brainglobe-atlasapi
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brainglobe
A lightweight python module to interact with atlases for systems neuroscience
**Describe the bug** https://github.com/brainglobe/bg-atlasgen/blob/8e71c2288a61efc063fdd19ddb407215f7c6b95e/bg_atlasgen/mesh_utils.py#L158C17-L158C17 `mesh_utils.py::extract_mesh_from_mask` uses a `smoothLaplacian` method which no longer exists. **To Reproduce** Run the `mesh_utils.py::create_region_mesh` function with `smooth=True` **Additional context** There are other calls to vedo functions...
https://doi.org/10.1007/s12021-023-09623-9
Some anisotropic atlases have been made isotropic and some have not. I think it's worth making them all isotropic for simplicity and to make it easier to develop downstream tools.
**Is your feature request related to a problem? Please describe.** Thanks to brainglobe/bg-atlasgen#116, we now have a mature-enough first version of a validation framework for BrainGlobe atlases, and have run...
**Is your feature request related to a problem? Please describe.** Once valid versions of all atlases are created, we won't be able to use them as test data for our...
**Is your feature request related to a problem? Please describe.** We currently need an extra check for whether the atlas is locally available or not before confidently calling `get_local_atlas_version` -...
Depends on https://github.com/brainglobe/brainglobe-atlasapi/issues/210
**Is your feature request related to a problem? Please describe.** When querying for structures as ID from coordinates, out of bounds coordinates return 0, but when asking for an acronym,...
See https://github.com/brainglobe/BrainGlobe/issues/26
Being able to access the metadata of each atlas though the atlas name, something like: ```python metadata = bg_atlasapi.get_metadata("example_mouse_100um") ``` might make the UX of the napari atlas viewer widget...
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A lightweight python module to interact with atlases for systems neuroscience