NDP.toolkit cropped images don't open properly in QuPath


I’ve noticed that QuPath 0.2.3 doesn’t like image crops generated by NDP.toolkit v When you open such a file, here’s how it looks:

I’m not sure if this is a problem with NDP.toolkit, QuPath or OpenSlide. OpenSlide v3.4.1 mentions NDP.toolkit by name in their Changelog: hamamatsu: Properly detect NDPI slides produced by NDP.toolkit. Maybe I should ask our Hamamatsu rep if there’s a newer version of NDP.toolkit I could try.

I’ve put my cropped image on Swiss Transfer in case that helps. The original slide is a demo image from OpenSlide: (OS-2) but ours produce exactly the same result in QuPath.


It seems to be an OpenSlide issue - if you choose Bio-Formats as the image provider when adding the image to a QuPath project it works fine.

You can also request that Bio-Formats is used by specifying the extension .ndpi with the Always use Bio-Formats for specified image extensions in the preferences.