Overview

Notes

The printer used by Chris Scholin is a custom printer. It can not output GAL files. It does put out a text file that I'm trying to parse and work with. A copy of the file is checked into SVN.

Piezzo Array Printer

The file that is used to describe the Piezzo array has lines that look like this:

SpotNum	SrcWell	SrcNum	TipNum	SubNum	SpotX	SpotY	SpotVol	Status
1	C-1	1	2	5	9380	45310	20	OK
2	A-1	1	1	5	9380	50590	20	OK
3	C-1	1	2	4	9380	74060	20	OK
4	A-1	1	1	4	9380	79340	20	OK
5	C-1	1	2	3	9380	102810	20	OK
6	A-1	1	1	3	9380	108090	20	OK

SpotX and SpotY are coordinates in micrometers starting in the upper left hand corner of the paper. The 0, 0 point is actually 6.5mm from the upper left hand side of the paper itself. Multiple arrays are usually printed on a single paper and then cut out.

SrcWell indicates the contents of the spots. For example, all spots from the C-1 source well will have identical chemistries applied.

Image Analysis

Maximum Entropy thresholding does a decent job of delineating the control spots. Unfortunately, I haven't found a technique for delineating the spots that don't go off. In fact those spots can contain values within the range of the background noise.

(view as slideshow)
	Raw ESP image		Masked Image

Possible avenues of exploration

The ESP folks would like an automated image analysis package that:

1. Reads the image
2. locates the spots (either with or without the help of the GAL-like file)
3. Read the highest 8x8 block (full size image) or 4x4 block (half-size image) average within the spot. The block average is square with no weighting applied.
4. Return a text file (Tab or comma delimited) with:
   • Average intensity associated with the SrcWell (i.e. C-1, A-1, etc.)
   • Standard deviation by SrcWell
   • Average intensity of background disk (excluding spot values)

Analysis Steps (in progress)

1. Read in layout description file with LayoutViewer
2. Generate a single assay image.
3. Select the control spots and export spot list to a new Layout Description File
4. Read in single control spot list
5. Read in measurement image.
   • Convert to binary image using maximum entropy threshold technique
6. Convert both images to polar and log-polar coordinates
7. Calculate translation and rotation of control spots using techniques described in Robust Image Registration Using Lo-Polar Transform

References

1. Old ESP Matlab toolbox at http://moonjelly/cgi-bin/cvsweb.cgi/ESP/matlab/

bac_neg_N12_P1_A608feb2717h0ml160s.png (image/png)
bac_neg_N12_P1_A608feb2717h0ml160s_threshold.png (image/png)