Working with QuPath often involved annotating images, and these annotations end up in the ‘object hierarchy’. Any changes to this could help make QuPath easier to use… or possibly just annoy people who prefer the old behavior.

The object hierarchy is one of the things I feel most ambivalent about in QuPath… it is easy and intuitive most of the time, but not always. In particular, things get tricky when annotations overlap with one another, rather than one annotation being completely contained within the other.

I’ve been exploring modifications to the annotation tools that I think might help.

The video below shows this in action: specifically, it’s possible here to clip annotations so that it’s possible to ensure that they end up in the expected place in the object hierarchy, and to control this behavior using shortcut keys.

Additionally, there are two more things visible in the video:

  • a new script to show keypresses on screen to help see what’s happening
  • a new ‘polyline’ tool for ‘open polygons’ (currently this has the same icon as the polygon tool)

It can take a little while to get the hang of the new behavior, and it isn’t yet available to try out, but I plan to experiment with it a while longer.

As ever, this video has no sound…