Hi, I’m a Consultant Pathologist and have been using QuPath for annotations for machine learning. It’s given us a massive head start and I’m really grateful for all the work that you have put (and continue to put) into creating it.
So that we can use annotations for training we are exporting them into a JSON as co-ordinates. When there is an annotation that sits as an island within a different annotation we run into trouble. We can create a negative space within the larger annotation using the alt key and can export the peripheral co-ordinates first followed by the internal co-ordinates of the negative space. However, if we try and reimport from the JSON back into QuPath then the co-ordinates from the negative space and the periphery get muddled up with lines joining between the two. This creates a shape that is quite different to what was intended.
Is it possible to either label the co-ordinates as indicating a negative space or to give a command that allows for the peripheral ring co-ordinates to be drawn separately to the negative space?
Hope that makes sense and hope you can help us.