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Add Cuttlebase cuttlefish atlas#338

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kjungwoo5 wants to merge 43 commits intobrainglobe:mainbrainglobe/brainglobe-atlasapi:mainfrom kjungwoo5:cuttlefish-atlaskjungwoo5/brainglobe-atlasapi:cuttlefish-atlasCopy head branch name to clipboard

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Commits on Aug 2, 2024

• Make empty cuttlefish.py file

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Commits on Aug 8, 2024

• Download cuttlefish hierarchy file from github and amend format

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Commits on Aug 10, 2024

• Tweaked region ID structure, loaded in region colour map from cuttlebase

  kjungwoo5

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Aug 26, 2024

• Applied RGB triplets and fixed acronyms for all regions

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Commits on Aug 29, 2024

• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Sep 15, 2024

• Revised hierarchy creation using annotation data, and added both left and right sides of regions to hierarchy file

  kjungwoo5

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Commits on Sep 29, 2024

• Fixed structure ID path of all regions using the new IDs found from annotation data

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Oct 4, 2024

• add wrapup function + minor tweaks

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• draft mesh creation

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Commits on Oct 21, 2024

• Added validation script to brainglobe main folder.

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Commits on Nov 26, 2024

• Updated mesh generation code to store meshes by correct ID. (In previous code, mesh name did not match the region ID)

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Commits on Dec 2, 2024

• Scaled, rotated and inverted mesh to match the size of the annotation image.

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Commits on Dec 4, 2024

• Corrected meshes_dict in wrapup function, changed mesh generation to use map_points_to, but currently the meshes are still not correctly aligned.

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Dec 5, 2024

• Edited validation script

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Dec 8, 2024

• Corrected the orientation of the meshes using map_points_to rather than matrix multiplication, and attempted to translate meshes.

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Dec 9, 2024

• Edited the atlas generation to be in 50um resolution, and changed scaling of meshes to match the annotation volume.

  kjungwoo5

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Jan 16, 2025

• test to check for functionality of new branch

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• Remove test of branch functionality

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• Remove mesh generation code from atlas generation script.

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Commits on Jan 28, 2025

• Added mesh generation code to create our own meshes, rather than using the Cuttlebase meshes.

  kjungwoo5

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Jan 31, 2025

• Removed temporary validation script, and cleaned up comments on atlas generation script

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Feb 4, 2025

• Removed mesh url, and added code to rescale template image to uint16

  kjungwoo5

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• Merge branch 'cuttlefish-atlas' of https://github.com/kjungwoo5/brainglobe-atlasapi into cuttlefish-atlas

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Commits on Feb 5, 2025

• rename script to match api name

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