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Published May 5, 2023 | Version v1.4.0
Software Open

TIAToolbox as an end-to-end library for advanced tissue image analytics

Authors/Creators

Description

1.4.0 (2023-04-24) Major Updates and Feature Improvements
  • Adds Python 3.11 support [experimental] #500
  • Removes Python 3.7 support
    • This allows upgrading all the dependencies which were dependent on an older version of Python.
  • Adds Neighbourhood Querying Support To AnnotationStore #540
    • This enables easy and efficient querying of annotations within a neighbourhood of other annotations.
  • Adds MultiTaskSegmentor engine #424
  • Fixes an issue with stain augmentation to apply augmentation to only tissue regions.
    • #546 contributed by @navidstuv
  • Filters logger output to stdout instead of stderr.
    • Fixes #255
  • Allows import of some modules at higher level for improved usability
    • WSIReader can now be imported as from tiatoolbox.wsicore import WSIReader
    • WSIMeta can now be imported as from tiatoolbox.wsicore import WSIMeta
    • HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN can now be imported as `from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN
  • Improves PatchExtractor performance. Updates WSIPatchDataset to be consistent. #571
  • Updates documentation for License for clarity on source code and model weights license.
Changes to API
  • Updates SCCNN architecture to make it consistent with other models. #544
Bug Fixes and Other Changes
  • Fixes Parsing Missing Omero Version NGFF Metadata #568
    • Fixes #535 raised by @benkamphaus
  • Fixes reading of DICOM WSIs at the correct level #564
    • Fixes #529
  • Fixes scipy, matplotlib, scikit-image deprecated code
  • Fixes breaking changes in DICOMWSIReader to make it compatible with latest wsidicom version. #539, #580
  • Updates shapely dependency to version >=2.0.0 and fixes any breaking changes.
  • Fixes bug with DictionaryStore.bquery and geometry=None, i.e. only a where predicate given.
    • Partly Fixes #532 raised by @blaginin
  • Fixes local tests for Windows/Linux
  • Fixes flake8, deepsource errors.
  • Uses logger instead of warnings and print statements to properly log runs.
Development related changes
  • Upgrades dependencies which are dependent on Python 3.7
  • Moves requirements*.txt files to requirements folder
  • Removes tox
  • Uses pyproject.toml for bdist_wheel, pytest and isort
  • Adds joblib and numba as dependencies.

Notes

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

Files

TissueImageAnalytics/tiatoolbox-v1.4.0.zip

Files (62.5 MB)

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md5:f3d115a56684b42dbc5a3c0e5031bf20
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Additional details

Related works

Is supplement to
https://github.com/TissueImageAnalytics/tiatoolbox/tree/v1.4.0 (URL)