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Recent Releases of https://github.com/adaptivemotorcontrollab/cellseg3d

https://github.com/adaptivemotorcontrollab/cellseg3d - v0.2.2

What's Changed

  • Mwm/colab updates by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/102
  • Update crf.py by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/101
  • Update Colabinferencedemo.ipynb by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/104
  • Update README.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/105
  • Colab notebooks update by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/103
  • CRF adjustments by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/106
  • Version bump 0.2.2 by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/107

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3D/compare/v0.2.1...v0.2.2

- Jupyter Notebook
Published by MMathisLab about 1 year ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Version 0.2.1

New features :

  • Utility to find best threshold for supervised models
  • Better defaults for provided demo data in inference
  • Default threshold is now updated per-model, to help obtain suitable predictions quicker

What's Changed

  • Update README.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/67
  • Small docs update for WNet by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/68
  • Some training fixes and improvements by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/65
  • Small inference docs update by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/69
  • Fix setup.cfg name by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/66
  • test directory and very small data cube by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/75
  • Add demo instructions by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/78
  • Create CODEOFCONDUCT.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/77
  • Update macbook conda by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/72
  • Small API changes for training by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/70
  • update training of WNet3D by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/79
  • Colab demo : Inference by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/80
  • v0.2.0 by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/73
  • Update README.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/82
  • small updates to Colab demo by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/81
  • Update README.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/84
  • Update README.md by @constantinpape in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/88
  • Add pyClEsperanto troubleshooting by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/90
  • correct readme install by @hausmanns in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/92
  • Fix dtype of demo data by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/94
  • Update tests by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/97
  • v0.2.1 : Update defaults and new utilities by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/98
  • Fix dependencies for deploy by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/100

New Contributors

  • @constantinpape made their first contribution in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/88
  • @hausmanns made their first contribution in https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/92

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3D/compare/v0.1.2...v0.2.1

- Jupyter Notebook
Published by C-Achard about 1 year ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Version 0.2.0

Test release of version 0.2.0

  • Fix deprecation warning regarding package name in setup.cfg
  • Refreshed installation procedure for ARM64 (Mac)
  • New example volumes and a Colab demo notebook
  • Added code of conduct

What's Changed

  • Update README.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/67
  • Small docs update for WNet by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/68
  • Some training fixes and improvements by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/65
  • Small inference docs update by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/69
  • Fix setup.cfg name by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/66
  • test directory and very small data cube by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/75
  • Add demo instructions by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/78
  • Create CODEOFCONDUCT.md by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/77
  • Update macbook conda by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/72
  • Small API changes for training by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/70
  • update training of WNet3D by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/79
  • Colab demo : Inference by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/80

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/compare/v0.1.2...v0.2.0rc1

- Jupyter Notebook
Published by C-Achard almost 2 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Version 0.1.2

  • Fix issue with napari manifest on PyPi

- Jupyter Notebook
Published by C-Achard almost 2 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Version 0.1.1

Hotfix for v0.1.0 :

  • Fixed an issue with models initialization in inference
  • Fixed artifact removal UI visibility

- Jupyter Notebook
Published by C-Achard about 2 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Version 0.1.1rc1

What's Changed

  • Update pyproject.toml; minimal conda for m1 by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/38
  • Voronoi-Otsu labeling + instance segmentation code overhaul by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/34
  • WNet + models code refactor by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/36
  • Additional tests by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/42
  • Temp fix for CRF by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/46
  • Improved Utilities by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/44
  • WNet training by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/47
  • WandB/Colab + docs by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/48
  • Feedback fixes by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/58
  • v1.0 Draft - Training improvements and fixes by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/43
  • Fixes for v0.1.0 by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/62

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/compare/v0.0.2rc6...v0.1.1rc1

- Jupyter Notebook
Published by C-Achard about 2 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Version 0.1.0

What's Changed

  • Update pyproject.toml; minimal conda for m1 by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/38
  • Voronoi-Otsu labeling + instance segmentation code overhaul by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/34
  • WNet + models code refactor by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/36
  • Additional tests by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/42
  • Temp fix for CRF by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/46
  • Improved Utilities by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/44
  • WNet training by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/47
  • WandB/Colab + docs by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/48
  • Feedback fixes by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/58
  • v1.0 Draft - Training improvements and fixes by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/43

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/compare/v0.0.2rc6...v0.1.0rc1

- Jupyter Notebook
Published by C-Achard about 2 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - Interface overhaul, v0.0.2rc6

  • Updated UI
  • Many fixes
  • New docs action/pre-commit hooks

- Jupyter Notebook
Published by C-Achard almost 3 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - v0.0.1rc4

What's Changed

  • Timer improvement by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/27
  • Inference on layer by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/26
  • Adding SwinUNetR by @vidalmaxime in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/12
  • v0.0.1rc4 by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/29

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/compare/v0.0.1rc3...v0.0.1rc4

- Jupyter Notebook
Published by MMathisLab over 3 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - v0.0.1rc3

What's Changed

  • Various fixes by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/11
  • Added more anisotropy handling + fix global in review by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/14
  • UI API overhaul + several features/fixes by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/17
  • Moved weights download + enhancements by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/19
  • Improved pretrained weights usage by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/24
  • v0.0.1rc3 by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/16

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/compare/v0.0.1rc2...v0.0.1rc3

- Jupyter Notebook
Published by MMathisLab over 3 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - v0.0.1rc2

What's Changed

  • Updated plugin visibility for napari-hub by @C-Achard in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/8
  • Mwm/download models by @MMathisLab in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/6
  • Bug fix in local installation & minor fixes in launch_review by @vidalmaxime in https://github.com/AdaptiveMotorControlLab/CellSeg3d/pull/10

New Contributors

  • @jeylau

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/compare/v0.0.1rc1...v0.0.1rc2

- Jupyter Notebook
Published by MMathisLab over 3 years ago

https://github.com/adaptivemotorcontrollab/cellseg3d - v0.0.1rc1

Hello World! This is cellseg3D, a napari plugin for 3D cell segmentation specifically geared towards mesoSPIM data. This is written primarily by @C-Achard at EPFL. This code will undergo development -- please get in touch if you want to hear more about our roadmap, we are very open to contributions and making these models are interoperable to other tools as possible.

Full Changelog: https://github.com/AdaptiveMotorControlLab/CellSeg3d/commits/v0.0.1rc1

- Jupyter Notebook
Published by MMathisLab over 3 years ago