I am trying to use make ROIs and measure co-localization within them using JACoP. Every time I make an ROI and split channels in order to assess colocalization between channels the ROI is removed and values stay the same as if I were measuring the entire image. Can you please point me towards a tutorial or provide some guidance?
Though - regarding ROIs specifically… have you ever taken a look at Coloc2 for these analyses? I have used it successfully with ROIs… The UI is not as pretty as JACoP - but it functions as it should and will get the job done for sure.
This email thread from the ImageJ mailing list a few years back might be of some interest to you as well. Just keep in mind - all those updates were made in Coloc2 for ROIs.