Colorizing greyscale channels in QuPath


I am new to fluorescence image analysis so maybe I am asking something very obvious.

I have a few “tiled tiff” images that were exported from 3D Histech scanner using Slide Converter. They are in greyscale and they represent different channels, DAPI and Cy5. After looking around this forum I found a link to this script Merge images along the channels dimension in QuPath v0.2.0 · GitHub which allowed me to merge my individual channels into one image.

However, what I am left with is a composite image that has my DAPI and Cy5 channels overlayed on top of each other as a greyscale, see the screenshot below.

Is there any way to map greyscale from my DAPI image to some kind of blue pseudocolor and Cy5 to some kind of green? Is there some obvious trick that I am missing out here? Thanks!

It looks like you either exported or saved RGB images. So while they look grayscale, they are not. That is why you end up with two sets of RGB channels. I would try to export them as a single channel image first.

If you are unable to, you could also change all three DAPI or all three Cy5 channels to the same color. I think.

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Yep, changing all three DAPI/Cy5 RGB channels to the same color works, thanks for tip! It’s a bit awkward to have three channel per stain but at least now I can see the difference between DAPI and Cy5!