When I take multi-channel images that have been captured using MicroManager (OME-TIFF format) and try to use the ColorToGray module set to split the channels up CellProfiler just gives me the first channel as each channel.
This doesn’t happen with other image formats so I think it’s specific to the file type. I searched the forum but couldn’t find anyone else having the same/ a similar issue recently (although I did found an older post - Multi Channel Tif and ColorToGray). But I have this issue is in 2.2.0 and also now in 3.0.0.
Currently, I’ve been running an ImageJ macro to open and re-save all the files as tifs as that fixes the issue but would love to be able to just use CellProfiler and delete the need to use two programs.