Good morning,
could anyone suggest me a pipeline to run in Cell Profiler? I need to quantify colocalization between two proteins Here, I attach pictures of the two channels, red and green(SOD2 and REST,respectively). I want to measure colocalization between them;
I also attach an image in which you can see the nuclear staining of cells with DAPI.
Thanks to anyone who could suggest me how to solve the problem.
Hello,I've had a similar problem couple of months ago and although I like cellprofiler and I use it a lot, I wasn't able to find or make any usable colocalization pipeline. Sure, it is a matter of skill, but for such analysis, ImageJ is probably better as there already are colocalization plugins (e.g. Coloc2) available that work fine.
Hello. I believe that cellprofiler is not the best option for studying colocalization between two proteins. For this purpose I have used image J
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074624/?report=reader
As others have mentioned, CellProfiler isn't really meant for giving "co-localization" in the traditional sense. However, if you had nicely segregated objects (in green here), then you could use the nuclei to identify primary objects, then the green channel to identify secondary objects per each nucleus. From that secondary object, you can measure the green and red signal and plot those as a green-red scatter plot, or the red channel alone as an intensity histogram. This would effectively give you a possibly meaningful distribution that could be extrapolated to a type of co-localization, but it would not be the type I think you want.
If you want the more standard Pearson/Spearman colocalization, then it's best just to use the Coloc2 plugin in ImageJ/FIJI.
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