Once we have images uploaded to Bisque, we might want to be able to overlay annotations on top of them so that users can interact with them. This post quickly goes through the conversation of a binary mask, in matlab, into an XML which can later be imported into Bisque.
Assuming we have the necessary files on our Bisque server (perhaps uploaded with our script), and we have a set of bisque compliant XML annotations (perhaps generated with our script), we would like to upload them to the Bisque server so that they can be evaluated or modified. That is what this post is about 🙂
In the previous post we discussed how to export annotations from a Ventana Image Viewer program and create binary masks. Now we explain how to do the opposite and import the mask back into Image Viewer.
One of the main purposes of having a digital format is to allow experts (e.g., pathologists) to annotate certain structures in the images. Be it nuclei, epithelium/stroma regions, tumor/non-tumor tissue etc. This is easily done with ImageScope and SVS files, but the trick is importing them into Matlab.
Continue reading Working with Aperio SVS files in Matlab – Converting Annotations to Binary Masks