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Add Cuttlebase cuttlefish atlas#338

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kjungwoo5 wants to merge 30 commits intobrainglobe:mainbrainglobe/brainglobe-atlasapi:mainfrom kjungwoo5:cuttlefish-atlaskjungwoo5/brainglobe-atlasapi:cuttlefish-atlasCopy head branch name to clipboard

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Commits

Commits on Aug 2, 2024

• Make empty cuttlefish.py file

  kjungwoo5

  committed
  45834a1

Commits on Aug 8, 2024

• Download cuttlefish hierarchy file from github and amend format

  kjungwoo5

  committed
  2ace3d2

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Commits on Aug 10, 2024

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

  kjungwoo5

  committed
  4f16ca5

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

  kjungwoo5

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  947d056

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Commits on Aug 26, 2024

• Applied RGB triplets and fixed acronyms for all regions

  kjungwoo5

  committed
  09ed09f

Commits on Aug 29, 2024

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

  kjungwoo5

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  93dcd64

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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

  committed
  74d47c1

Commits on Sep 29, 2024

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

  kjungwoo5

  committed
  57d7f5b

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

  kjungwoo5

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  ab5256d

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Commits on Oct 4, 2024

• add wrapup function + minor tweaks

  alessandrofelder

  committed
  b42a409

• draft mesh creation

  alessandrofelder

  committed
  6dd72b9

Commits on Oct 21, 2024

• Added validation script to brainglobe main folder.

  kjungwoo5

  committed
  0bae2f6

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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)

  kjungwoo5

  committed
  ce5fecd

Commits on Dec 2, 2024

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

  kjungwoo5

  committed
  411fe4d

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.

  kjungwoo5

  committed
  a8c23aa

• 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

  kjungwoo5

  committed
  98b3b3a

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

  kjungwoo5

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  407c874

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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.

  kjungwoo5

  committed
  84f9d47

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

  kjungwoo5

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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

  committed
  f215042

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

  kjungwoo5

  committed
  82195e5