I know that it’s possible to export color images out of cell profiler to use in Cell profiler analyst (specifically I want to use color cells for the cell categorizer) but I don’t see how to do this since I had to convert to grayscale to count individual cells. I also could split the original image into RGB instead of combining it and using one of the channels to count cells but I don’t know how to set the recombined image (using graytocolor) as the output.
For importing images into CPA, that you should select “Yes” for the “Record the file and path information to the saved images.” This can be useful, for example, to export outline images of your objects in order to visualize the segmentation results within CellProfiler Analyst.
I’d recommend saving the individual grayscale channels and then adjusting the color of each channel as you want in CellProfiler Analyst using the menu bar.
Hope this helps!