Other - Fix missing license info. (#391)
Bug Fix
- Fix pixel_overlap of adjacent tiles in GridTiler. (#372)
- Fix bug of thumbnail dimensions when using large_image. (#390)
New Features
- Tissue mask on Tile is sharper. (#364)
- Allow custom filters in TissueMask. (#377)
- Allow custom filters in BiggestTissueBoxMask. (#387)
Maintenance
Dependencies
- Support scikit-image up to 0.19.2. (#365 and #384)
- Support NumPy up to 1.22.3 (#366, #373, #382 and #386)
- Upgrade sphinx to 4.5.0. (#367, #374 <histolab#374> and #388 <histolab#388>)
- Pin large_image to 1.8.11. (#368)
- Support scipy up to 1.8.0. (#383)
- Upgrade black to fix click dependency issue. (#389)
Bug Fix
- None as default level for Tile, instead of 0. (#355)
- Fix Tile's tissue mask in case of a full tissue tile. (#360)
New Features
- Use BICUBIC for upsampling and LANCZOS for downsampling. (#361)
Maintenance
Dependencies
Bug Fix
- Fix SlideSet not passing along args to Slide. (#351)
New Features
- Add RAG threshold parameters to allow return labels and masking. (#300)
- Support fetching exact MPP resolutions. (#301)
- Allow only keeping a subset of slides for SlideSet. (#303)
Documentation
- Fix link to installation instructions. (#350)
Bug Fix
- Map TCGA old UUID with new UUID to fix data module. (#346)
Dependencies
Other
- Add test for np_to_pil with float values [0,1] array. (#347)
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)
- Fix the mismatch between row-column / X-Y coordinates in the RandomTiler (#317)
- Fix return type of RGB to LAB filter. (#323)
- Filter kmeans_segmentation is now applied only to RGB images. (#328)
- Conversion from RGB to HED preserves HED color space range (#334)
- Conversion from RGB to HSV preserves HSV color space range (#337)
- Remove HSV and YCBCR references in wrong value range in tests (#343)
New Features
- Add RGB to OD filter. (#290 and #331)
- Add method dispatcher compatible with older Python versions. (#312)
- Add LAB to RGB filter. (#323)
- Finer control of locate_tiles (pass tiles to avoid re-extraction and color tiles' border individually). (#304)
- Add TissueMask mask for Tile with type dispatcher. (#313)
- Add conversion level - magnification factor in Slide. (#319)
- Add CellularityScorer. (#320)
Maintenance
- Link automatically issues in PR template. (#291)
- Include histolab version in issue template. (#296)
- Add security linter with Bandit in pre commit and CI. (#316)
- Get rid of src directory in favor of histolab dir within the root. (#324)
- Use Python 3.9 for benchmarks. (#342)
Dependencies
- Support scikit-image 0.18.3. (#196, #200 and #327)
- Support scipy 1.7.1. (#305)
- Upgrade sphinx to 4.2.0 to fix incompatibility with docutils 0.18. (#339)
- Support numpy 1.21.4. (#344)
Documentation
- Fix docs links in tissue_mask module. (#321)
- Add note on data module for TCGA example data not available. (#325 and #333)
Bug Fix
- Fix
polygon_to_mask_arrayreturn mask shape. (#268) - Fix overlapping extraction grids in
GridTiler. (#270)
New Features
Documentation
- Docs fixes about Slide's processed_path. (#276)
- Add instructions on how to install Pixman 0.40. (#280)
Bug Fix
- RandomTiler coordinates selection within the binary mask. (#256)
- LocalOtsuThreshold filter: now it returns correct type (PIL Image). (#258)
- Coordinate definition in the scale coordinates of RandomTiler were reversed. (#261)
New Features
- Support and test for IHC-stained slides. (#262)
Documentation
- Extended documentations to include examples, images, and tutorials. Added IHC-stained slides in the data module. (#232)
Bug Fix
- RandomTiler now respects the given tile size (#243)
- Use logger object instead of logging module when logging tiler updates (#237)
New Features
- New masks module to create binary masks from slides with different strategies: BiggestTissueBoxMask and TissueMask (#234)
- Refactor locate_mask to draw mask contours on the slide from an arbitrary BinaryMask object (#248)
Breaking Changes
- Refactor Slide: return thumbnail and scaled image instead of saving them (#236)
New Features
- Allow pathlib.Path as Slide path parameter (#226)
- Tilers extract method now has log_level param that set the threshold level for the log messages (#229)
Bug Fix
- Fix of np_to_pil in case float input but in a correct range (#199)
- Fix tiles extractor checking if the tile size is larger than the slide size (#202)
- Fix RandomTiler border wackiness extraction (#203)
New Features
- New parameter tissue_percent for all the tilers' to be used during the has_enough_tissue check (#204)
- Expose wsi properties. The Slide.properties returns the whole OpenSlide WSI properties (#209)
- Allow negative indexing for slide.level (#210)
- New Filter Protocol available (#213)
Breaking Changes
- Remove pen marks filter (#201)
Maintenance
- Pin dependencies in requirements.txt to avoid discrepancy with scikit-image v0.18.0
Bug Fix
- Bug: Fix grid tile coordinates calculation (#186)
- Bug: Fix quickstart tutorial slides' paths (#154 and #165)
New Features
- Add diagnostic method to locate tiles on a slide with every Tiler (#179)
- Add diagnostic method to locate the biggest tissue bounding box on a slide (#188)
- SlideSet is iterable and its slides property has been dropped (#177)
New Features
- Add RgbToLab image filter (#147)
- Add Watershed segmentation filter (#153)
- Support Python 3.8 on Linux and macOS (#151)
Bug Fix
New Features
- Add Lambda filter (#124)
- Add ScoreTiler and RandomScorer (#129)
- Add NucleiScorer (#132)
- Add Ovarian Tissue sample in data module (#136)
Bug Fix
New Features
- Grid Tiler (#99)
Bug Fix
- Fix kmeans segmentation image filter default parameters
- Fix rag threshold image filter default parameters
- Fix check tissue on Tile to discard almost white tiles
.. toctree::