Fetch atlas meshes by loading meshio and converting to vedo mesh by IgorTatarnikov · Pull Request #461 · brainglobe/brainrender

IgorTatarnikov · 2026-07-17T10:00:08Z

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Description

What is this PR

Bug fix
Addition of a new feature
Other

Why is this PR needed?
Following the release of brainglobe-atlasapi==3.0.0rc0 meshes are no longer stored on disk as .obj files. brainrender accesses these files directly to load meshes into vedo.

What does this PR do?
Alters the loading path for atlas meshes. brainrender now requests the mesh directly from brainglobe-atlasapi receiving a meshio.Mesh, this is converted into a vedo.Mesh and passed through as before.

References

#460

How has this PR been tested?

All tests pass locally and local examples involving atlas meshes have been inspected in an environment with brainglobe-atlasapi==3.0.0rc0 and brainglobe-atlasapi==2.3.1

Is this a breaking change?

No, this change is backwards compatible with brainglobe-atlasapi<3.0.0

Does this PR require an update to the documentation?

No

Checklist:

The code has been tested locally
Tests have been added to cover all new functionality (unit & integration)
The code has been formatted with pre-commit

codecov · 2026-07-17T10:15:52Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.52%. Comparing base (e1b1969) to head (0f8a341).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #461      +/-   ##
==========================================
+ Coverage   89.48%   89.52%   +0.03%     
==========================================
  Files          27       27              
  Lines        1294     1298       +4     
==========================================
+ Hits         1158     1162       +4     
  Misses        136      136

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adamltyson

This all looks sensible to me, although for some reason everything is failing locally for me. Not sure what's going on with my installation.

Could load_mesh_from_file be deleted at this point?

IgorTatarnikov · 2026-07-17T10:24:14Z

I don't think load_mesh_from_file can be removed. It's used to support adding external .obj or .stl files to a scene.

IgorTatarnikov · 2026-07-17T10:25:10Z

This all looks sensible to me, although for some reason everything is failing locally for me. Not sure what's going on with my installation.

Is this with 2.3.1 or 3.0.0rc0?

Could you try deleting ~/.brainglobe/brainglobe-atlasapi?

adamltyson · 2026-07-17T10:29:14Z

Even after deleting .brainglobe, I still get:

Traceback

(atlasapiv3test) tigger:brainrender adamtyson$ python examples/volumetric_data.py 
Running example: volumetric_data.py
Downloading allen_mouse_25um atlas v3.0 manifest:
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/adamtyson/projects/brainglobe/brainrender/brainrender/atlas.py:39 in __init__             │
│                                                                                                  │
│    36 │   │   logger.debug(f"Generating ATLAS: {atlas_name}")                                    │
│    37 │   │                                                                                      │
│    38 │   │   try:                                                                               │
│ ❱  39 │   │   │   super().__init__(atlas_name=atlas_name, print_authors=False)                   │
│    40 │   │   except TypeError:                                                                  │
│    41 │   │   │   # The latest version of BGatlas has no print_authors argument                  │
│    42 │   │   │   super().__init__(atlas_name=atlas_name, check_latest=check_latest)             │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: BrainGlobeAtlas.__init__() got an unexpected keyword argument 'print_authors'

During handling of the above exception, another exception occurred:

╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/adamtyson/projects/brainglobe/brainrender/examples/volumetric_data.py:24 in <module>      │
│                                                                                                  │
│   21                                                                                             │
│   22 print(f"[{orange}]Running example: {Path(__file__).name}")                                  │
│   23                                                                                             │
│ ❱ 24 scene = Scene(inset=False)                                                                  │
│   25                                                                                             │
│   26 data = np.load(volume_file)                                                                 │
│   27 print(data.shape)                                                                           │
│                                                                                                  │
│ /Users/adamtyson/projects/brainglobe/brainrender/brainrender/scene.py:69 in __init__             │
│                                                                                                  │
│    66 │   │   self.actors = []  # stores all actors in the scene                                 │
│    67 │   │   self.labels = []  # stores all `labels` actors in scene                            │
│    68 │   │                                                                                      │
│ ❱  69 │   │   self.atlas = Atlas(atlas_name=atlas_name, check_latest=check_latest)               │
│    70 │   │                                                                                      │
│    71 │   │   self.screenshots_folder = (                                                        │
│    72 │   │   │   Path(screenshots_folder)                                                       │
│                                                                                                  │
│ /Users/adamtyson/projects/brainglobe/brainrender/brainrender/atlas.py:42 in __init__             │
│                                                                                                  │
│    39 │   │   │   super().__init__(atlas_name=atlas_name, print_authors=False)                   │
│    40 │   │   except TypeError:                                                                  │
│    41 │   │   │   # The latest version of BGatlas has no print_authors argument                  │
│ ❱  42 │   │   │   super().__init__(atlas_name=atlas_name, check_latest=check_latest)             │
│    43 │                                                                                          │
│    44 │   @property                                                                              │
│    45 │   def zoom(self) -> float:                                                               │
│                                                                                                  │
│ /Users/adamtyson/miniforge3/envs/atlasapiv3test/lib/python3.13/site-packages/brainglobe_atlasapi │
│ /bg_atlas.py:110 in __init__                                                                     │
│                                                                                                  │
│   107 │   │   │   │   # If internet is up, then the atlas name was invalid                       │
│   108 │   │   │   │   raise ValueError(f"{atlas_name} is not a valid atlas name!")               │
│   109 │   │   │   else:                                                                          │
│ ❱ 110 │   │   │   │   self.download()                                                            │
│   111 │   │   │   │   assert self.local_full_name is not None, (                                 │
│   112 │   │   │   │   │   "Download failed: local atlas manifest not found after "               │
│   113 │   │   │   │   │   "download."                                                            │
│                                                                                                  │
│ /Users/adamtyson/miniforge3/envs/atlasapiv3test/lib/python3.13/site-packages/brainglobe_atlasapi │
│ /bg_atlas.py:249 in download                                                                     │
│                                                                                                  │
│   246 │   │   │   f"Downloading {self.atlas_name} atlas "                                        │
│   247 │   │   │   f"v{remote_version_str.replace('_', '.')} manifest:"                           │
│   248 │   │   )                                                                                  │
│ ❱ 249 │   │   self.fs.get(remote_path, local_path, callback=TqdmCallback())                      │
│   250 │   │   self.metadata = read_json(local_path)                                              │
│   251 │   │                                                                                      │
│   252 │   │   try:                                                                               │
│                                                                                                  │
│ /Users/adamtyson/miniforge3/envs/atlasapiv3test/lib/python3.13/site-packages/fsspec/spec.py:1007 │
│ in get                                                                                           │
│                                                                                                  │
│   1004 │   │   │   │   (has_magic(rpath) and source_is_file)                                     │
│   1005 │   │   │   │   or (not has_magic(rpath) and dest_is_dir and not trailing_sep(rpath))     │
│   1006 │   │   │   )                                                                             │
│ ❱ 1007 │   │   │   lpaths = other_paths(                                                         │
│   1008 │   │   │   │   rpaths,                                                                   │
│   1009 │   │   │   │   lpath,                                                                    │
│   1010 │   │   │   │   exists=exists,                                                            │
│                                                                                                  │
│ /Users/adamtyson/miniforge3/envs/atlasapiv3test/lib/python3.13/site-packages/fsspec/utils.py:414 │
│ in other_paths                                                                                   │
│                                                                                                  │
│   411 │   │   │   else:                                                                          │
│   412 │   │   │   │   path2 = [p.replace(cp, path2, 1) for p in paths]                           │
│   413 │   else:                                                                                  │
│ ❱ 414 │   │   assert len(paths) == len(path2)                                                    │
│   415 │   return path2                                                                           │
│   416                                                                                            │
│   417                                                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: object of type 'PosixPath' has no len()
Exception ignored in: <function Scene.__del__ at 0x14ba9de40>
Traceback (most recent call last):
  File "/Users/adamtyson/projects/brainglobe/brainrender/brainrender/scene.py", line 114, in __del__
    self.close()
  File "/Users/adamtyson/projects/brainglobe/brainrender/brainrender/render.py", line 322, in close
    self.plotter.close()
AttributeError: 'NoneType' object has no attribute 'close'

IgorTatarnikov · 2026-07-17T10:47:01Z

I can replicate on Mac, weird that CI passes!

I'll move this to draft for now

IgorTatarnikov · 2026-07-17T13:52:58Z

Issue should be solved by brainglobe/brainglobe-atlasapi#860

adamltyson · 2026-07-17T14:43:27Z

Works for me with a clean installation :)

IgorTatarnikov · 2026-07-17T14:52:09Z

Perfect! I'll merge this now to unblock brainglobe-heatmap.

IgorTatarnikov added 3 commits July 17, 2026 10:26

Fetches atlas meshes by loading meshio and converting to vedo mesh

f4137c5

Explicitly adds meshio to dependencies

1844aa7

Adds tests for the new convert_meshio_to_vedo function

0f8a341

IgorTatarnikov changed the title ~~Fetches atlas meshes by loading meshio and converting to vedo mesh~~ Fetch atlas meshes by loading meshio and converting to vedo mesh Jul 17, 2026

IgorTatarnikov requested a review from a team July 17, 2026 10:00

adamltyson approved these changes Jul 17, 2026

View reviewed changes

This was referenced Jul 17, 2026

[Feature] Ensure all BrainGlobe tools are compatible with the new format brainglobe/brainglobe-atlasapi#780

Open

[Feature] brainglobe-atlasapi V3 compatibiltiy brainglobe/brainglobe-heatmap#146

Open

IgorTatarnikov marked this pull request as draft July 17, 2026 10:47

IgorTatarnikov marked this pull request as ready for review July 17, 2026 13:52

IgorTatarnikov merged commit 5dab17e into main Jul 17, 2026
12 checks passed

IgorTatarnikov deleted the update-atlas-mesh-fetch branch July 17, 2026 14:52

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Fetch atlas meshes by loading meshio and converting to vedo mesh#461

Fetch atlas meshes by loading meshio and converting to vedo mesh#461
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Description

References

How has this PR been tested?

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Does this PR require an update to the documentation?

Checklist:

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IgorTatarnikov commented Jul 17, 2026 •

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