TIAToolbox as an end-to-end library for advanced tissue image analytics

TIAToolbox v1.6.0 (2024-12-12)

Major Updates and Feature Improvements

• Foundation Models Support via timm API (#856, contributed by @GeorgeBatch)
  • Introduced TimmBackbone for running additional PyTorch Image Models.
  • Tested models include UNI, Prov-GigaPath, and H-optimus-0.
  • Added an example notebook demonstrating feature extraction with foundation models.
  • timm added as a dependency.
• Performance Enhancements with torch.compile (#716)
  • Improved performance on newer GPUs using torch.compile.
• Multichannel Input Support in WSIReader (#742)
• AnnotationStore Filtering for Patch Extraction (#822)
• Python 3.12 Support
• Deprecation of Python 3.8 Support
• CLI Response Time Improvements (#795)

API Changes

• Device Specification Update (#882)
  • Replaced has_gpu with device for specifying GPU or CPU usage, aligning with PyTorch's Model.to() functionality.
• Windows Compatibility Enhancement (#769)
  • Replaced POWER with explicit multiplication.

Bug Fixes and Other Changes

• TIFFWSIReader Bound Reading Adjustment (#777)
  • Fixed read_bound to use adjusted bounds.
  • Reduced code complexity in WSIReader (#814).
• Annotation Rendering Fixes (#813)
  • Corrected rendering of annotations with holes.
• Non-Tiled TIFF Support in WSIReader (#807, contributed by @GeorgeBatch)
• HoVer-Net Documentation Update (#751)
  • Corrected class output information.
• Citation File Fix for cffconvert (#869, contributed by @Alon-Alexander)
• Bokeh Compatibility Updates
  • Updated bokeh_app for compatibility with bokeh>=3.5.0.
  • Switched from size to radius for bokeh>3.4.0 compatibility (#796).
• JSON Extraction Fixes (#772)
  • Restructured SQL expression construction for JSON properties with dots in keys.
• VahadaneExtractor Warning (#871)
  • Added warning due to changes in scikit-learn>0.23.0 dictionary learning (#382).
• PatchExtractor Error Message Refinement (#883)
• Immutable Output Fix in WSIReader (#850)

Development-Related Changes

• Mypy Checks Added
  • Applied to utils, tools, data, annotation, and cli/common.
• ReadTheDocs PDF Build Deprecation
• Formatter Update
  • Replaced black with ruff-format.
• Dependency Removal
  • Removed jinja2.
• Test Environment Update
  • Updated to Ubuntu 24.04.
• Conda Environment Workflow Update
  • Implemented micromamba setup.
• Codecov Reporting Fix (#811) Full Changelog: https://github.com/TissueImageAnalytics/tiatoolbox/compare/v1.5.1...v1.6.0