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brainglobe / brainrender-napari

A napari plugin to render BrainGlobe atlases and associated data as layers.
BSD 3-Clause "New" or "Revised" License
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[BUG] Atlas entries do not show on fresh install #148

Closed TimMonko closed 2 months ago

TimMonko commented 4 months ago

Describe the bug On a fresh pip install of either brainrender-napari or brainglobe when I open brainrender there is no atlases in the atlas viewer. I have never used brainglobe before, so maybe this is the expected behavior? Documentation makes me think otherwise.

Expected behaviour There would be a list of atlases I can click on as according to the tutorial.

Screenshots image

Computer used (please complete the following information): napari: 0.4.19.post1 Platform: Windows-10-10.0.22631-SP0 Python: 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:40:08) [MSC v.1938 64 bit (AMD64)]

alessandrofelder commented 4 months ago

Thanks for reporting @TimMonko

You're right, the tutorial is out-of-sync with the latest version. The widget currently only shows the atlases you have already downloaded.

Our plan is to have two separate `brainrender-napari widgets - one for downloading atlases, and one for visualising them.

To get it to work in the meantime, you should be able to use the command line to download the atlas you're interested in. For example, for the Allen Mouse atlas at 50 um resolution, you would do:

brainglobe install -a allen_mouse_25um

Then you should be able to close and reopen napari, and continue the tutorial from step 3.

alessandrofelder commented 2 months ago

Thanks again for reporting this @TimMonko - I'll update the documentation now, but if you upgrade your brainrender-napari by running pip install -U brainrender-napari in your activate conda-environment, you will get an additional widget to download/update atlases via BrainGlobe - let us know how you get on!