Importing NDPA annotation files into QuPath (code attached)


this is to follow on the Google groups thread about importing NDPA annotation files into QuPath.

I adapted the groovy script written by John Pan to

  • work with 0.2.0-m8
  • be able to import a few more shapes besides polygons (rectangles, circles, polylines, pins, lines).

The script isn’t super clean (sorry if I butchered John’s code, I’m very new to groovy) but works for us (Hamamatsu NanoZoomer NDPI files / NDPA generated with NDP.view 2.6.8).

Once launched, it will look for an NDPA file which has the same name as the NDPI file selected in QuPath and load all the annotations.

Then for each annotation:

  • The title becomes the QuPath annotation’s class
  • The details are transferred to the QuPath annotation’s description


Attachment: (2.4 KB)