I am worker at UCSD and we have been trying to use cell profiler to identify autophagy in cells. These spots are very small and I have been having only moderate success using a pipeline I made and was wondering if anyone has any tips or a better pipeline to use instead?
The biggest problem I’ve had is the variation in spots size and brightness/intensity. I can’t seem to find a good parameter for Cell Profiler to pick up these spots for a big sample size of images.
I have attached my pipeline and some sample images to the post. Hope someone can provide some advice and/or tips!
AutophagyValidationPipeline.cp (10.4 KB)