For some reason Cell profiler does not split my images into channels correctly. I separate the images using ImageJ and then merge them/make a composite picture, but when I upload the merged picture to cell profiler it does not split them (red, blue and far red channel). The pictures of the split channels do differ from each other to some extent (so it’s not 3 times the same picture), but they are not split correctly into the 3 different channels. What could be the problem here?
I then tried to upload the different channels separately by using one image for each channel (again; red, blue and far red). Cell profiler treats each channel as a different picture, but I want to use all 3 in the same pipeline. What settings should I use to analyze these 3 images of each channel in 1 pipeline?