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Published July 5, 2022 | Version 1.2.0
Software Open

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

Description

Major Updates and Feature Improvements
  • Adds support for Python 3.10
  • Adds short description for IDARS algorithm #383
  • Adds support for NGFF v0.4 OME-ZARR.
  • Adds CLI for launching tile server.
Changes to API
  • Renames stainnorm_target() function to stain_norm_target().
  • Removes get_wsireader
  • Replaces the custom PlattScaler in tools/scale.py with the regular Scikit-Learn LogisticRegression.
Bug Fixes and Other Changes
  • Fixes bugs in UNET architecture.
    • Number of channels in Batchnorm argument in the decoding path to match with the input channels.
    • Padding 0 creates feature maps in the decoder part with the same size as encoder.
  • Fixes linter issues and typos
  • Fixes incorrect output with overlap in predictor.merge_predictions() and return_raw=True
    • Thanks to @paulhacosta for raising #356, Fixed by #358.
  • Fixes errors with JP2 read. Checks input path exists.
  • Fixes errors with torch upgrade to 1.12.
Development related changes
  • Adds pre-commit hooks for consistency across the repo.
  • Sets up GitHub Actions Workflow.
    • Travis CI will be removed in future release.

Notes

If you use this software, please cite it as below.

Files

TissueImageAnalytics/tiatoolbox-v1.2.0.zip

Files (59.6 MB)

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