I am counting the number of y-H2AX foci per nuclei in a microscopy slide. The original image had two channels and was in ‘.lsm’ format. I split the channels and created two ‘.tif’ format images, one having nuclei and the other having y-H2AX foci using ImageJ. I segmented the nuclei and foci using watershed algorithm in opencv. After that, I overlay one image over other. Finally, I have an image that looks like below.
I am unable to count the foci (yellow) that lie inside these nuclei contours (green). Could somebody help me here?