Cell counting with 2 channels

Hi all,

I am wondering if there is a way to get ImageJ to automatically count cells based on whether signals from 2 channels are present? I am trying to count oligodendrocytes and have DAPI and p25a as markers. I want to be able to count only the particles which show both signals as the image contains different combinations of these. I was thinking maybe a mask of one channel overlaid on the other could work but I am not sure if this is possible. I would appreciate any suggestions. Thank you!

Hi and welcome to the forum,

one way to achieve what you want would be to first segment each channel individually and thereby generate masks.

Than you can use to generate the intersection of those using the image calculator using the Multiply or AND command:
Process > Image Calculator

This leaves with binary masks only the intersection.

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And if you are willing to try something slightly different, Pete wrote about this problem here:


Further information on both programs here:

I tend to prefer the QuPath route since I can click a few buttons and run it for the whole project of images, but I am also far more familiar with it :slight_smile: YMMV