We loaded SVS (Aperio) scanner files using Qupath for annotation, and we’re now attempting to extract matching pathology and corresponding annotation images. In order to extract TIF from SVS, we used Aperio’s Digital Slide Studio, and was only able to extract an area of interest due to the size of each file. We are able to independently extract our annotation as images (below). However, because the two extractions were done independently, they don’t match in size, edge and dimension, and x,y-coordinates.
Could you help us with if there’s a way to register/match these two independently extracted images? Is there a way to do this with a one-step process using Qupath? Any idea is welcome.
Thank you very much,