Issue splitting channels with ColorToGray for images captured with MicroManager


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.

I’ve put an example file here -



CellProfiler unfortunately doesn’t yet nicely read OME-XML metadata (which is how MicroManager encodes how many Z planes vs channels, etc), so the reason that ColorToGray isn’t producing the results you expect is when I load your image into CP it doesn’t actually known it’s multichannel (see all the “Size” columns below).

There are hacky ways to get around this in the meantime; it is definitely an area we want to improve though, and hopefully we will soon. Sorry!

Splitting multistack TIFF and merging colors