Hello,
I am new to CellProfiler, and this type of software in general. I went through some posts but couldn’t get past pipelines to load (I am using version 2.1.1)
I have some feline cells I am trying to analyze- for now just cell counts and size of both stained and unstained (see attached)
Whenever I run some modified pipelines (from the sample HumanImages) it ends up counting the interstitial fluid as cells. How can I get it to recognize the cells I want?
Thanks!
Hi,
The quick answer is that:
(1) CellProfiler expects that foreground objects be brighter than background. For fluorescently labeled objects, that is no problem, but for histological sections or any traditionally stained bright-field samples, you’d first have to transform the images (try the UnmixColors module!).
(2) Bright-field image analysis is hard! 
If it is at all viable, add a fluorescent marker, e.g. DAPI. The added benefit is that you will be able to get a much simpler count of all cells (by counting separated DAPI-marked nuclei, and then count the stained cells too. As it is, I find it hard to distinguish between adjacent brown cells, but even harder is counting the unstained cells!
I did create pipeline to segment the stained cells (attached). Even this is difficult as it is, and I don’t think that counting the unstained cells will be that viable without a change in staining (nuclear, or possibly a better and more continuous membrane stain), though feel free to try and post your pipeline attempt!
Cheers,
David
DL_attempt_stained.cppipe (5.6 KB)
