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>_)

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>_)

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
  ​
• 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 large_image to 1.8.11. #368
• Support scipy up to 1.8.0. #383
• Upgrade black to fix click dependency issue. #389

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

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

• 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

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_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

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