Histolab

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**Bug Fix**

- Map TCGA old UUID with new UUID to fix `data` module. (`346 <https://github.com/histolab/histolab/pull/346>`_)

**Dependencies**

- Support Python 3.10. (`336 <https://github.com/histolab/histolab/pull/336>`_)
- Support scipy 1.7.2. (`345 <https://github.com/histolab/histolab/pull/345>`_)
- Upgrade sphinx to 4.2.3. (`349 <https://github.com/histolab/histolab/pull/349>`_)

**Other**

- Add test for `np_to_pil` with float values [0,1] array. (`347 <https://github.com/histolab/histolab/pull/347>`_)

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**Bug Fix**

- Fix `GridTiler`'s `_are_coordinates_within_extraction_mask` method where tile coordinates are off by 1 or 2 pixels due to conversion of floats to ints. (`308 <https://github.com/histolab/histolab/pull/308>`_)
- Fix the mismatch between row-column / X-Y coordinates in the RandomTiler (`317 <https://github.com/histolab/histolab/pull/317>`_)
- Fix return type of RGB to LAB filter. (`323 <https://github.com/histolab/histolab/pull/323>`_)
- Filter `kmeans_segmentation` is now applied only to RGB images. (`328 <https://github.com/histolab/histolab/pull/328>`_)
- Conversion from RGB to HED preserves HED color space range (`334 <https://github.com/histolab/histolab/pull/334>`_)
- Conversion from RGB to HSV preserves HSV color space range (`337 <https://github.com/histolab/histolab/pull/337>`_)
- Remove HSV and YCBCR references in wrong value range in tests (`343 <https://github.com/histolab/histolab/pull/343>`_)

**New Features**

- Add RGB to OD filter. (`290 <https://github.com/histolab/histolab/pull/290>`_ and `#331 <https://github.com/histolab/histolab/pull/331>`_)
- Add method dispatcher compatible with older Python versions. (`312 <https://github.com/histolab/histolab/pull/312>`_)
- Add LAB to RGB filter. (`323 <https://github.com/histolab/histolab/pull/323>`_)
- Finer control of `locate_tiles` (pass tiles to avoid re-extraction and color tiles' border individually). (`304 <https://github.com/histolab/histolab/pull/304>`_)
- Add `TissueMask` mask for `Tile` with type dispatcher. (`313 <https://github.com/histolab/histolab/pull/313>`_)
- Add conversion level - magnification factor in `Slide`. (`319 <https://github.com/histolab/histolab/pull/319>`_)
- Add `CellularityScorer`. (`320 <https://github.com/histolab/histolab/pull/320>`_)

**Maintenance**

- Link automatically issues in PR template. (`291 <https://github.com/histolab/histolab/pull/291>`_)
- Include histolab version in issue template. (`296 <https://github.com/histolab/histolab/pull/296>`_)
- Add security linter with Bandit in pre commit and CI. (`316 <https://github.com/histolab/histolab/pull/316>`_)
- Get rid of `src` directory in favor of `histolab` dir within the root. (`324 <https://github.com/histolab/histolab/pull/324>`_)
- Use Python 3.9 for benchmarks. (`342 <https://github.com/histolab/histolab/pull/342>`_)

**Dependencies**

- Support scikit-image 0.18.3. (`196 <https://github.com/histolab/histolab/pull/196>`_, `#200 <https://github.com/histolab/histolab/pull/200>`_ and `#327 <https://github.com/histolab/histolab/pull/327>`_)
- Support scipy 1.7.1. (`305 <https://github.com/histolab/histolab/pull/305>`_)
- Upgrade sphinx to 4.2.0 to fix incompatibility with docutils 0.18. (`339 <https://github.com/histolab/histolab/pull/339>`_)
- Support numpy 1.21.4. (`344 <https://github.com/histolab/histolab/pull/344>`_)

**Documentation**

- Fix docs links in `tissue_mask` module. (`321 <https://github.com/histolab/histolab/pull/331>`_)
- Add note on data module for TCGA example data not available. (`325 <https://github.com/histolab/histolab/pull/325>`_ and `#333 <https://github.com/histolab/histolab/pull/333>`_)

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**Bug Fix**

- Fix ``polygon_to_mask_array`` return mask shape. (`268 <https://github.com/histolab/histolab/pull/268>`_)
- Fix overlapping extraction grids in ``GridTiler``. (`270 <https://github.com/histolab/histolab/pull/270>`_)

**New Features**

- Add DAB filter. (`277 <https://github.com/histolab/histolab/pull/277>`_)
- Allow slide name to contain dot. (`281 <https://github.com/histolab/histolab/pull/281>`_)

**Documentation**

- Docs fixes about Slide's processed_path. (`276 <https://github.com/histolab/histolab/pull/276>`_)
- Add instructions on how to install Pixman 0.40. (`280 <https://github.com/histolab/histolab/pull/280>`_)

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**Bug Fix**

- `RandomTiler` coordinates selection within the binary mask. (`256 <https://github.com/histolab/histolab/pull/256>`_)
- `LocalOtsuThreshold` filter: now it returns correct type (PIL Image). (`258 <https://github.com/histolab/histolab/pull/258>`_)
- Coordinate definition in the scale coordinates of `RandomTiler` were reversed. (`261 <https://github.com/histolab/histolab/pull/261>`_)

**New Features**

- Support and test for IHC-stained slides. (`262 <https://github.com/histolab/histolab/pull/262>`_)

**Documentation**

- Extended documentations to include examples, images, and tutorials. Added IHC-stained slides in the data module. (`232 <https://github.com/histolab/histolab/pull/232>`_)

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**Bug Fix**

- `RandomTiler` now respects the given tile size (`243 <https://github.com/histolab/histolab/pull/243>`_)
- Use logger object instead of logging module when logging tiler updates (`237 <https://github.com/histolab/histolab/pull/237>`_)

**New Features**

- New `masks` module to create binary masks from slides with different strategies: `BiggestTissueBoxMask` and `TissueMask` (`234 <https://github.com/histolab/histolab/pull/234>`_)
- Refactor locate_mask to draw mask contours on the slide from an arbitrary BinaryMask object (`248 <https://github.com/histolab/histolab/pull/248>`_)

**Breaking Changes**

- Refactor `Slide`: return thumbnail and scaled image instead of saving them (`236 <https://github.com/histolab/histolab/pull/236>`_)

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**New Features**

- Allow pathlib.Path as Slide path parameter (`226 <https://github.com/histolab/histolab/pull/226>`_)
- Tilers `extract` method now has `log_level` param that set the threshold level for the log messages (`229 <https://github.com/histolab/histolab/pull/229>`_)