TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics

Major Updates and Feature Improvements

• Adds nucleus instance segmentation base class
  • Adds HoVerNet architecture
• Adds multi-task segmentor HoVerNet+ model
• Adds <a href="https://www.thelancet.com/journals/landig/article/PIIS2589-7500(2100180-1/fulltext">IDaRS</a> pipeline
• Adds SlideGraph pipeline
• Adds PCam patch classification models
• Adds support for stain augmentation feature
• Adds classes and functions under tiatoolbox.tools.graph to enable construction of graphs in a format which can be used with PyG (PyTorch Geometric).
• Add classes which act as a mutable mapping (dictionary like) structure and enables efficient management of annotations. (#135)
• Adds example notebook for adding advanced models
• Adds classes which can generate zoomify tiles from a WSIReader object.
• Adds WSI viewer using Zoomify/WSIReader API (#212)
• Adds README to example page for clarity
• Adds support to override or specify mpp and power

• Replaces models.controller API with models.engine
• Replaces CNNPatchPredictor with PatchPredictor

• Fixes Fix filter_coordinates read wrong resolutions for patch extraction
• For PatchPredictor
  • ioconfig will supersede everything
  • if ioconfig is not provided
    • If model is pretrained (defined in pretrained_model.yaml )
      • Use the yaml ioconfig
      • Any other input patch reading arguments will overwrite the yaml ioconfig (at the same keyword).
    • If model is not defined, all input patch reading arguments must be provided else exception will be thrown.
• Improves performance of mask based patch extraction

• Improve tests performance for Travis runs
• Adds feature detection mechanism to detect the platform and installed packages etc.
• On demand imports for some libraries for performance
• Improves performance of mask based patch extraction