View multiple channels simultaneously in qupath

Hi Qupath users,
Is it possible with a brightfield image type to view multiple channels? I have 3 channels of interest: H, E, and DAB. I can’t find a way to view, for example H+DAB (simultaneously and without E)
Also how can I customize the number of channels/stains? It seems to be limited to 3?

Hi @alk,

I think the Channel viewer might be useful to you.
You can access it with View → Mini viewers → Show channel viewer. :slight_smile:
Also, in Brightness and contrast you should be able to pick the specific channel(s) that you would like to visualise.

Additionally, you can toggle on and off specific channels by pressing the channel number on your keyboard (1, 2, 3, …).

Finally, I don’t think you can set more than 3 stains for H-DAB/H&E, but that would need confirmation.
Good luck!

1 Like

Confirmed! Color deconvolution (at least in its ‘standard’ form, as implemented in QuPath) is limited to three stains.

You’ll need to be using a v0.2.0 milestone release (rather than v0.1.2) to get the Channel viewer, which will also provide a pixel classifier. Color-based pixel classification is one potential way to overcome the stain number limitation… depending on what exactly you need to do.

Thanks very much for your replies.
I agree you can use channel viewer (or number shortcuts) to switch channels but you cannot toggle the channels independently. I have three channels - H, E, and DAB, I can either view all channels at once or one at a time . I cannot to my knowledge view two channels simultaneously. We be useful to be able to do this for phenotyping some tissues.
Thanks, Alan

I’m not sure from your answer if you’re mixing up the Brightness/Contrast dialog with Show channel viewer?

As @melvingelbard writes, the Show channel viewer command lets you see multiple channels side-by-side - precisely to help with phenotyping some tissues.

You can view multiple fluorescence channels simultaneously as composite images with the Brightness/Contrast tool but not multiple brightfield channels. But composite images aren’t terribly good for phenotyping anyway… which is why Show channel viewer exists.