Count particles with different colors at once

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maybe this was already discussed elsewhere, but I couldn’t find it.

I have optical microscopy images with cells and background tissue stained brown. My aim is to count all stained cells (stained are both cytoplasm and nuclei) and of those asses the number of the cells that show weak in the nucleus. I can manually pick the cells in an image editor and assign them two colors, e.g. red for those fully stained and blue for those with negative nuclei, and export the image as red and blue dots on white background.
What I was trying to achieve and totally failed in is to tell the ImageJ to give me the count of all dots (particles) and tell me how many of them are red and how many are blue and also to process all images at once using batch analysis (I have around 300 images) with tabulated results that I can export as one big table.
I have tried Cell Counter plugin, and this essentially did what I need but I couldn’t analyse more than one image without losing the previous results and I didn’t get summarized results table.
I also tried to make RGB stack that allowed me to correctly assess one image but again, I failed to generate summary result table with all analysed images (I tried to batch analyse five images and got summary with particle counts only for one).

I think that I am missing something elementary and that this can be also done using some trivial macro, but I have virtually no coding capabilities and the only thing I can do is to record the macro and then use it on the batch of images which I already did in different projects successfully.

Could anyone please help me with this?

Thanks a lot,


Hello @zdenekrohan and welcome to the ImageJ forum!

If you can open all your images as a stack, you can move among images while counting and won’t loose the results.


Thanks a lot Ignacio, that worked!