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TIAToolbox 0.6.0

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@shaneahmed shaneahmed released this 11 May 20:41
v0.6.0
6ee13c7
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Learn about vigilant mode.

Major and Feature Improvements

  • Add TissueMasker class to allow tissue masking using Otsu and Morphological processing.
  • Add helper/convenience method to WSIReader(s) to produce a mask. Add reader object to allow reading a mask conveniently as if it were a WSI i.e., use same location and resolution to read tissue area and mask area.
  • Add PointsPatchExtractor returns patches that can be used by classification models. Takes csv, json or pd.DataFrame and returns patches corresponding to each pixel location.
  • Add feature FixedWindowPatchExtractor to run sliding window deep learning algorithms.
  • Add example notebooks for patch extraction and tissue masking.
  • Update readme with improved instructions to use the toolbox. Make the README file somewhat more comprehensible to beginners, particularly those with not much background or experience.

Changes to API

  • tiatoolbox.dataloader replaced by tiatoolbox.wsicore

Bug Fixes and Other Changes

  • Minor bug fixes

Development-related changes

  • Improve unit test coverage.
  • Move test data to tiatoolbox server.
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