Is it possible to quantify the number of cells that are double or maybe triple positive for fluorescence markers in imagej?

I am mainly interested in quantifying cells that are double positive for two fluorescence marker. Specifically DAPI and SOX10 which are both localized to the nucleus. I have been reading around and it does not seem that imagej is solely capable of this and maybe an additional software maybe needed.

If I understood it right what you are trying to do you should have a look at the different colocalization plugins. I think the EZColocalisation plugin can help with two markers, see:

See also:

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Thank you for the suggestions but the colocalization plugin (i.e colo2) does not give me what I need. It does not give you any quantitative output just how well your images aligned with each other. EZcolocalisation seems to be ideal but do you happen to know where I can find the plugin for that

If you want to try EZcolocalization, you need to manually add their update sire to your Fiji installation, following these instructions .
Since it is not listed, you need to add it by giving the URL

I hope it helps

The download and install instructions are cited in the article I cited before: