Congrats for this forum, specially for the whole community around cell profiler.
First, I’m more a sequencing guy, so sorry for my naive perspective about image matters and comments/questions.
Here is my post: I’m trying to differentiate colonies (fungi) expressing GFP from the ones which don’t (mutants) on a petri dish. In theory, the problem seems easy to solve, though I’m getting steps-back on the way. We’re talking about look at hundreds of dishes and thousands of colonies; so I’m looking into a more computer based solution. And my second biggest problem is that non-fluorescence colonies have a rather auto-fluorescence which make it harder (not to mention the auto-fluorescence coming from the media).
So, my pipeline at first was to take one pic with epifluorescence light (using BioRad Chemidoc MP) of the plate. Then use the same plate with white light and with the help of ImageJ (after background correction and transform into grey scale) using an Image Ratio plugin to determine which of the colonies present (whites) habe more (GFP expression) or less (mutants) intensity on the epifluorescence image. So far, not really good results.
Then I met Cell Profiler, and the all its capabilities. I have checked a couple of protocols, like Yeast colonies measurement cp project or colocalization cp project. But I’m not sure if I’m going in the right direction. Any input would be appreciated. I can attach a couple of pics, so you can see the nature of the problem.
Colonies-GFP after background correction and grey conversion
tip: the ones on the left side seem to be more intense
Colonies-White after background correction and grey conversion