job everyone!!

Despite the realization that football (see also: soccer) is, in fact, not coming home, it's been a good week. qPCR is going well, and have finally got some data for my project - which is always useful. Not a huge amount to update on, except that for the next week I will be shackled to the lab getting through the remainder of my PCRs.

On Tuesday I attended a seminar at the Naval Postgraduate School on how humpback whales produce their vocalizations. It's fascinating that these mammals are able to produce sounds with no vocal folds. Instead they pass air from their lungs to laryngeal sac, opening and closing their arytenoid cartilages!

Since I now have labeled a handful of songs, I am beginning to run some statistics on them. I installed MATLAB and yesterday I created a bar graph (with error bars) of the average durations of song units for the labeled songs. It is apparent that the means are not significantly different as all the error bars overlap.

Good morning everyone!

I have been working with my mentor, Danelle Cline, to ensure the right components of our revised Mbarivision.C file includes Mayra's BoxObjectDetection code. I have put together everything needed in the main file, but ran into 2 changes needed in order to see results of detection. I will be finishing these 2 changes today. Today, I'm planning to meet with my mentors to discuss further steps and receive help on existing code.

Changes needed:
1) Converting showAllWinners(list<Winner>, ...) to showAllWinners(list<Rectangle>, ...) to output the frame from the MbariResultViewer.

2) run() method from the BoxObjectDetection class had been changed to adapt to using a "Colored" image than a "Grayscale" image. (Received help from Danelle)

Hello everyone!

My work this week consisted of understanding what is needed in the BoxObjectDetection class and working with Raymond to put together our revised Mbarivision.C. I have been receiving help from my mentor, Danelle Cline, to ensure my BoxObjectDetection class contains the right components and the correct revised algorithm. Today, Raymond has informed me what different problems we have ran into before running the main file and we will begin working on that. Also, we will be having a meeting with our mentors today to discuss about future work and receive help on the code we have as of now.

This week I did a little statistics to decide on optimal parameters for our spectrograms so that 95% of units have reasonably high (but not too high) resolution. I then computed spectrograms for all humpback songs in the dataset and attempted to cluster the fft frames on my local machine. It turned out that my local machine's memory isn't even enough to load all the data so my mentor Danelle set me up with an account on a more powerful machine. I am currently putting together a docker image that I can transfer to the beefier machine and cluster on there. Hopefully I can at least get all the data into memory. Once I have the cluster labels and centroids, I can move on to training the topic model and see some (hopefully good) results. Fingers crossed.

This week was mostly returning intern things for me (organizing the bbq, organizing the t-shirts, continuing to try and contact breakwater scuba, etc.), so thanks for all your help with those things! It is muchly appreciated.

I did get to do some work on my vampy project - I went up to UCSC to get trained on their Mass Spec machine (and ran into John Ryan in the parking lot, haha), and decided to start working on the octopoteuthis luciferase/symplectin-like protein. I am also waiting for some material for pichia yeast expression (for the vampy luiferase gene), so I can start working with this new expression system. The next few weeks are going to be a combination of furiously working to express my vamp luciferase in yeast, and during its long incubations, trying to extract and assay the octopoteuthis protein.

Happy Thursday! Is it just me or does this week feel like it's been reaaaaallllyyyy loooong (maybe it's due to the fact that last week was a two-day work week). Nevertheless, it feels good to get back and continue the work. This week has been exciting! Monday was spent prepping for my chaetognath time sequence experiment And then Tuesday, I actually got to run the real thing! Basically Tuesday and yesterday consisted of me running back and forth to the lab every 1-3 hours to assay my homogenate for light. After talking with my mentor about the results I was getting, we decided that I needed to change my concentration of coelenterazine (what I add to my crushed up chaetognath to start the light reaction) because it seemed like I had too much. So today, I'm going to make the new coelenterazine solution and test it on my samples. I'm also going to do some troubleshooting for the rest of the week so that on Monday, I can redo the experiment and get cleaner results. This first time was kind of my trial run.

Hi everyone!

This week has mostly been the same stuff for me down in the sea lab. We've been going though our daily routine of feeding abalone, checking for mortalities, flow, and temperature in the tanks. Yesterday was more eventful though, since all of us at the Barry lab got to meet with Nina at 9am to talk about her research on OA effects on pteropods. We also got to show her our own upwelling system we have in our lab as well! The BBQ was also fun, and I'm glad we pulled it all off! Otherwise, my weeks are mostly spent taking care of abalone and doing more image analysis.

Hello everyone,

this week has been, again, very eventful.
Last week my advisors left me with a long list of what I should work on, since they are absent for two weeks. So I started working my way through the list, and am reporting to them over e-mail about my findings, as well as to get advice on how they'd like me to approach certain situations or problems.

Right now, I am mostly focusing on two things:
1. We noticed many irregularities in the calculation of our BIC values, implying we might have been using inaccurate BIC values after switching to them from AIC. So I am mostly focusing on researching the equations and investigating what is the cause of these irregularities in our code, comparing multiple methods. This takes priority, since even if all the code is running correctly, if the BIC values are wrong or inaccurate, this could lead to results that are not optimal, although they should still be usable (the number of optimal change points could be under or over-estimated, but to what degree is undetermined).

2. I am writing a separate script to run through all SOCCOM floats available and collect the best correction for each. For this, I am using the calculation that finds the optimal change points at depth only (~1500m), and then corrects the data to these. The purpose of this is to eventually compare the new, automated method with what has been done manually in the past, seeing as most of these floats have already been manually corrected. Then we can compare them and better assess how accurate each method has been.
I have started writing this, however to fully run it and compare methods, the BIC values have to be fixed. Then the analysis can be much more reliable.

To accomplish this, I have been looking into more papers and sources that explain more in depth about BIC calculations, as well as change point detection algorithms overall. I am also happy to find that other sources/studies have relied on BIC values to perform accurate change point detection, so I can trust that it will be an accurate approach once we correct our calculations.

Besides this, we put on our first BBQ this Wednesday, and I was happy to help prepare and clean up alongside all the interns. It was a really fun experience, and the interns are pretty impressive at preparing and cooking food! I hope everyone else enjoyed it as well.

Have a great week

Hello,

This week, we were doing abalone husbandry like last week. We saw some mortality in the small size class.

Yesterday, our Lab met with Dr. Nina Bednarsek and she was really interested in our upwelling System.

This week I have been working on getting better surface normals from my data. Surface normals are vectors that are associated with each 3d point and indicate the direction of the surface created by the point and it's nearest neighbors. There is a variant of the algorithm I am using that works much better if I can have one scan with normals in it, so that it can be treated like a plane. It works very well in my some test scrips I have written but, but not as well in the production code so I am still trying to figure that out.

Besides that I also talked with my mentor and came up with a plan for quantifying the "fitness" of the match one it is done, and will work on that next week.

Today and tomorrow I am out at sea, observing the deployment of AUVs for testing new localization programs.

This week began with meeting with my mentor after she came back from her vacation. It was very helpful in figuring out what were some of the next steps to begin building a prototype of the jellyfish device. Since we want to include a spring, I began researching int springs and seeing which type would be best to implement into our design. I finally began to build the prototype by Wednesday after the BBQ. I recently just tested it out and I was able to get a successful release. Of course, the current spring I am using makes the whole package far too heavy, but it shows that the design works in a very basic background. So I will spend the rest of today testing it once more and then seeing what kind of spring to order, that we will be implementing into our actual design and not just the prototype.

This week feels like a long week back in the office after hiking in Yosemite! I'm preparing all the content for my Open House exhibit to test the activities I've been developing. We're hoping to 3D print some phytoplankton models, have a phytoplankton sorting game and have some coloring sheets, as well as some graphics about phytoplankton, HABs and digital screens showing the live data and images of phytoplankton out in Monterey Bay.

Kristen and I went to a school in Salinas this morning and ran an STEM workshop with them, blindfolding kids and getting them to pretend to be ROVs as their classmates guided them around the room to find pens. It went really well - hopefully we've got a few budding scientists in that class!

And my exhibition officially opened two hours ago! First reviews are out, I particularly like 'spine-tingling': https://www.theguardian.com/artanddesign/2018/jul/12/life-in-the-dark-natural-history-museum-cave-diving-tham-luang-thailand I'll bombard you all with more videos/images as they come in.

This week I mostly worked on the Matlab script to analyze the kinematics of my model. It is going well so far, except for small modifications I have had to do along the way, and trying to figure out a way to accurately measure amplitude. Today Brian and I did a STEM workshop at an elementary school, and it was really nice to be able to talk to really young kids about aerospace and ocean engineering to inspire them to want to go into stem in the future.

Hi all,

 This week, I've been working almost entirely on the Mesobot project. I developed a simple (and very flawed) process for background subtraction to isolate moving targets in a moving environment. If you want to check it out, I made a short clip: https://drive.google.com/open?id=1nWLf3embMBtvPAMpPU5PqPkGAPiiOcxL

The overall procedure for that process is 1. stabilizing the frame (tracking keypoints, calculating optical flow using the Lucas-Kanade method, then estimating a matching 4-DoF affine transformation between successive frames), 2. pre-processing the frame to cut down on marine snow (opening morphology transformation and a slight Gaussian blur), then 3. applying a background subtraction model (MOG2) to make a mask of the foreground. The green dots in the video are just from a simple blob tracker. The goal here is to be able to separate the giant larvacean from its house visually and eventually be able to track them separately.

Other than that, I've been working on making the data visualizations for the external collaborators on the FathomNet project. I'm currently building a library of tools to help visualize the database that I've assembled. I should finish up with the image watermarking process today, if all goes well.

Hi all,

Sorry for the delayed post, but I've been out of the office all week and canyonhead wasn't letting me log in. For some reason, it finally let me log in today. Go figure.

This week hasn't been the most productive, but I've been working on writing code for a couple of different functions as I look at this data analysis. I've been working more on despiking my velocity data and then trying to rotate my velocity vectors. I spent a lot of time thinking about this idea this past semester working with electrodynamics, so the math, thankfully, isn't too bad. I've never coded it though, so that is creating a new challenge.

I'm looking forward to being back next week. See you all on the kayaks.

Hi everyone,

My post is late because I was on the Western Flyer on Thursday! The ship was supposed to leave on Monday night, but a part for the steering was broken (apparently that's kind of important) and had to be ordered. On the bright side, this meant I was able to attend the Wednesday seminar and help with the intern BBQ. I continued analyzing video footage from Sur Ridge until getting on the boat on Wednesday evening to go see some of the same locations in real time. The dives at Sur Ridge were amazing, but I'll save those details for the next update!