I have some confocal images that are Z stacks in 3 channels as .lsm files. I order to analyze them I created MIPs in Image J and saved them as tifs.
However, when I attempt to load them into cell profiler it does not recognize that there are 3 channels.
I’ve tried several different ways of saving the file and when I open the files up in other software there are clearly 3 channels.
An example image is attached.