Atlases do not overlay on data registered by brainreg

[adamltyson]

The atlases are displayed in real, micron space. I assume this is so that the images overlay with the meshes. However this causes (what I think is) undesired behaviour, in that if you register your data to an atlas, this registered image doesn't overlay with the atlas in the plugin.

Should the atlases be scaled to the "correct" voxel space?

See image.sc issue for context.

[imagesc-bot]

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

https://forum.image.sc/t/brainglobe-brainrender-region-names-on-mouse-hover/94962/2

[alessandrofelder]

Not sure - I'd argue we should find a way to scale the registered data on import into napari in microns?

• There are efforts underway to make napari have units
• Not having the image and the meshes overlay can lead to its own confusing issues?

Either way, this should be made consistent across brainglobe and documented well!

[adamltyson]

Not having the image and the meshes overlay can lead to its own confusing issues?

They should overlay, I was suggesting resampling the meshes to the image. It's not ideal but I don't see another way, other than users needing to load their data and set the scale every time.

[alessandrofelder]

I see!
We should do that at the atlas generation stage, I guess, to avoid unnecessary compute time?

[adamltyson]

I think we should just downscale them in napari. brainrender-napari is the only time that the meshes and images are overlaid.

In an ideal world, all image data would have correct metadata, and every image visualisation tool would scale appropriately, but until then, we should fudge it.