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.
Is it possible to quantify the number of cells that are double or maybe triple positive for fluorescence markers in imagej?
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:
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 https://imagej.net/Following_an_update_site#Add_update_sites .
Since it is not listed, you need to add it by giving the URL http://sites.imagej.net/EzColocalization/
I hope it helps
The download and install instructions are cited in the article I cited before: