brainglobe-atlasapi

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Distributing custom atlases

8

I have the first occurrence in the lab of a scenario where I would need to generate an high res atlas of a subregion of fish brain. We mentioned this...

vigji

Artifacts when visualizing Atlas Structure Meshes

6

Hi, I tried doing some visualization of the atlas meshes in Napari, which takes in the mesh vertices (`mesh.points`) and the mesh faces (`mesh.cells[0].data`), and noticed quite a bit of...

nickdelgrosso

Feature Proposal: Conversion method between Numpy and Physical Coordinate Spaces

9

Hi, Sometimes I'd like to know where a particular pixel in the reference or annotations template is located in microns or millimeters. The data for calculating this is already present...

nickdelgrosso

Adding pycln

4

Hi, Opening it here but valid throughout the org. We could add [pycln](https://github.com/hadialqattan/pycln) to our pre-commit stack. It automatically removes unused imports from all files. I have set it up...

FedeClaudi

Sort out confusion with cartesian/ij indexing

55

As per the slack discussion: There is some ambiguity when working on displaying numpy arrays, coming from the fact that image-first applications (eg: matplotlib, brainrender) have the convention that as...

vigji

Should handle asymmetric and uncentered atlases as well as atlases with only one hemisphere. Might require adding some info about this to the metadata.

FedeClaudi

[BUG]Mesh issues with perens (20um) and kim (10um)

1

**Describe the bug** I'm using brainrender in napari to look at the perens (20um) and kim (10um) atlases and their meshes. When I load in meshes along with the reference...

pderdeyn

Create validator script to ensure packaged atlas meet certain criteria (maybe also with an option to display images for a visual check?)

1

```[tasklist] ### Tasks - [ ] https://github.com/brainglobe/bg-atlasgen/issues/97 - [ ] https://github.com/brainglobe/bg-atlasgen/issues/98 - [ ] https://github.com/brainglobe/brainglobe-atlasapi/issues/207 - [ ] https://github.com/brainglobe/bg-atlasgen/issues/100 - [ ] checking that files have expected format (internal columns,...

adamltyson

**Is your feature request related to a problem? Please describe.** Our validation functions take a `BrainGlobeAtlas` object. It is unclear to me how easy it is to run them on...

alessandrofelder

Add human brain atlases

2

Could we leverage [TemplateFlow](https://github.com/templateflow) somehow?

adamltyson