Editing QuPath annotations after saving and reloading

Hello QuPath people,

If I create an annotation in QuPath using the brush tool and then want to slightly edit the shape of the region, I can do so by clicking on the square boxes which appear on the yellow line around my highlighted area and dragging them.

However, if I save my annotations, restart QuPath and open the image again, I lose the ability to edit the annotations in this way, which precludes me from tweaking them in response to advice from colleagues et cetera.

I would be incredibly grateful if anyone has any suggestions or workarounds for this problem; am I missing something obvious?


Hi Jim,

You should still be able to edit your annotations in the same way, even after saving and restarting QuPath.
I think that your annotations are ‘locked’, which prevents any further modification. To unlock your annotations, do the following:

  1. Select your annotation
  2. Right click on them.
  3. Click on Annotation > Unlock.
  4. Edit your annotation!

Good luck :slight_smile:

Hi Melvin,

Thank you for your reply! I should have specified in my post: my annotations are definitely unlocked, which suggests something has gone awry. Apologies, and thank you!



You can edit an unlocked annotation with the brush tool just by clicking inside it (to ensure its selected) and then dragging – like with the original brush.

You’ll only see the little squares for some ‘simple’ annotations that can be entirely represented by outer vertices (rectangles, ellipses, simple polygons), but fortunately with the brush/wand editing is possible even without the squares.

You can see some gifs demonstrating annotation tricks at https://twitter.com/petebankhead/status/1295965136646176768?s=20

If you still find something isn’t working as it should, please check under View → Show log for error messages and make sure you’re using the latest version (currently v0.2.3). If you’re importing annotations from an old version then this may be relevant.

Hi Pete,

Thank you very much; these gifs are really cool and helpful.