TIAToolbox 1.2.0

1.2.0 (2022-07-05)

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.