Image analysis in ImageJ


I’m new to ImageJ, so any help would be appreciated! I have 3 channels of 1 sample. The first channel is stained for the nuclei, the second channel is stained for the mRNA spots, and the third is a stain for a specific protein (not relevant for this question).

I want to assign the mRNA spots to the closest cell. I know that I can count the mRNA spots within a nucleus using “Analyze Particles” feature of ImageJ, but I wish to assign mRNA that is outside of this nucleus to the cell and count that as well.

Any idea of how to do this?


Threshold the cells, analyse particles and number each found cell (x,y coordinates from Analyse Particles, flood fill with cell counted so far), make region on mRNA spot, measure average value, if not zero, then find maximum value in region by
getRawStatistics(nPixels, mean, min, max);
run(“Find Maxima…”, “noise=”+max+" output=[Point Selection]");
that will give you the cell number of the nearest cell.
If zero, grow region by 1 (run(“Enlarge…”, “enlarge=1”) and repeat until hit.