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first draft of symmetrical 25um blackcap atlas #314

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first draft of symmetrical 25um blackcap atlas #314

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alessandrofelder
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@alessandrofelder alessandrofelder commented Jun 27, 2024 •
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Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

What does this PR do?
This PR

  • adds the packaging script for the new blackcap atlas, at 25um resolution
  • adds one-off scripts used to help anatomists create and refine annotations, for reproducibility

How has this PR been tested

  • generated atlas passes our validation script ✅

Does this PR require an update to the documentation?

Yes, we need to update at least

  • website list of atlases
  • website list of contributors
  • website blackcap blog
  • readme of this repo
  • readme of GIN atlases repo

once we have uploaded the atlas to GIN.

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 changed the title first draft of symmetrical 50um blackcap atlas first draft of symmetrical 25um blackcap atlas Jul 25, 2024
@adamltyson
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Once this PR is merged, we should remember to add everyone involved to the list of BrainGlobe collaborators. We may forget as they're not authors of this PR.

@alessandrofelder alessandrofelder requested a review from a team December 6, 2024 13:41
@alessandrofelder alessandrofelder self-assigned this Dec 6, 2024
@alessandrofelder alessandrofelder marked this pull request as ready for review December 6, 2024 13:41
adamltyson
adamltyson reviewed Dec 6, 2024
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brainglobe_atlasapi/atlas_generation/atlas_scripts/blackcap.py Outdated
# setup folder for downloading

atlas_path = Path(
"/media/ceph/margrie/sweiler/AnalyzedData/"
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Does this atlas fail our "normal" requirement that all data is available online, and the script should run without access to any specific filesystem?

Should we create a blackcap repo on GIN and upload these files?

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Done: https://gin.g-node.org/BrainGlobe/blackcap_materials

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@alessandrofelder @adamltyson