Changelog¶
v0.6.0¶
Bug Fix
Fix missing relate parameter in OtsuThreshold. (#415)
New Features
Stain Normalization with Macenko’s method. (#394)
Stain normalization with Reinhard’s method. (#409)
Use non-deprecated resampling constants after upgrading to Pillow 9.1.0 (#408)
Maintenance
Poetry migration. (#353)
Dependencies - Support large-image up to 1.19.1 (#496) and (#494) - Support openslide-pyrthon up to 1.2.0 (#416) - Support numpy up to 1.23.0 (#418) - Support scipy up to 1.8.1 (#405)
Documentation
v0.5.1¶
Other - Fix missing license info. (#391)
v0.5.0¶
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
v0.4.1¶
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
v0.4.0¶
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)
v0.3.1¶
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)
v0.3.0¶
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 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 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
v0.2.6¶
Bug Fix
Fix
polygon_to_mask_array
return mask shape. (#268)Fix overlapping extraction grids in
GridTiler
. (#270)
New Features
Documentation
v0.2.5¶
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)
v0.2.4¶
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)
v0.2.3¶
New Features
v0.2.2¶
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)
v0.2.1¶
Maintenance
Pin dependencies in requirements.txt to avoid discrepancy with scikit-image v0.18.0
v0.2.0¶
Bug Fix
Bug: Fix grid tile coordinates calculation (#186)
New Features
v0.1.1¶
New Features
v0.0.1¶
Bug Fix
New Features
v0.0.5b¶
Bug Fix
New Features
Grid Tiler (#99)
v0.0.4b¶
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