v0.2.3: Python 3.10-3.12 support

napari-cellseg3d v0.2.3

Summary

• Python 3.10-12 support added
• Several fixes to deprecation errors on newer Python versions
• Upgraded packaging to use only pyproject.toml
• Added uv.lock to repository for more reproducible installs

Warning

If you are still getting errors related to in_channels on the SwinUNetR model, please open an issue and report your MONAI version. Thanks!

What's changed

• Fix brainreg URL in docs by @C-Achard in #108
• Update docs build to py3.9 by @C-Achard in #109
• Update README.md by @MMathisLab in #111
• Update README with links to publication by @C-Achard in #114
• Fix Swin for latest MONAI by @C-Achard in #113
• Fix preprint link in README by @ajinkya-kulkarni in #118
• Upgrade python support to 3.10-3.12, fix deprecation errors by @C-Achard in #120
• Additional fixes for py3.12: Fix Swin args, update docs workflow by @C-Achard in #124
• Add uv lock + bump MONAI lower bound by @C-Achard in #123
• Update and run all pre commit hooks by @C-Achard in #121
• Update README & docs CI for Python 3.12 support by @C-Achard in #125

New Contributors

• @ajinkya-kulkarni made their first contribution in #118

Full Changelog: v0.2.2...v0.2.3

v0.2.2

What's Changed

• Mwm/colab updates by @MMathisLab in #102
• Update crf.py by @MMathisLab in #101
• Update Colab_inference_demo.ipynb by @MMathisLab in #104
• Update README.md by @MMathisLab in #105
• Colab notebooks update by @C-Achard in #103
• CRF adjustments by @C-Achard in #106
• Version bump 0.2.2 by @C-Achard in #107

Full Changelog: v0.2.1...v0.2.2

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

New Contributors

• @constantinpape made their first contribution in #88
• @hausmanns made their first contribution in #92

Full Changelog: v0.1.2...v0.2.1

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

Full Changelog: v0.1.2...v0.2.0rc1

Version 0.1.2

• Fix issue with napari manifest on PyPi

Version 0.1.1

Hotfix for v0.1.0 :

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

Version 0.1.1rc1

What's Changed

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

Full Changelog: v0.0.2rc6...v0.1.1rc1

Interface overhaul, v0.0.2rc6

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

v0.0.1rc4

What's Changed

• Timer improvement by @C-Achard in #27
• Inference on layer by @C-Achard in #26
• Adding SwinUNetR by @vidalmaxime in #12
• v0.0.1rc4 by @C-Achard in #29

Full Changelog: v0.0.1rc3...v0.0.1rc4

v0.0.1rc3

What's Changed

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

Full Changelog: v0.0.1rc2...v0.0.1rc3