Mesh issue with the Princeton Mouse Brain Atlas

[adamltyson]

As reported on image.sc there seems to be an issue with the meshes of the Princeton Mouse Brain Atlas. They have some additional transform that means they don't align with e.g. the Allen atlas.

@viktorpm @alessandrofelder is this something that was caught in the validation scripts?

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/princeton-mouse-brain-atlas-offset-in-3d-space/92868/8

[alessandrofelder]

Hey, yes, this does indeed fail our validation test for the root mesh and the annotation have the same bounding box:

AssertionError: ('Mesh coordinate 618.5 and annotation coordinate 12360.0', 'differ by more than 10 times pixel size 20.0')

which is not surprising, seeing as opening the mesh and the annotations in napari looks like:

[alessandrofelder]

There's a dorso-ventral flip and a scale issue...

[alessandrofelder]

On the rotation/flip side here, a suspect is

brainglobe-atlasapi/brainglobe_atlasapi/atlas_generation/atlas_scripts/princeton_mouse.py

Line 130 in e5296d7

rotated_annotations = np.rot90(annotated_volume, axes=(0, 2))

@viktorpm to test manually whether not rotating the annotation used to create meshes would help.

[dbirman]

Hey this seems to be closed but I haven't seen any update for the version in bgatlas, do I need to do something to see the new version? I get this currently:

╭───────────────────────────────── Brainglobe Atlases ─────────────────────────────────╮
│                                                                           Latest     │
│  Name                              Downloaded  Updated  Local version    version     │
│  princeton_mouse_20um                  ✔          ✔          1.0           1.0       │

Or was it updated without changing the version number and I just need to re-download?

[alessandrofelder]

Thanks for checking in @dbirman - we haven't managed to make time to upload the new version just yet - but aiming to do so on Monday! Thanks for your patience.

[dbirman]

Thanks @alessandrofelder, wanted to make sure I wasn't missing something on my end. Appreciate your time on this!

[alessandrofelder]

hey @dbirman
this has been released now - thanks a lot to @viktorpm for his efforts on this! 🎉

Make sure you have brainglobe-atlasapi == 2.0.5 (e.g. by running pip install --upgrade brainglobe-atlasapi in your conda env) before attempting to update the atlas with the command line (we recently seem to have lost the entry point to do things like brainglobe -update, which is now restored!).

Please shout if you run into problems, and thanks for your patience!

[dbirman]

Thank you @viktorpm and @alessandrofelder, there are a bunch of people who have been asking for this atlas. Really appreciate you spending time on this!