How to count cells from immunohistochemistry using Cell Profiler?

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Hi, I am new to CellProfiler and I’m looking for some suggestions on which modules I would need to use to count cells, such as those in the image linked; or any pipelines which are already up and running which I can tweak? The goal is to work out the ratio of brown cells/foci to blue cells (percentage of positive cells of the total in the image). The cells have undergone immunohistochemistry and imaging using a brightfield microscope. I have been doing this by hand using ImageJ, but the volume of images I will be taking makes this time consuming and unfeasible in the long run.

So far using Cell Profiler, I have managed to isolate the nuclei by changing the image to HSV and assigning one of the primary objects as OrigSaturation, as I found that it was easier to work with a darker background and brighter cells however, I am unsure how to distinguish the blue cells from the brown cells. Unfortunately, I am not sure that this method will work as my background is white and my distinguishing feature is the colour. I have tried using the RGB setting, but no luck. Thank you!

Hi @ABarry,

Try the Module “UnmixColors” in cellprofiler. Check here for details,

Hope this helps.


Thanks very much! I think I worked it out, but it can always be improved!