Virtual double stain with QuPath

Happy New Year everyone. This question has probably been asked before, but I have not been able to find an answer yet. I would like to do a virtual double stain, whereby, one slide is stained with cytokeratin and a sequential slide is stained with a biomarker of interest, such as Ki-67. Is there a way of overlaying the first image to provide a “mask”, so that you get a more accurate count of your biomarker.
As always, thank you and really appreciate the effort from the QuPath team in constructing a very robust image analysis platform.

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You can fairly easily overlay slides, either visually or with regards to their detected objects, or combine them into fluorescent images.

However sequential slices do not contain quite the same information, and may be stretched or distorted. QuPath only performs affine transformations for the alignment of the two images.

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