Image patch extraction from annotated whole slides in QuPath v0.2.0

Dear All,

Is there anyone who has an experience of image path extraction from annotated whole slides in QuPath v0.2.0? For some reason I cant open images in previous version. Any help will be very much appreciated.


I understand from your blog comment you’re using .vsi images. Just to be clear, which of the following is true… or none of them?

  • the images open in v0.1.2, but not v0.2.0-m2?
  • the images open in v0.2.0-m2, but never opened in v0.1.2?
  • the images previously opened in v0.1.2 but now only open in v0.2.0-m2?

It is also important to specific if your images are brightfield (i.e. 8-bit RGB) or fluorescence. There are more options to export RGB than fluorescence.

The third option is true, it was previously opened in v0.1.2 but now it opens only in v0.2.0-m2

In that case, check the extensions directory for v0.1.2. The Bio-Formats extension needs to be installed, along with bioformats_package.jar. It’s important that only one Bio-Formats extension is there - so if you see more than one, I’d suggest deleting them both and downloading and reinstalling the most recent extension from

Note that v0.2.0-m2 includes Bio-Formats by default, and it must not have the old extension installed because it is incompatible. But you can potentially use different extensions directories for v0.2.0-m2 and v0.1.2 so it is possible to use both versions of QuPath on the same machine.

All right, thats a good advice, thank you so much and I will try it!

Thank you so much!!! It works perfectly now! :slight_smile: