v1.8.2

What's Changed

⚠️ Breaking Changes

• Use Geary's C normality variance in spatial_autocorr (fixes #1183) by @gaoflow in #1197

Added

• Functions to QC histopathology images by @timtreis in #1036
• Add derive_mpp_from_shapes utility by @timtreis in #1172
• Add tiling QC metric for tile-boundary segmentation artifacts by @timtreis in #1157
• Stain normalization: foundations by @timtreis in #1178
• spatial_neigbours extensibility features and clarification by @selmanozleyen in #1147
• Stain normalization: Reinhard color transfer by @timtreis in #1191
• Stain normalization: Macenko/Vahadane decomposition + background estimator by @timtreis in #1196
• feat: add cells SpatialData dataset and update S3 key paths in registry by @selmanozleyen in #1211
• [2/4] Add calculate_image_features with skimage + squidpy-native features by @timtreis in #1190

Changed

• Add explicit error handling in _make_tiles.py by @timtreis in #1130
• fix: remove unused parameters in co_occurence by @selmanozleyen in #1121
• feat: remove unnecessary parallelize usage in sepal by @selmanozleyen in #1120
• Parallelize spatial neighbors by @grst in #1198

Deprecated

• Deprecate Napari Interactive by @selmanozleyen in #1082

Removed

• remove mask_polygon by @selmanozleyen in #1148

Fixed

• fix: require spatialdata>=0.7.2 to drop the xarray-schema/pkg_resources break by @timtreis in #1117

New Contributors

• @gaoflow made their first contribution in #1197

Full Changelog: v1.8.1...v1.8.2

v1.8.1

What's Changed

Other Changes

• Fix for pandas 3 CoW policy by @selmanozleyen in #1106
• Lower bound spatialdata>=0.7.1 by @selmanozleyen in #1114

Full Changelog: v1.8.0...v1.8.1

v1.8.0

What's Changed

Other Changes

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1080
• Fix for spatial_neighbors breaks when transform='spectral' by @selmanozleyen in #1028
• Adding a registry to have the hashes of datasets (restructured for aws s3) by @selmanozleyen in #1076
• make_tiles now properly copies the transformations from source img by @timtreis in #1084
• Add SpatialLeiden as clustering method by @melocery in #1019
• Update exampledata URL to point to cloudfront by @grst in #1092
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1083
• fix: Support SpaceRanger v3 format by @selmanozleyen in #1097
• Fix: _set_default_colors_for_categorical_obs import fix by @selmanozleyen in #1103
• Lower bound spatialdata and unpin dask by @selmanozleyen in #1108
• ci: mark test_parallelize as flaky by @selmanozleyen in #1105

New Contributors

• @melocery made their first contribution in #1019
• @grst made their first contribution in #1092

Full Changelog: v1.7.0...v1.8.0

v1.7.0

What's Changed

Changed

• refactor: Import fewer private modules by @selmanozleyen in #1069
• Raised lower pin for zarr to >=3.0.0 by @timtreis in #1075

Added

• Added more complex tissue detection method for complexer tissues by @timtreis in #1074

Full Changelog: v1.6.6...v1.7.0

v1.6.6

What's Changed

Changed

• Updating CI/CD by @timtreis in #981
• Docs: Edit the argument documentation of n_jobs of the parallelize function by @selmanozleyen in #987
• parallelize sets numba cores to 1 by @selmanozleyen in #1008
• Re-implementating co_occurrence() by @wenjie1991 in #975
• Deprecate Python 3.10 by @selmanozleyen in #1031
• Replacing fixed size tuples as return types by @selmanozleyen in #1043
• zarr v3 support by @LucaMarconato in #1040* Change niche flavor to cellcharter_simple and default distance = 3 by @marcovarrone in #978

Fixed

• Fix outline color behavior by @Sonja-Stockhaus in #1006
• Fix IO warning by @Zethson in #979
• Ligrec Reproducibility and Bug Fix in Sparse Data. by @selmanozleyen in #991
• Fix logger warnings by @emmanuel-ferdman in #1004
• Numba warning fix by @selmanozleyen in #1002
• Fix: sepal numba compilation options changes the results significantly by @selmanozleyen in #1045
• Fix the __version__ deprecated warning by @selmanozleyen in #1056

Added

• Run notebooks in CI by @selmanozleyen in #1013
• Method to detect specimens in H&E images by @timtreis in #1044
• fix: repair the docs by @flying-sheep in #1062
• Add helper functions to tile image for inference by @timtreis in #1053

Other Changes

• chore: fix messed-up yaml formatting by @flying-sheep in #1024
• Update CI by @flying-sheep in #1025
• Moving to uv + hatch by @selmanozleyen in #1029
• chore: remove unused imports by @flying-sheep in #1058
• Update template to v0.6.0 by @scverse-bot in #1041
• remove duplicated issue templates by @Zethson in #1064
• now creating folder if it doesn't exist by @timtreis in #1066

New Contributors

• @selmanozleyen made their first contribution in #987
• @Sonja-Stockhaus made their first contribution in #1006
• @emmanuel-ferdman made their first contribution in #1004
• @wenjie1991 made their first contribution in #975
• @LucaMarconato made their first contribution in #1040

Full Changelog: v1.6.5...v1.6.6

v1.6.5

What's Changed

Added

• Added Artifact action to CI/CD so we can download test images from runners by @timtreis in #973
• Add function for calculating niches by @LLehner in #831

Full Changelog: v1.6.4...v1.6.5

v1.6.4

What's Changed

Added

• Added NumFOCUS trademark and statement to README by @melonora in #965

Removed

• Removed leiden as hard dep to stay BSD3 compliant by @Intron7 in #972

Fixed

• Fixed bug in CICD by @timtreis in #971

New Contributors

• @Intron7 made their first contribution in #972

Full Changelog: v1.6.3...v1.6.4

v1.6.3

What's Changed

Added

• Added function to download Visium as SpatialData by @timtreis in #949

Changed

• Upper bound zarr to <3 by @ilan-gold in #935
• Pin xarray to >=2024.10.0 by @timtreis in #954
• Mirror SpatialData release action by @timtreis in #960

Fixed

• Fixes to var_by_distance functionalities by @LLehner in #929
• Rename count_file in internal API to counts_file; Improves error message when wrongly specified by @flying-sheep in #944
• Updated linkcheck times for sphinx to prevent timeouts by @timtreis in #955
• Fixed error in tox.ini by @timtreis in #956

Full Changelog: v1.6.2...v1.6.3