Microscopy Image Analysis

Hi All,

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?

Thank you.

Sachin Dev

Try to make an histogram. Read tutorial herehttps://docs.opencv.org/master/d1/db7/tutorial_py_histogram_begins.html

In the first step use findContoures to find nuclei Contoures .In next step by floodfill process content of each contour for each foci .

please post the full size picture, not a thumbnail.