CP assigning my green image to "Red: 1" and my red image to "Green: 1" in ColorToGrey

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

Thank you!

Let me clarify something really quickly- if you’re splitting based on channels and it’s really a multichannel image (as opposed to RGB) as yours is, you only need to worry about the numbers; no matter what dye was used to take the image in channel 1, CP will recognize it as channel 1- the “Red:1” nomenclature is just about the fact that for RGB images the internal channel order is (Red, Green, Blue). So since the order of your channels is Green, Red, Blue, when you split by channels set the Red:1 to whatever your green channel name should be (pretend it’s “GFP”) and your Green:2 to whatever your red channel name should be (“RFP” eg). Does that make more sense?

Yes, that makes sense, and is the work-around that I identified as well. It just looks odd and is a bit confusing if I were to be looking at the pipeline down the road and wondering why it was set up that way. You are correct that it has no functional consequence so long as I correct for it. It’s merely aesthetics and I was hoping there was a way to eliminate or change CP’s default naming for channels 1,2,3.

Thanks again.