histolab - v0.7.0

v0.7.0

Bug Fix - Fix tissue mask calculation to accommodate slides with large dimensions. (#500 <https://github.com/histolab/histolab/pull/500>_)

Maintenance - Support python 3.11. (#688 <https://github.com/histolab/histolab/pull/688>) - Remove support for python 3.7 and Windows (#683 <https://github.com/histolab/histolab/pull/683>) - Update Openslide to 4.0.0 (#682 <https://github.com/histolab/histolab/pull/682>_)

- Python
Published by ernestoarbitrio about 2 years ago

histolab - v0.6.0

v0.6.0

Bug Fix

• Fix missing relate parameter in OtsuThreshold. (#415 <https://github.com/histolab/histolab/pull/415>_)

New Features

• Stain Normalization with Macenko's method. (#394 <https://github.com/histolab/histolab/pull/394>_)
• Stain normalization with Reinhard's method. (#409 <https://github.com/histolab/histolab/pull/409>_)
• Use non-deprecated resampling constants after upgrading to Pillow 9.1.0 (#408 <https://github.com/histolab/histolab/pull/408>_)

Maintenance

• Poetry migration. (#353 <https://github.com/histolab/histolab/pull/353>_)

Dependencies - Support large-image up to 1.19.1 (#496 <https://github.com/histolab/histolab/pull/496>) and (#494 <https://github.com/histolab/histolab/pull/494>) - Support openslide-pyrthon up to 1.2.0 (#416 <https://github.com/histolab/histolab/pull/416>) - Support numpy up to 1.23.0 (#418 <https://github.com/histolab/histolab/pull/418>) - Support scipy up to 1.8.1 (#405 <https://github.com/histolab/histolab/pull/405>_)

Documentation

• Fix typo in documention for Slide._thumbnail_size(). (#495 <https://github.com/histolab/histolab/pull/495>_)
• Add citation guidelines using citation file. (#497 <https://github.com/histolab/histolab/pull/497>_)
• Add conda installation info. (#399 <https://github.com/histolab/histolab/pull/399>_)
• Update Contributing guidelines after poetry migration. (#425 <https://github.com/histolab/histolab/pull/425>_)

- Python
Published by ernestoarbitrio about 3 years ago

histolab - Version 0.5.1

Other

Fix missing license info. (https://github.com/histolab/histolab/pull/391)

- Python
Published by ernestoarbitrio almost 4 years ago

histolab - Version 0.5.0

Bug Fix ​ - Fix pixel_overlap of adjacent tiles in GridTiler. #372 - Fix bug of thumbnail dimensions when using largeimage. #390 ​ ​ New Features ​ - Tissue mask on Tile is sharper. #364 - Allow custom filters in TissueMask. #377 - Allow custom filters in BiggestTissueBoxMask. #387 ​ Maintenance ​ - Add Gitpod configuration file. #379 - Try to fix dependabot. #369 ​ 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 and #388 - Pin largeimage to 1.8.11. #368 - Support scipy up to 1.8.0. #383 - Upgrade black to fix click dependency issue. #389

- Python
Published by ernestoarbitrio almost 4 years ago

histolab - Version 0.4.1

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

• Use http instead of ftp to download TGGATES slide in CI. #352
• Add cache for WSI files. #358

Dependencies

• Support scipy 1.7.3. #356
• Only support scikit-image 0.19.0. #362

- Python
Published by ernestoarbitrio about 4 years ago

histolab - Version 0.4.0

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

- Python
Published by ernestoarbitrio over 4 years ago

histolab - Version 0.3.1

Bug Fix - Map TCGA old UUID with new UUID to fix data module. #346

Dependencies - Support Python 3.10. #336 - Support scipy 1.7.2. #345 - Upgrade sphinx to 4.2.3. #349

Other - Add test for np_to_pil with float values [0,1] array. #347

- Python
Published by ernestoarbitrio over 4 years ago

histolab - Version 0.3.0

Bug Fix

• Fix GridTiler's arecoordinateswithinextraction_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)

- Python
Published by ernestoarbitrio over 4 years ago

histolab - Version 0.2.6

Bug Fix

• Fix polygon_to_mask_array return mask shape. #268
• Fix overlapping extraction grids in GridTiler. #270

New Features

• Add DAB filter. #277
• Allow slide name to contain dot. #281

Documentation

• Docs fixes about Slide's processed_path. #276
• Add instructions on how to install Pixman 0.40. #280

- Python
Published by ernestoarbitrio over 4 years ago

histolab - Version 0.2.5

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

- Python
Published by ernestoarbitrio almost 5 years ago

histolab - Version 0.2.4

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 locatemask 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>_)

- Python
Published by ernestoarbitrio almost 5 years ago

histolab - Version 0.2.3

v0.2.3

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

- Python
Published by ernestoarbitrio about 5 years ago

histolab - Version 0.2.2

Bug Fix

• Fix of np_to_pil in case float input but in a correct range (https://github.com/histolab/histolab/pull/199)
• Fix tiles extractor checking if the tile size is larger than the slide size (https://github.com/histolab/histolab/pull/202)
• Fix RandomTiler border wackiness extraction (https://github.com/histolab/histolab/pull/203)

New Features

• New parameter tissue_percent for all the tilers' to be used during the has_enough_tissue check (https://github.com/histolab/histolab/pull/204)
• Expose wsi properties. The Slide.properties returns the whole OpenSlide WSI properties (https://github.com/histolab/histolab/pull/209)
• Allow negative indexing for slide.level (https://github.com/histolab/histolab/pull/210)
• New Filter Protocol available (https://github.com/histolab/histolab/pull/213)

Breaking Changes

• Remove pen marks filter (https://github.com/histolab/histolab/pull/201)

- Python
Published by ernestoarbitrio about 5 years ago

histolab - Version 0.2.1

• Pin dependencies in requirements.txt to avoid discrepancy with scikit-image v0.18.0

- Python
Published by ernestoarbitrio about 5 years ago

histolab - Version 0.2.0

• 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)
• Bug: Fix grid tile coordinates calculation (#186,)
• Bug: Fix quickstart tutorial slides' paths (#154 and #165)

- Python
Published by ernestoarbitrio about 5 years ago

histolab - Version 0.1.1

• Add RgbToLab image filter https://github.com/histolab/histolab/pull/147
• Add Watershed segmentation filter https://github.com/histolab/histolab/pull/153
• Support Python 3.8 on Linux and macOS https://github.com/histolab/histolab/pull/151

- Python
Published by ernestoarbitrio over 5 years ago

histolab - Version 0.1.0

• Add Lambda filter (#124)
• Add ScoreTiler and RandomScorer (#129)
• Add NucleiScorer (#132)
• Add Ovarian Tissue sample in data module (#136)
• Fix tiles's save path (#126)
• Fix critical memory issue when extracting biggest tissue box (#128)

- Python
Published by ernestoarbitrio over 5 years ago