Separating Stains in QuPath

In this video, I show you how to separate stains in different types of images using QuPath. We will follow the docs: qupath.readthe... for this. We will learn about colour deconvolution, working with stain vectors, and viewing the scatter plots that represent our stains. You'll also hearm me complain about ICC profiles.
The images used in this video can be found in : openslide.cs.c...

[@SERDARBALCIMD]

Hi, just my two cents: 1:16 brown stains are in fact melanin pigment produced by melaocytes and engulfed by keratinocytes. So they are the natural elements of this biopsy. 1:22 the green is artifical, we ink the surgical margins with tissue dyes or commercial indian ink. they are used to identify if there is remaining tissue at the surgical margin. They can be in value to assess automatic surgical margin evaluation.

[@LauraNicolasSaenz]

That is super interesting and helpful! I'll be sure to include that info next time I find that in an image. Thank you!!!!!!

[@joshuasamsoondar]

Nice walkthrough! Can you explain how the H&E images differ? Are they the same slide from different scanners? Or different scanner settings?