v0.1.0

CAREamics v0.1.0 freezes the historical API (CAREamist and corresponding Lightning modules), which has barely changed since v0.0.7. Does that mean that CAREamics will no longer change? Quite the opposite!

Apart from some bug fixes and slight API adjustments, all the changes since v0.0.7 consist in a massive refactoring effort, with the aim to bring about a much more powerful modular dataset (Next-Gen Dataset) and increase the maintainability of the code base. The result, known as Next-Gen CAREamics, will be made the default API in a future v0.2.0 release.

In summary, v0.1.0 is used as reference release for future archiving purposes before we can unveil in the next weeks the newly refactored Next-Gen CAREamics!

What's Changed

• Feat: per_channel and global normalization options by @veegalinova in #777
• Chore(deps): Update tifffile requirement from <=2026.2.15 to <=2026.2.16 by @dependabot[bot] in #776
• Chore(deps-dev): Update onnxscript requirement from <=0.6.0 to <=0.6.2 by @dependabot[bot] in #765
• Chore(deps): Update typer requirement from <=0.23.1,>=0.12.3 to >=0.12.3,<=0.24.0 by @dependabot[bot] in #775
• Feat: add AGENTS.md file by @jdeschamps in #704
• Chore(deps): Update tifffile requirement from <=2026.2.16 to <=2026.2.20 by @dependabot[bot] in #783
• Chore(deps): Update typer requirement from <=0.24.0,>=0.12.3 to >=0.12.3,<=0.24.1 by @dependabot[bot] in #782
• Feat(Next-Gen Dataset): Validation split function (not integrated) by @melisande-c in #771
• Feat: Add seed to N2V pixel manipulation by @CatEek in #759
• Restore original prediction shape by @CatEek in #762
• Chore(deps): Update tifffile requirement from <=2026.2.20 to <=2026.2.24 by @dependabot[bot] in #788
• Feat(Next-Gen CAREamics): CAREamist v2 training methods by @CatEek in #761
• Feat: Add website examples to the main repo by @jdeschamps in #786
• Feat(Next-Gen): add CARE and N2N configurations and factories by @jdeschamps in #778
• Feat(Next-Gen CAREamics): add checkpoint loading strategy by @CatEek in #760
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #795
• Feat(Next-Gen CAREamist): improved array reshaping and restoring by @jdeschamps in #790
• Chore(docstrings): fix docstring error by @jdeschamps in #797
• Chore(deps): Update tifffile requirement from <=2026.2.24 to <=2026.3.3 by @dependabot[bot] in #802
• Chore: add AI disclaimer in PR template, and CONTRIBUTING.md by @jdeschamps in #800
• Feat(Next-Gen CAREamist): prediction methods by @CatEek in #754
• Feat: add residual connection to UNet by @jdeschamps in #801
• Feature(Next-Gen): Integrate validation splitting with refactor of CareamicsDataModule by @melisande-c in #789
• Fix: fix ng config loading by @jdeschamps in #805
• Feat: integrate new reshaping/restoring implementations, zarr tile shape restoration by @jdeschamps in #798
• Feat: Add monitor_metric config option for Noise2Void by @Callidior in #806
• Feat: raise error when batch_size is in dataloader_params by @diyasrivas in #808
• Refac: replace transforms by augmentations for clarity and coherence by @diyasrivas in #809
• Feat: improve checkpoints name by adding experiment name and val loss by @diyasrivas in #807
• Feat: explicit supervised error in CAREamistV2 by @jdeschamps in #815
• Feat: torchmetrics-compatible (scale invariant) PSNR implementations by @jdeschamps in #699
• Feat(Next-Gen): various fixes by @jdeschamps in #818
• Chore(deps-dev): Update pylibczirw requirement from <6.0.0,>=4.1.2 to >=4.1.2,<7.0.0 by @dependabot[bot] in #814
• Tests(Next-Gen): new testing structure draft and example for NGDataConfig by @jdeschamps in #811

Full Changelog: v0.0.22...v0.1.0

v0.0.22

What's Changed

• Chore(deps): Update torch requirement from <=2.9.1,>=2.0 to >=2.0,<=2.10.0 by @dependabot[bot] in #695
• Chore(deps): Update torchvision requirement from <=0.24.1 to <=0.25.0 by @dependabot[bot] in #694
• MS performance testing by @CatEek in #615
• Refac(Next-Gen Dataset): Remove inheritance from lightning modules by @veegalinova in #701
• Fix: prevent file overwriting when predicting with CachedTiles and WriteImage by @diyasrivas in #702
• Chore(deps): Update tifffile requirement from <=2026.1.14 to <=2026.1.28 by @dependabot[bot] in #705
• Chore(deps): Update psutil requirement from <=7.2.1 to <=7.2.2 by @dependabot[bot] in #706
• Chore(deps-dev): Update onnxscript requirement from <=0.5.7 to <=0.6.0 by @dependabot[bot] in #707
• Chore(deps): Update pytorch-lightning requirement from <=2.6.0,>=2.2 to >=2.2,<=2.6.1 by @dependabot[bot] in #711
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #716
• Bug: Check whether model_desc.root is a dir or a zip before extraction by @mese79 in #719
• Feat: add default value for TrainingConfig in NGConfiguration by @jdeschamps in #725
• Fix: update _auto_chunking in zarr tile writer to not chunk in Z by @jdeschamps in #723
• Chore: remove unused extract_patch method in ImageStack implementations by @jdeschamps in #724
• fix:prevent file overwriting when S_dim > batch_size in WriteImage by @diyasrivas in #726
• Feature(NG Dataset): Stratified Patching Strategy by @melisande-c in #710
• Provide parameters in convenience function for normalization by @diyasrivas in #713
• Feature: Next-Gen CAREamist API by @melisande-c in #717
• Chore: rename flag by @jdeschamps in #747
• Implement stop_training, get_losses, and export_to_bmz for CAREamistV2 by @diyasrivas in #748
• Updated WriteTilesZarr to support tiff and array as the prediction so… by @mese79 in #735
• Feat: split convenience function into standard and advanced. by @jdeschamps in #743
• Chore: rename flag in prediction writer by @jdeschamps in #751
• CareamistV2: initialization cleanup by @veegalinova in #744
• Add StopPredictionCallback to lightning callbacks by @diyasrivas in #756
• Chore: rename parameter and prevent override by @jdeschamps in #755
• Feature(Next-Gen Dataset): Integrate new stratified patching into the dataset by @melisande-c in #745
• Chore(deps): Update tifffile requirement from <=2026.1.28 to <=2026.2.15 by @dependabot[bot] in #772
• Chore(deps): Update typer requirement from <=0.21.1,>=0.12.3 to >=0.12.3,<=0.23.1 by @dependabot[bot] in #773
• Chore(deps): Update pillow requirement from <=12.1.0 to <=12.1.1 by @dependabot[bot] in #764
• Fix: EarlyStopping callback initialisation in CAREamist by @melisande-c in #774
• Fix: 3D case for StructN2V + N2V2 with refac of median pixel manipulation by @melisande-c in #767

New Contributors

• @diyasrivas made their first contribution in #702

Full Changelog: v0.0.21...v0.0.22

v0.0.21

What's Changed

• Feat(Next-Gen Dataset): Configurable normalization by @veegalinova in #655
• Fix: allow images to have dimensions equal to patch size by @jdeschamps in #682
• Chore: improve error message when patch_size failed validation by @jdeschamps in #686
• Fix: add zero padding to 3rd dimension in CZI by @jdeschamps in #688

Full Changelog: v0.0.20...v0.0.21

v0.0.20

What's Changed

• Chore(deps): Update tifffile requirement from <=2025.12.20 to <=2026.1.14 by @dependabot[bot] in #677
• Fix: Struct N2V 3D by @melisande-c in #678

Full Changelog: v0.0.19...v0.0.20

v0.0.19

What's Changed

• Typo: configuration docstring by @lamteteeow in #608
• Chore(deps): Update pytorch-lightning requirement from <=2.5.5,>=2.2 to >=2.2,<=2.5.6 by @dependabot[bot] in #609
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #603
• Chore(deps): Update pydantic requirement from <=2.12.3,>=2.11 to >=2.11,<=2.12.4 by @dependabot[bot] in #610
• Feature(Next-Gen Dataset): Lateral context patch construction for MicroSplit by @melisande-c in #612
• Chore(deps): Update torch requirement from <=2.9.0,>=2.0 to >=2.0,<=2.9.1 by @dependabot[bot] in #619
• Chore(deps): Update torchvision requirement from <=0.24.0 to <=0.24.1 by @dependabot[bot] in #618
• Feature(Next-Gen Dataset): MicroSplit Input and Target Generation (Proof of Principle) by @melisande-c in #617
• Feat: Enable Zarr CAREamics DataModule by @jdeschamps in #616
• Feat: Add prediction utilities and callbacks to NG Dataset by @jdeschamps in #620
• Refac(Next-Gen Dataset): Factory functions & Directory structure by @melisande-c in #624
• PN2V Lightning Draft by @CatEek in #557
• Refac: Rename test to pred in NG Dataset Config by @jdeschamps in #627
• Chore: update tests to prevent writing files outside of tmp folders by @jdeschamps in #628
• Feat(Next-Gen Dataset): Enable CZI by @jdeschamps in #629
• Chore: rename all configuration Pydantic models and reorganize modules by @jdeschamps in #623
• Chore(config): Add imports to __init__ by @jdeschamps in #633
• Feat(Next-Gen Dataset): return sources from convert_prediction in order by @jdeschamps in #631
• Feat(Next-Gen Dataset): enforce axes in CZI image stack loader by @jdeschamps in #635
• Feat(Next-Gen Dataset): allow selecting which channels to extract by @jdeschamps in #640
• Chore(Tests): rename test files by @jdeschamps in #641
• Chore(deps): Update pydantic requirement from <=2.12.4,>=2.11 to >=2.11,<=2.12.5 by @dependabot[bot] in #643
• Feat(Next-Gen Dataset): add in_memory parameter to configuration by @jdeschamps in #642
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #647
• Feat(Next-Gen Dataset): add mode parameter to NGDataConfig and add config conversion by @jdeschamps in #645
• Chore(deps): Update pytorch-lightning requirement from <=2.5.6,>=2.2 to >=2.2,<=2.6.0 by @dependabot[bot] in #646
• Chore(deps): Update matplotlib requirement from <=3.10.7 to <=3.10.8 by @dependabot[bot] in #656
• Chore(deps): Update tifffile requirement from <=2025.10.16 to <=2025.12.12 by @dependabot[bot] in #657
• Feat(Next-Gen Dataset): Better Zarr tile writing (prediction with S, sharding/chunking, error handling) by @jdeschamps in #653
• Chore(deps-dev): Update onnxscript requirement from <=0.5.6 to <=0.5.7 by @dependabot[bot] in #659
• Fix(Next-Gen Dataset): fix issue causing empty channels when predicting on channel subset by @jdeschamps in #661
• Chore(deps): Update tifffile requirement from <=2025.12.12 to <=2025.12.20 by @dependabot[bot] in #665
• Chore(deps): Update scikit-image requirement from <=0.25.2 to <=0.26.0 by @dependabot[bot] in #663
• Chore(deps): Update pillow requirement from <=12.0.0 to <=12.1.0 by @dependabot[bot] in #673
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #674
• Chore(deps): Update typer requirement from <=0.20.0,>=0.12.3 to >=0.12.3,<=0.21.1 by @dependabot[bot] in #675
• Chore(deps): Update psutil requirement from <=7.1.3 to <=7.2.1 by @dependabot[bot] in #670
• Feat(Next-Gen CAREamics): draft convenience functions for NG-compatible CAREamics (N2V only) by @jdeschamps in #662

New Contributors

• @lamteteeow made their first contribution in #608

Full Changelog: v0.0.18...v0.0.19

v0.0.18

What's Changed

• Chore(deps): Update torch requirement from <=2.8.0,>=2.0 to >=2.0,<=2.9.0 by @dependabot[bot] in #583
• Chore(deps): Update torchvision requirement from <=0.23.0 to <=0.24.0 by @dependabot[bot] in #581
• Chore(deps): Update pillow requirement from <=11.3.0 to <=12.0.0 by @dependabot[bot] in #582
• Chore(deps): Update tifffile requirement from <=2025.10.4 to <=2025.10.16 by @dependabot[bot] in #585
• Chore(deps): Update psutil requirement from <=7.1.0 to <=7.1.1 by @dependabot[bot] in #590
• Feature(Next-Gen Dataset): Pad patches queried outside of data range by @melisande-c in #587
• Chore(deps): Update typer requirement from <=0.19.2,>=0.12.3 to >=0.12.3,<=0.20.0 by @dependabot[bot] in #591
• Chore(deps): Update pydantic requirement from <=2.12.2,>=2.11 to >=2.11,<=2.12.3 by @dependabot[bot] in #589
• Fix: fix structN2V handling of batches by @jdeschamps in #593
• Feat: Generalizes ZarrImageStack by @jdeschamps in #594
• Chore(deps): Update psutil requirement from <=7.1.1 to <=7.1.3 by @dependabot[bot] in #599
• Feature(Next-Gen Dataset): Iterative file loading by @melisande-c in #596

Full Changelog: v0.0.17...v0.0.18

v0.0.17

What's Changed

• Improve NG dataset reproducibility; pin torchmetrics by @veegalinova in #565
• Fix pre-commit by @jdeschamps in #564
• Chore(deps): Update matplotlib requirement from <=3.10.6 to <=3.10.7 by @dependabot[bot] in #570
• Chore(deps): Update tifffile requirement from <=2025.9.30 to <=2025.10.4 by @dependabot[bot] in #566
• Chore(deps): Update torchmetrics requirement from <1.5.0,>=0.11.0 to >=0.11.0,<1.9.0 by @dependabot[bot] in #569
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #567
• Chore: add monkeypatching for MPS by @jdeschamps in #571
• Feat: Exclude background patches during training by @jdeschamps in #532
• Chore(deps): Update pydantic requirement from <=2.12,>=2.11 to >=2.11,<=2.12.1 by @dependabot[bot] in #574
• Convert CI to uv by @jdeschamps in #572
• Chore: revert torchmetrics change and update dependabot by @jdeschamps in #575
• Chore(deps): Update pydantic requirement from <=2.12.1,>=2.11 to >=2.11,<=2.12.2 by @dependabot[bot] in #576
• Chore: make CI run doctests by @jdeschamps in #577
• Fix: fix publish CI by @jdeschamps in #578

Full Changelog: v0.0.16...v0.0.17

v0.0.16

What's Changed

• Chore(deps): Update pytorch-lightning requirement from <=2.5.2,>=2.2 to >=2.2,<=2.5.4 by @dependabot[bot] in #525
• Chore(deps): Update matplotlib requirement from <=3.10.3 to <=3.10.6 by @dependabot[bot] in #524
• Chore(deps): Update torch requirement from <=2.7.1,>=2.0 to >=2.0,<=2.8.0 by @dependabot[bot] in #518
• Chore(deps): Update torchvision requirement from <=0.22.1 to <=0.23.0 by @dependabot[bot] in #519
• ci(pre-commit.ci): autoupdate by @pre-commit-ci[bot] in #517
• Chore(deps): Update pillow requirement from <=11.2.1 to <=11.3.0 by @dependabot[bot] in #502
• Chore(deps): Update typer requirement from <=0.16.0,>=0.12.3 to >=0.12.3,<=0.17.3 by @dependabot[bot] in #529
• Chore(deps): Update pytorch-lightning requirement from <=2.5.4,>=2.2 to >=2.2,<=2.5.5 by @dependabot[bot] in #530
• Chore(deps): Update typer requirement from <=0.17.3,>=0.12.3 to >=0.12.3,<=0.17.4 by @dependabot[bot] in #531
• Lightning API refac for HDN example by @CatEek in #511
• MicroSplit config for lightning api draft by @CatEek in #512
• Expose lightning trainer params by @CatEek in #505
• MicroSplit noise model config changes for Lightning API by @CatEek in #513
• MicroSplit DataModule by @CatEek in #514
• Chore(deps): Update psutil requirement from <=7.0.0 to <=7.1.0 by @dependabot[bot] in #547
• Chore(deps): Bump bioimageio-core from 0.9.0 to 0.9.1 by @dependabot[bot] in #548
• Chore: Upgrade python, Zarr and numpy versions by @jdeschamps in #545
• Chore(deps): Update tifffile requirement from <=2025.5.10 to <=2025.9.20 by @dependabot[bot] in #554
• Chore(deps): Update typer requirement from <=0.17.4,>=0.12.3 to >=0.12.3,<=0.19.2 by @dependabot[bot] in #555
• Chore(deps): Update pyyaml requirement from !=6.0.0,<=6.0.2 to !=6.0.0,<=6.0.3 by @dependabot[bot] in #559
• Chore(deps): Update tifffile requirement from <=2025.9.20 to <=2025.9.30 by @dependabot[bot] in #562

Full Changelog: v0.0.15...v0.0.16

v0.0.15

What's Changed

• chore: Only run codecov on releases by @jdeschamps in #506
• chore: Ignore ruff errors on module import in CZI tests by @jdeschamps in #507
• chore: Bump BMZ dependency to 0.9.0 by @jdeschamps in #508
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #509

Full Changelog: v0.0.14...v0.0.15

v0.0.14

What's Changed

• Fix(UNet): Remove top level skip connection for N2V2 and reduce number of parameters in decoder by @melisande-c in #503

Full Changelog: v0.0.13...v0.0.14