Allow different values in each hemisphere.

[adamltyson]

Raising an issue based on this image.sc issue.

It would be useful to allow users to visualise different values in each hemisphere.

[imagesc-bot]

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

https://forum.image.sc/t/allen-spinal-cord-atlas-is-off-axis/99539/4

[AdityaGupta716]

Hey @adamltyson opened a PR for this — #114
Tried using brainrender's hemisphere= param first but it crashes on numpy>=2.0 (float(np.diff(...)) in get_plane()), so I bypass it entirely and cut meshes manually with vedo's cut_with_plane() — this also fixes the existing hemisphere= param as a side effect. The other tricky bit was the 2D projection: the slicer uses actor names as dict keys so two "TH" actors would overwrite each other, fixed by temporarily renaming them "TH__left" / "TH__right" before slicing. Also fixed the spinal cord atlas off-axis issue from the forum — was using center_of_mass() as midplane which is skewed; now uses bounding box midpoint for symmetric atlases matching brainrender's own logic.

[adamltyson]

Thanks @AdityaGupta716, we will take a look (but could be some time, as the core team are very busy currently!).

Tried using brainrender's hemisphere= param first but it crashes on numpy>=2.0 (float(np.diff(...)) in get_plane()), so I bypass it entirely and cut meshes manually with vedo's cut_with_plane()

I'm curious about this, it would be great to not bypass brainrender if there are issues. It's also our tool, so I'd rather any issues were fixed if possible!

[AdityaGupta716]

@adamltyson Looks like it's already fixed in brainrender's main with [0], just not in the latest release yet. Kept the manual cutting here so it works on the current installed version, but happy to revert to add_brain_region(hemisphere=) once a new brainrender release is out.

[AdityaGupta716]

@adamltyson Checked PypI the fix with [0] is already in brainrender 2.1.18, so anyone on the latest release is fine. Our manual cutting is just a safety net for anyone still on 2.1.17 or older. Happy to drop it and use add_brain_region(hemisphere=) directly if you'd rather keep things simple and just document a minimum brainrender version requirement.

[adamltyson]

Thanks, yes I think it's fine to just set a new minimum brainrender version. It should be backwards compatible (very little has changed in the last ~2 years).