Code

Merge with atlasgen#199

Code

Merged

willGraham01 merged 119 commits intomainbrainglobe/brainglobe-atlasapi:mainfrom atlasgen-mergebrainglobe/brainglobe-atlasapi:atlasgen-mergeCopy head branch name to clipboardFeb 23, 2024

+7,052-1,863

Commits

Commits on Sep 2, 2020

• Initial commit

  vigji

  authored
  636d801

• Update README.md

  vigji

  authored
  f06c2d5

• First commit

  vigji

  committed
  c42e115

• gitignore

  vigji

  committed
  8173167

• Almost at complete atlas autogeneration

  vigji

  committed
  921c007

Commits on Sep 3, 2020

• Finalized script for automatic atlas generation

  vigji

  committed
  6ca9c7e

• Added template script for atlas generation

  vigji

  committed
  461820f

• Template description

  vigji

  committed
  b42ea88

• First working version of script for auto deployment

  vigji

  committed
  e6c7ed6

• Fixed metadata link

  vigji

  committed
  252f806

Commits on Sep 4, 2020

• Trying to fix windows permission error when deleting folders

  vigji

  committed
  24c9e8a

• add 50um to allen mouse

  adamltyson

  committed
  2fcf04f

• Merge pull request #1 from brainglobe/add_res

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  adamltyson

  authored
  b05c2db

Commits on Oct 21, 2020

• v1.2 for allen mouse

  vigji

  committed
  97e4d1c

• blacked

  vigji

  committed
  375a03c

Commits on Oct 23, 2020

• Update requirements

  adamltyson

  committed
  bc32f7f

• vtkplotter -> vedo

  adamltyson

  committed
  6132575

• Format with black

  adamltyson

  committed
  2bcd6f3

• Update kim mouse atlas generation

  adamltyson

  committed
  dfcadc8

• Improve downsampling

  adamltyson

  committed
  c0cbf69

• revert roations

  adamltyson

  committed
  1c63191

• add kim to main script

  adamltyson

  committed
  e821b8d

Commits on Oct 26, 2020

• rotate annotation volume for meshes

  adamltyson

  committed
  2d82ad7

• Merge pull request #2 from brainglobe/kim_atlas

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  adamltyson

  authored
  837cff9

Commits on Dec 3, 2020

• add osten mouse atlas

  adamltyson

  committed
  2c0962f

Commits on Dec 4, 2020

• Merge pull request #3 from brainglobe/osten_atlas

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  adamltyson

  authored
  86caab9

Commits on Jun 30, 2021

• Added function for creating intermediate hierarchy structures masks

  vigji

  committed
  4264649

• Merge branch 'master' of https://github.com/brainglobe/bg-atlasgen

  vigji

  committed
  068d04e

Commits on Jul 21, 2021

• Fix extract_largest_region and compare_mesh_volume

  MathieuBo

  committed
  bc7518d

Commits on Jul 31, 2021

• Merge pull request #7 from MathieuBo/fix-mesh-utils

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  adamltyson

  authored
  f944baa

Commits on Aug 6, 2021

• reformat with black

  adamltyson

  committed
  370dfb0

• save additional metadata

  adamltyson

  committed
  707905a

Commits on Aug 10, 2021

• consistent syntax for empty dict

  adamltyson

  committed
  fb22377

• Update docstring

  adamltyson

  committed
  56b2e00

• Add atlas packager metadata

  adamltyson

  committed
  7c0c4bf

• python 3.8 compatibility

  adamltyson

  committed
  8140a82

Commits on Aug 12, 2021

• Merge pull request #9 from adamltyson/metadata

  Show description for 547b3e6
  adamltyson

  authored
  547b3e6

• Add mouse spinal cord atlas

  adamltyson

  committed
  9612e91

Commits on Aug 27, 2021

• Merge pull request #10 from MetaCell/cord-atlas

  Show description for f37ee5d
  adamltyson

  authored
  f37ee5d

Commits on Oct 31, 2021

• add WHS SD Rat atlas

  bkntr

  committed
  19ef461

Commits on Nov 4, 2021

• add xmltodict to requirements.txt

  bkntr

  committed
  f9e1d85

Commits on Nov 7, 2021

• remove structures that are missing from annotation volume

  bkntr

  committed
  79a6446

• remove structures that are missing from annotation volume

  bkntr

  committed
  ca31ce7

Commits on Nov 9, 2021

• Fixed vedo Slicer import issue

  kailynkfields

  authored
  2e44cca

• Update mesh_utils.py

  kailynkfields

  authored
  3276068

• Merge branch 'brainglobe:master' into master

  kailynkfields

  authored
  016c4ff

Commits on Nov 19, 2021

• Create azba_zfish.py

  kailynkfields

  authored
  55f52d4

Commits on Nov 21, 2021

• Merge pull request #12 from bkntr/master

  Show description for 05f043e
  adamltyson

  authored
  05f043e

• Standardise temporary output directory

  adamltyson

  authored
  53e23db

Commits on Nov 26, 2021

• add [allenmouse] extra dependency (#17)

  adamltyson

  authored
  844592b

Commits on Nov 30, 2021

• Allow multiple downloads at once, updated citation

  kailynkfields

  authored
  74b08ee

Commits on Dec 1, 2021

• Merge pull request #14 from kailynkfields/master

  Show description for cda0d3e
  vigji

  authored
  cda0d3e

Commits on Jan 19, 2022

• Mesh cleaning improvements (#15)

  Show description for 4384efb
  

  FedeClaudi

  and

  vigji

  authored
  4384efb

Commits on Jan 28, 2022

• Update azba_zfish.py

  Show description for 4b6f765
  kailynkfields

  authored
  4b6f765

Commits on Jan 31, 2022

• Merge pull request #19 from kailynkfields/patch-1

  Show description for 670b214
  vigji

  authored
  670b214

Commits on Feb 9, 2022

• some fixes for mpin atlas

  vigji

  committed
  d6ac454

Commits on Feb 10, 2022

• Merge pull request #20 from brainglobe/improved-mpin

  Show description for 51c79dc
  vigji

  authored
  51c79dc

Commits on May 30, 2022

• Fix tiny typo (#22)

  adamltyson

  authored
  eea5259

Commits on May 31, 2022

• Update README.md

  adamltyson

  authored
  2e4320b

• Add lsfm atlas script (#18)

  Show description for fcd5f87
  

  3 peopleauthored
  fcd5f87

• Update requirements.txt

  adamltyson

  authored
  7530600

Commits on Jul 1, 2022

• Add ADMBA 3D developing mouse atlases (#25)

  Show description for 6e2f8c7
  yoda-vid

  authored
  6e2f8c7

Commits on Aug 31, 2022

• Add script for the Princeton mouse brain atlas. (#27)

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  samclothier

  and

  Sam

  authored
  c9d090d

Commits on Jan 6, 2023

• KimLabDevCCFv001 (neuroinformatics team form) (#31)

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  3 peopleauthored
  9190e1e

Commits on Feb 1, 2023

• Add testing config (#35)

  Show description for d5dbe27
  dstansby

  authored
  d5dbe27

Commits on Feb 3, 2023

• Replace brainglobe with NI actions (#37)

  dstansby

  authored
  577cd06

Commits on Feb 21, 2023

• Use pyproject.toml

  dstansby

  committed
  a226d5d

Commits on Feb 24, 2023

• Update supported Python metadata

  dstansby

  committed
  c9b04b9

• Clean manifest check

  dstansby

  committed
  d00db2f

• Remove cibuildwheel config

  dstansby

  committed
  ebdb976

• Merge pull request #38 from dstansby/pyproject

  Show description for c536ed4
  dstansby

  authored
  c536ed4

Commits on Feb 27, 2023

• Catch warnings during tests (#39)

  dstansby

  authored
  ea9acb6

• Add standard pre-commit config (#40)

  Show description for 3b92d54
  dstansby

  authored
  3b92d54

Commits on Mar 20, 2023

• Fix branches that CI is run on (#42)

  dstansby

  authored
  423598b

Commits on Jun 19, 2023

• Update link (#48)

  adamltyson

  authored
  b1ee389

Commits on Jun 20, 2023

• [pre-commit.ci] pre-commit autoupdate (#49)

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  pre-commit-ci[bot]

  authored
  a7e10ee

Commits on Jun 27, 2023

• [pre-commit.ci] pre-commit autoupdate (#50)

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  pre-commit-ci[bot]

  authored
  fdf3190

Commits on Jul 4, 2023

• [pre-commit.ci] pre-commit autoupdate (#52)

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  pre-commit-ci[bot]

  authored
  ad79edb

Commits on Jul 11, 2023

• [pre-commit.ci] pre-commit autoupdate (#53)

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  pre-commit-ci[bot]

  authored
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Commits on Jul 18, 2023

• [pre-commit.ci] pre-commit autoupdate (#54)

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  pre-commit-ci[bot]

  authored
  ec229da

Commits on Jul 25, 2023

• [pre-commit.ci] pre-commit autoupdate (#55)

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  pre-commit-ci[bot]

  authored
  21a3162

Commits on Aug 1, 2023

• [pre-commit.ci] pre-commit autoupdate (#57)

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  pre-commit-ci[bot]

  authored
  f9e4cc1

Commits on Aug 8, 2023

• [pre-commit.ci] pre-commit autoupdate (#59)

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  pre-commit-ci[bot]

  authored
  2140031

Commits on Aug 10, 2023

• Update to newer vedo API (#58)

  alessandrofelder

  authored
  c732275

Commits on Aug 17, 2023

• [pre-commit.ci] pre-commit autoupdate (#64)

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  pre-commit-ci[bot]

  authored
  5dd3890

Commits on Aug 21, 2023

• scale mesh points before mapping to new anatomical space (#62)

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  3 peopleauthored
  fc4e4cb

Commits on Aug 22, 2023

• [pre-commit.ci] pre-commit autoupdate (#66)

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  pre-commit-ci[bot]

  and

  adamltyson

  authored
  399b6b2

Commits on Aug 29, 2023

• [pre-commit.ci] pre-commit autoupdate (#67)

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  pre-commit-ci[bot]

  authored
  d946d4f

• Set pre-commit autoupdate frequency to monthly (#68)

  adamltyson

  authored
  70fd901

Commits on Sep 5, 2023

• [pre-commit.ci] pre-commit autoupdate (#70)

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  pre-commit-ci[bot]

  authored
  495cdc3

Commits on Oct 3, 2023

• [pre-commit.ci] pre-commit autoupdate (#83)

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  pre-commit-ci[bot]

  authored
  510f7d3

Commits on Nov 7, 2023

• [pre-commit.ci] pre-commit autoupdate (#95)

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  pre-commit-ci[bot]

  authored
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Commits on Dec 5, 2023

• [pre-commit.ci] pre-commit autoupdate (#107)

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  pre-commit-ci[bot]

  authored
  d304152

Commits on Jan 2, 2024

• [pre-commit.ci] pre-commit autoupdate (#109)

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  pre-commit-ci[bot]

  authored
  24bae47

Commits on Jan 22, 2024

• draft validation functions (#90)

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  3 peopleauthored
  93e95ab

Commits on Jan 23, 2024

• Structure validation (#110)

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  3 peopleauthored
  a4acdb4

Commits on Jan 29, 2024

• simplify validation function (#113)

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  alessandrofelder

  and

  pre-commit-ci[bot]

  authored
  9259796

Commits on Feb 6, 2024

• [pre-commit.ci] pre-commit autoupdate (#117)

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  pre-commit-ci[bot]

  authored
  12252af

• Add manifest to ci (#118)

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  willGraham01

  authored
  ae19fad

Commits on Feb 12, 2024

• printing data frames with validation function information (#115)

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  3 peopleauthored
  03392f3

• bg-atlasapi -> brainglobe-atlasapi

  willGraham01

  committed
  795bddd

• bg_atlasapi -> brainglobe_atlasapi, package restructure

  willGraham01

  committed
  120c3b2

• Move tests for API into separate subfolder

  willGraham01

  committed
  639aafc

• Revert "bg_atlasapi -> brainglobe_atlasapi, package restructure"

  Show description for 80152d1
  willGraham01

  committed
  80152d1

• bg_atlasapi -> brainglobe_atlasapi, package restructure

  willGraham01

  committed
  7d585e9

• Update manifest

  willGraham01

  committed
  c055cb4

• [pre-commit.ci] auto fixes from pre-commit.com hooks

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  pre-commit-ci[bot]

  committed
  d96b91e

• Pre-commit pass

  willGraham01

  committed
  7ca6f63

• fixing small bug: validation_functions function argument as variable instead of all_validation_functions (#119)

  viktorpm

  authored
  b195cb6

• Bump NIU action versions

  willGraham01

  committed
  eb37112

Commits on Feb 14, 2024

• Move conftest back to top-level directory

  willGraham01

  committed
  dd314e7

• First pass merge

  willGraham01

  committed
  ae673a2

• Refactor atlasgen into a submodule

  willGraham01

  committed
  8da5382

• pre-commit pass

  willGraham01

  committed
  ab6432d

Commits on Feb 21, 2024

• test functions for validate_mesh_structure_pairs (#114)

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  3 peopleauthored
  76a513a

Commits on Feb 23, 2024

• Revert "Prepare for merge and rename (#198)"

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  willGraham01

  committed
  c9d9136

• Merge branch 'revert-depre' into atlasgen-merge

  willGraham01

  committed
  8f1245a

• Merge remote-tracking branch 'atlasgen/main' into atlasgen-merge

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  willGraham01

  committed
  58c5d94

• Update pyproject.toml

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  willGraham01

  and

  alessandrofelder

  authored
  33498a0