In the ColorToGrey module, when splitting by channels, the channel number fields are set to “Red: 1” “Green: 2” “Blue: 3” and “Alpha: 4”. In the images that I am processing, what is actually the green channel staining is being assigned to “Red: 1” and what is truly my red channel staining is being assigned to “Green: 2”. Blue is being assigned to the correct channel. I recently posted about a similar issue that ended up not being a problem with CP, but this is a different problem all together
What is causing CP to think think that that my green channel is my red channel image?
The link below is to a zipped folder on google drive with the .tif that is being processed in CP, the original .czi which was converted to .tif using ImageJ Process>Convert function, and my CP pipeline.
What the channels should actually show:
Green: bright cellular staining, entire surface of cells
Red: no staining or much less than green
Blue: DAPI staining, nuclear