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TIAToolbox 1.5.0
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@shaneahmed shaneahmed released this 15 Dec 22:30
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v1.5.0
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1.5.0 (2023-12-15)

Major Updates and Feature Improvements

  • Adds the bokeh visualization tool. #684
    • The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines.
    • This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/.
  • Extends Annotation to Support Init from WKB #639
  • Adds IOConfig for NuClick in pretrained_model.yaml #709
  • Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724
  • Adds Support for QuPath Annotation Imports #721

Changes to API

  • Adds model.to(device) and model.load_model_from_file() functionality to make it compatible with PyTorch API. #733
  • Replaces pretrained with weights to make the engines compatible with the new PyTorch API. #621
  • Adds support for high-level imports for various utility functions and classes such as WSIReader, PatchPredictor and imread #606, #607,
  • Adds tiatoolbox.typing for type hints. #619
  • Fixes incorrect file size saved by save_tiles, issue with certain WSIs raised by @TomastpPereira
  • TissueMasker transform now returns mask instead of a list. #748

Bug Fixes and Other Changes

  • Fixes pixman incompability error on Colab #601
  • Removes shapely.speedups. The module no longer has any affect in Shapely >=2.0. #622
  • Fixes errors in the slidegraph example notebook #608
  • Fixes bugs in WSI Registration #645, #670, #693
  • Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712
  • Fixes #738 raised by @xiachenrui

Development related changes

  • Replaces flake8 and isort with ruff #625, #666
  • Adds mypy checks to root and utils package. This will be rolled out in phases to other modules. #723
  • Adds a module to detect file types using magic number/signatures #616
  • Uses poetry for version updates instead of bump2version. #638
  • Removes setup.cfg and uses pyproject.toml for project configurations.
  • Reduces runtime for some unit tests e.g., #627, #630, #631, #629
  • Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644
  • Set up parallel tests locally #671

Full Changelog: v1.4.0...v1.5.0

Contributors

xiachenrui and TomastpPereira
Assets 2
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