What is the maximum number of channels that can be analyzed with CellProfiler?
Channels of a single image? I don’t think there’s a limit other than potentially the memory of the computer you’re doing the processing on. I’ve never personally tried pushing the limits beyond 5 at a time, but I don’t think there’s anything in the software that stops you after a certain number of images.
She’s right, AFAIK. We’ve heard of some using CP for multi-spectral images. The only hassle is needing to set NamesAndTypes for each channel, but LoadData can be a way to enter this into CP.