Hi I am segmenting and annotating the different nuclei of the human amygdala on brightfield sections in QuPath and I would like to import these annotations into 3D Slicer. The common file format used for export of QuPath annotations is GeoJSON. Is this possible to import in 3D Slicer?
I don’t think there’s an existing parser for GeoJSON but it should be easy to write a python script for it, maybe with this package. If you try and run into questions you could post an example file and image and someone can probably help you out (e.g. include a screenshot of what it looks like in QuPath, the json, and an image file).