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Fixing admba #322

Merged
merged 6 commits into from
Aug 8, 2024
Merged

Fixing admba #322

merged 6 commits into from
Aug 8, 2024

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viktorpm
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What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

What does this PR do?

Fixes admba meshes and annotations mismatch, implements pooch to handle atlas downloading

How has this PR been tested?

Tested locally, and atlases were regenerated on the HPC

Is this a breaking change?

No

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 documentation has been updated to reflect any changes
  • The code has been formatted with pre-commit

@alessandrofelder alessandrofelder mentioned this pull request Jul 18, 2024
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@alessandrofelder @viktorpm @sfmig
quickfix wrapup for admba, fix admba orientation/resolution
03c4a13 
Result of mob-programming!

Co-authored-by: Viktor Plattner <[email protected]>
Co-authored-by: sfmig <[email protected]>
@alessandrofelder
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Hey @viktorpm
I'll let you continue on this after the various debugging sessions last week (thanks also to @sfmig for maths help, and to @niksirbi for helpful anatomical eyeballing 😁 )

I haven't changed all the resolutions in the config yet, but we have concluded that

  • for anisotropic atlases that don't come in ASR, we need to keep track of resolution in source space (to scale mesh points correctly) and in target space (to write output metadata correctly)
  • the ADMBA are in RSA according to our convention
  • as part of Refactor scripts to simplify code base as much as possible #219 we should generate the mesh points from the transformed annotation stack (ie in target space)
  • for now, we've implemented a hacky way of dealing with this that won't affect other atlases.

alessandrofelder
alessandrofelder reviewed Jul 22, 2024
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brainglobe_atlasapi/atlas_generation/atlas_scripts/admba_3d_dev_mouse.py
@@ -314,8 +319,13 @@ def create_atlas(
species="Mus musculus",
atlas_link="https://search.kg.ebrains.eu/instances/8ab25629-bdac-47d0-bc86-6f3aa3885f29",
atlas_file_url="https://data.kg.ebrains.eu/zip?container=https://object.cscs.ch/v1/AUTH_4791e0a3b3de43e2840fe46d9dc2b334/ext-d000023_3Drecon-ADMBA-E11pt5_pub",
orientation="lsa",
resolution=(16, 16, 20),
orientation="rsa",
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This is the correct way around, others need to be adapted!

alessandrofelder
alessandrofelder approved these changes Aug 8, 2024
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Amazing - thank you @viktorpm

@alessandrofelder alessandrofelder merged commit c1e80ee into main Aug 8, 2024
11 of 13 checks passed
@alessandrofelder alessandrofelder deleted the fixing_admba branch August 8, 2024 13:54
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@alessandrofelder alessandrofelder alessandrofelder approved these changes

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@viktorpm @alessandrofelder