Intensity at center of mass

Posted by MuchMaas on Sep 11, 2015; 6:43pm
URL: http://imagej.273.s1.nabble.com/Intensity-at-center-of-mass-tp5014319.html

Trying to write a script that will identify the center of mass of a fluorescent foci, and give me an intensity at that point as well as an average intensity of the entire roi.

I can select all the foci present with a mask, split them into individual rois, then measure average intensity, area, and center of mass.

But I have no clue, after hours of searching, what to do with the XM and YM center of mass values. The best I can figure is they correspond to pixel coordinates relative to the selection and not to the image as a whole. In other words, when I try to use these coordinates to measure intensity at the center of my roi, the selection is in entirely the wrong part of the image.

Quite lost, quite frustrated.

Can anyone help me A)understand how to use the XM YM values, and B)write a simple for loop to find and measure intensities at the centers of all my rois?

Any thoughts would be greatly appreciated.