Using ImageJ (Fiji), is there a way to threshold and get a count of colocalized channels? I have tried the JACoP plugin and it gives me interesting data and it gives me a count, but it doesn’t show a map of what was actually thresholded. Further, the Coloc threshold under analyze in Fiji gives me a map, but no counts. Is there a way to get both an overlaid map of the colocalized signal and an accurate count? This is for colocalizing Propidium Iodine and nuclear staining.
I realized this is a bit late, but I am just looking around the forums for fun and this sounded like something that might be a good test for a new QuPath script, if you were willing to give it a try.