Hi CellProfiler Team,
Before I start:
Great job, thanks a lot for that tool! We really appreciate your work.
So my aim is to identify foci within a nucleus. Therefore two pictures DAPI (nucleus) and TRITC (foci).
First step recognition of Nuclei works ok.
Second step identification of foci does not.
I think my problem is that just playing around with the threshold is not sufficient, because I have slightly different signal to background ratios within one image from nucleus to nucleus.
My solution would be normalizing the intensities from nucleus to nucleus whereas the nuclei detection works great. I wanted to set the max intensity in each foci stain within one nucleus to one, thereby getting the chance to put the threshold to a certain range that is then fitting to each foci stain in each nucleus.
I also tried saving each object from the first nuclei identification as a separate image to process each nucleus on its own, but the ‘save object’ just saves the shape of the object and did not help me much.
All image illumination corrections and rescaling functions just work on the whole image not on individual outlined objects… so either did not help.
Perhaps there are other ways to do it I am open for suggestions.
PS.: using CellProfiler v.10415
original images, pipeline and two different threshold settings for the identification of the foci are attached
pipeline.cp (12.6 KB)