I am doing some FISH analysis to assess ploidy in cells by counting the number of copies of a given chromosome. I’d be interested in using Cell Profiler to do the counting for me. Basically, I would need to count the number of blue nuclei in a field, then count the number of green or red dots (each representing one chromosome) within each nucleus to get a

quantitation of the number of nuclei within the field that have one, two, three, four, etc., copies of that chromosome. Do you know if Cell Profiler could do this, and if there are any modules out there already? I saw one on the web page for counting nuclear speckles, but it seems like what it does is give the number of nuclei and the total number of speckles in the field, which is not exactly what I’m looking for.

Andy