Advice about code

Hello guys, I’m new on the forum.
I would like to have an advice. I’m writing a code to count the number of cell inside a gel. I want to count the cells positive to Dapi (blu) and the cells positive to the green staining. When i was analyzing a single slice of the gel I was using the function FindMax() but now i have to analyze the whole gel and there is too much noise to use this function. That’s why now i use the sequence make binary, watershed and analyze particles on each channel.
This is what i obtain:

Do you think it could be a good analysis or do you have an advice for me?
I’m not able to use cellprofiler yet and i would like to do with it the same thing i did with imagej.
Thanks for your help


if you just want a detection and noise is a problem then you could combine it with filter to suppress the noise. I would usually use a Gaussian filter which effectively reduces noise in the signal and allows a robust maximum detection.


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thank you schmiedc,
do you have an idea to write a pipelines in cellprofiler?

I do not have so much experience with Cell Profiler. You can have a look at existing pipelines here: