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

v0.0.13

What's Changed

• feat: Expose Optimizer, LR Scheduler and Checkpoint parameters in convenience functions by @jdeschamps in #483
• Expose BatchNorm flag for UNet by @Callidior in #477
• Support CZI file format with NextGen datasets by @Callidior in #476
• fix: Fix pre-commit by adding missing docstrings by @jdeschamps in #484
• Chore(deps): Update torch requirement from <=2.6.0,>=2.0 to >=2.0,<=2.7.1 by @dependabot in #487
• ci(pre-commit.ci): autoupdate by @pre-commit-ci in #388
• Chore(deps): Update torchvision requirement from <=0.21.0 to <=0.22.1 by @dependabot in #493
• Fix: N2V masking bugs by @melisande-c in #491
• Chore(deps): Update typer requirement from <=0.15.2,>=0.12.3 to >=0.12.3,<=0.16.0 by @dependabot in #494
• Refac(Next-Gen): Fold patching strategies into a subconfiguration of DataConfig by @jdeschamps in #486
• chore: CZI format as optional dependency by @jdeschamps in #492
• chore: Drop support for 3.9 by @jdeschamps in #485
• Chore(deps): Update pytorch-lightning requirement from <=2.5.0.post0,>=2.2 to >=2.2,<=2.5.1rc0 by @dependabot in #433
• Chore(deps): Update pytorch-lightning requirement from <=2.5.1rc0,>=2.2 to >=2.2,<=2.5.2 by @dependabot in #499
• Chore(deps): Update matplotlib requirement from <=3.10.1 to <=3.10.3 by @dependabot in #498
• Chore(deps): Update tifffile requirement from <=2025.3.13 to <=2025.5.10 by @dependabot in #497

New Contributors

• @Callidior made their first contribution in #477

Full Changelog: v0.0.12...v0.0.13