Cell Counting Script for the Biomedical Sciences

Question

I want to talk to you about something I envision will be of great use in the biological/medical community. This involves the creation of an Adobe PS script that will count cells manually with the click of a button. First let me tell you a bit about my research. As a medical student, I’m interested in ophthalmology and I hope to make it a career out of fighting preventable forms of blindness like glaucoma, macular degeneration and diabetic retinopathy. Here’s some background of my work in Glaucoma:
Glaucoma is currently the second most common cause of irreversible blindness in the world. This usually presents as increased Intraocular Pressures (IOP) that damage a certain subpopulation of cells within the retina called Retinal Ganglion Cells (RGC).
We have mice that work as great models for glaucoma. These mice are imaged before the onset of glaucoma and treated with pharmacological agents throughout their glaucomatous state that we hope will 1.) reduce IOP and 2.) spare the RGCs.
I’m attaching an example of the images I am taking from mice and also a sketch of what I envision the Cell Counting Interface to look like.  This is something that other researchers would definitely use specially if they are doing multi channel work with fluorescent antibodies.
Ideas for a cell counting script:
1.     The script should ask for a file or multiple files to open.
2.     Once image file is open,  the script will ask to highlight a working area. Multiple areas can be created within one image file but only one area can be active. There should be a button that creates a new area that is easy to expand its width and length and is also easy to rotate and move similar to the Free Transform function on PS CS3.
3.     Cells will either be Red, Green, Blue or Yellow (overlap between red+green signals). When a specific area is toggled active and the researcher has the Red Channel toggled in preparation to count all the Red cells within the toggled active area, each Left click of the mouse will put a small solid red circle (adjustable to account for larger or smaller cell sizes) over the clicked cell on the image. This cell will be counted under the Red Channel for that particular “Active” area. There will automatically be a “Total Area toggle that, when active, will sum all the areas and will take a tally of the total number of Red, Green, Blue and Yellow cells that have been manually counted. As an example, say the researcher wants to work in an area of the image file whose cells have not yet been counted. The user clicks the button, “Create Area” and an “Area N” line is created below the button. The “Area N” line has a corresponding toggle switch that is clickable in order to activate. Simultaneously to creating the line below the button, the user will hold the Left click on the mouse, drag it to create Area N, and release when the desired size is attained. The user can then rotate and make final adjustments to make sure it is in the desired spot in the image file.
4.     When the area is active, a thicker bright outline distinguishable from the rest of the areas will be seen. Clicks will only be allowed within an active area. If the “Total Area” toggle is selected, all areas become active, yet the script will be robust enough to keep track of which cells came from what area and add these to the Total Area numbers
5.     If a Channel is deselected all dots of that color (Red, Green or Blue) will be invisible until the channel is selected again. 
6.     Two  or more scripts can run at the same same time.
7.     A print out will print the raw image plus the image with the dots, the filename, the individual area statistics (cell counts per channel) and the total Area and total cells counted (Total Red, Total Green, Total Blue, Total Yellow)
8.     The user has to manually interact and click on spots he/she thinks are cells.  (Automated programs are not as good at picking out cells from artifacts left
9.     Oh, Right clicking on a dot should remove the dot and subtract it from the cell counts.
Conversion for Area calculation:
x pixels = y microns
Area in microns squared =  ((H pixels X y microns)/ x pixels) X ((W pixels X y microns)/ x pixels)

Answer 1

Some of what you want is possible. Take a look at the Count Tool in CS3/4. It may only be available in the Extended versions. That provides a
reasonable interface for marking items in a image like you are wanting to do with cells. Take a look at that and see what kind of manual process
you can get worked out.
However, to get the workflow you want (or anything close to it) would require more than a little code.