[Feature] Force all atlas 3D meshes to be in consistent "brainglobe" space, aligned to the annotations

[dbirman]

The annotation volumes are set up so that the origin (0,0,0) is at the front/left/top corner. Some of the 3D mesh files are aligned with this so that the origin in 3D space is also at this same point (e.g. see the CCF files), but many of the atlases are not (see e.g. the human atlas or AZBA). It's possible to apply the trasform_to_brainglobe affine transform to move the brains to the correct position in some cases, but in other cases the transform appears to be incorrect.

It would be a big benefit for users to simply move all the 3D meshes into the annotation space for consistency (i.e. so that the transform is the identity matrix with a (0,0,0) translation)

[adamltyson]

There was a reason why this wasn't enforced originally, but I can't think what this was. This is a good idea, and I'm transferring this to the atlas generation repo.

[adamltyson]

Thanks for raising this @dbirman. The problems with those two specific atlases have now been fixed, and we're working through all the others.

[dbirman]

Amazing! I'll add the human atlas and AZBA to Pinpoint then, if there's a way to be notified when the other atlases are fixed I'd appreciate it so I can trigger the compile process for adding them to Pinpoint as well. Thanks!

[adamltyson]

So far updated versions have been released for azba_zfish, allen_human (this now has both hemispheres too), perens_lsfm_mouse and kim_mouse.

Shall we just post on the zulip when new versions are released @viktorpm, @alessandrofelder?