overlapping 2 sets of ROIs

Posted by itzpapalotl on Aug 06, 2014; 9:24am
URL: http://imagej.273.s1.nabble.com/overlapping-2-sets-of-ROIs-tp5009043.html

Hi,

I am a PhD student and a beginner with ImageJ. I recently started doing immunofluorescence experiments and I am looking for a way how to analyze the pictures.

I have 2 channels, first one with DAPI stained nuclei and the second with some of the cells stained for a cytoskeletal marker. I need to count the number of nuclei that are only in the cells marked in second channel. So far I figured out how to count the total number of nuclei in DAPI channel and I can make ROIs with stained cells from the second channel. Now I need to make an overlap between those 2 sets of ROIs and then count the resulting ROIs (the nuclei that were present only in marked cells).

I tried to search the forum, but I only found topics about overlapping single ROIs, not whole sets of them.

I would be very grateful for any kind of advice.

Lenka