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TIAToolbox 0.8.0

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@shaneahmed shaneahmed released this 28 Oct 07:56
· 24 commits to master since this release
v0.8.0
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Learn about vigilant mode.

Major Updates and Feature Improvements

  • Adds SemanticSegmentor which is Predictor equivalent for semantic segmentation.
  • Add TIFFWSIReader class to support OMETiff reading.
  • Adds FeatureExtractor API to controller.
  • Adds WSI Serialization Dataset which support changing parallel workers on the fly. This would reduce the time spent to create new worker for every WSI/Tile (costly).
  • Adds IOState data class to contain IO information for loading input to model and assembling model output back to WSI/Tile.
  • Minor updates for get_coordinates to pave the way for getting patch IO for segmentation.
  • Migrates old code to new variable names (patch extraction, patch wsi model).
  • Change in API from pretrained_weight to pretrained_weights.
  • Adds cli for semantic segmentation.
  • Update python notebooks to add read_rect and read_bounds examples with mpp read.

Changes to API

  • Adds WSIReader.open. get_wsireader will deprecate in the next release. Please use WSIReader.open instead.
  • CLI is now POSIX compatible
    • Replaces underscores in variable names with hyphens
  • Models API updated to use pretrained_weights instead of pretrained_weight.
  • Move string_to_tuple to tiatoolbox/utils/misc.py

Bug Fixes and Other Changes

  • Fixes README git clone instructions.
  • Fixes stain normalisation due to changes in sklearn.
  • Fixes a test in tests/test_slide_info
  • Fixes readthedocs documentation issues

Development related changes

  • Adds dependencies for tiffile, imagecodecs, zarr.
  • Adds more stringent pre-commit checks
  • Moved local test files into tiatoolbox/data.
  • Fixed Manifest.ini and added tiatoolbox/data. This means that this directory will be downloaded with the package.
  • Using pkg_resources to properly load bundled resources (e.g. target_image.png) in tiatoolbox.data.
  • Removed duplicate code in conftest.py for downloading remote files. This is now in tiatoolbox.data._fetch_remote_file.
  • Fixes errors raised by new flake8 rules.
    • Remove leading underscores from fixtures.
  • Rename some remote sample files to make more sense.
  • Moves all cli commands/options from cli.py to cli_commands to make it clean and easier to add new commands
  • Removes redundant tests
  • Updates to new GitHub organisation name in the repo
    • Fixes related links
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