colocalization on stack with threshold?

Posted by jvanleuven on Jan 30, 2014; 5:12pm
URL: http://imagej.273.s1.nabble.com/colocalization-on-stack-with-threshold-tp5006343.html

Hi,

I am trying to do a simple non-colocalization analysis and keep running into problems. I hope that someone can help me out.

I have a 84 slice stack with two channels. I want to measure non-colocalization (i want the cross-correlation function) of these two channels across all 84 slices. Also, I would like to estimate the number of pixels belonging to each channel in the image (e.g. 40% chan 1, 60% chan2).

Issues:

high background: would like to measure the average intensity of user defined background ROI (of each slice) and subtract it from the image. I would also use this value to threshold.

need to calculate non-colocalization on specified ROI because the imaged tissue is complex and has areas of autofluorescence. One ROI WILL work for the entire stack.

Many thanks for any suggestions.

-james