Issue Setting Channel Colors for Multiplex Image Analysis


I’ve been trying to use QuPath (v.0.2.3) to analyze IHC samples that have been triple stained for nuclei and three different markers. My goal is to be able to tell exactly which markers each identified nucleus stains positive for so that I get the percentage of cells in each possible combination of positive/negative for the three markers. All of my images are set to fluorescent.

I’ve been referring to the instructions here, which state that the channel names can simply be changed by double-clicking on them in the Brightness/Contrast dialog box. However, I’m not able to change them from the default Red/Blue/Green. I tried running the script to set channel names mentioned on the same page (shown below), which didn’t work either. I also hunted around old threads for channel-editing scripts (like the one here), but those didn’t seem to work.

setChannelNames( 'PDL1', 'CD8', 'FoxP3', 'CD68', 'PD1', 'CK' )

This is also an issue because I have four stains (red, blue, green, and orange) and it’s preventing me from setting an orange channel. Does anyone know what might be causing this?

Thank you!

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You saved your image as an RGB image - try using the original image as saved by the microscope/the manufacturer’s default image type, or some sort of multichannel file (.tif, CZI, etc).
I can also see that the image is .jpg, which is not really appropriate for careful scientific analysis since the values are all corrupted/altered.

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