I'm using tifffile in python to save out 3-channel tiff stacks, which I then want to read into ImageJ or FIJI. These tiff stacks open as composites in ImageJ with each channel assigned a (presumably default) colormap/LUT. However, the colors that are assigned aren't the colors that make sense for my images. My problem is that I can't figure out how to specify the colormap for each channel when saving the image using tifffile . For example, I'd like to have the following colormap assignments: ch 0: grays ch 1: green ch 2: red Here's the code that I'm using to save the files: # save hyperstack