P: Provide image analysis for Microbiology

Adobe should be looking at ImageJ, which has all sorts of scientific tools and features, and is public domain.

https://imagej.nih.gov/ij/features.html

If anyone at Adobe is looking for something to point Sensei towards... Cell counting, identifying, analyzing, counting...these are still big, difficult image data tasks.

I was searching to see if there is any way to record count groups and found this thread. I'd like to see an Analysis feature where count groups would be recorded. As it is now, only the total Count Tool count data is listed. I'm working with double labeled tissue and we want to record green cells in one count group, red cells in another and doubled-labeled yellow cells in a third count group and have that data recorded and exported.

that feature could be usefull for other purposes too!

David, this is fantastic!

Bingo--I agree completely, Christoph. It's funny, when I look at the photos above, it's completely trivial to determine what is a cell and what isn't, even though the cells overlap in some places (incomplete shapes), vary in intensity, and even vary in signal-to-noise. It feels like there's got to be some way to capture that, which would advance selections in general in Photoshop. Selecting by approximate shape and volume would, I suspect, really make a difference.

Adobe folks: There's a free tool called Cell Profiler (http://www.cellprofiler.org/) that is designed to count cells in an image. While I think that having a selection tool that could target shape, area, intensity range, and signal-to-noise would be a universally valuable feature, it may be useful to see what other folks have done already with regards to this problem.

The formulas mentioned in that software are probably a good starting point, although I have to admit, the math is not my area of expertise. Cell Profiler's main limitations, acording to the folks using it:
1) Post-acquisition pre-processing. The software demands images to be prepped to clearly distinguish cells, and provides channel filters and contrast adjustments. These are rarely effective alone due to varying intensities and noise; Photoshop is frequently used to prep images
2) Adaptability. Cell Profiler requires the user to choose a type of cell, which results in a shape-based analysis. Some cell shapes aren't in the menu or aren't identified correctly.
3) The software chokes on large image sizes.

I hope this sort of thing is something you guys would be interested in!

Zorana--I did not know that, and it's magnificent; thank you for your insight!! 🙂

The issue reminds me a bit of a topic concerning archeological photographs that has brought up in the user-to-user Fora; it concerned automating scaling large numbers of images according to a ruler in the photographs.

I think some form of shape recognition that users could run based on a path or a channel might be quite useful to the scientific users – possibly not with the spindly cells above but in other cases maybe.
And I have the somewhat vague suspicion that Photoshop performs such tasks already in bank-note recognition and possibly also in Auto-Aligning.

Are you aware that you can run an auto-count from your selection? If you have Extended, and using PS tools to select out what it is you want selected, got to Analysis > Record Measurements (make sure that you Select that Data Point from the same menu). This will spit out the total count in the Measurements Panel (and you can also export this as csv).

Are you aware that you can run an auto-count from your selection? If you have Extended, and using PS tools to select out what it is you want selected, got to Analysis > Record Measurements (make sure that you Select that Data Point from the same menu).

Indeed. Always awesome to see the scripting junkies swoop in with a great solution! Well done.