TIAToolbox 1.6.0

TIAToolbox v1.6.0 (2024-12-12)

Major Updates and Feature Improvements

• Foundation Models Support via timm API (#856, contributed by @GeorgeBatch)
  • Introduced TimmBackbone for running additional PyTorch Image Models.
  • Tested models include UNI, Prov-GigaPath, and H-optimus-0.
  • Added an example notebook demonstrating feature extraction with foundation models.
  • timm added as a dependency.
• Performance Enhancements with torch.compile (#716)
  • Improved performance on newer GPUs using torch.compile.
• Multichannel Input Support in WSIReader (#742)
• AnnotationStore Filtering for Patch Extraction (#822)
• Python 3.12 Support
• Deprecation of Python 3.8 Support
• CLI Response Time Improvements (#795)

API Changes

• Device Specification Update (#882)
  • Replaced has_gpu with device for specifying GPU or CPU usage, aligning with PyTorch's Model.to() functionality.
• Windows Compatibility Enhancement (#769)
  • Replaced POWER with explicit multiplication.

Bug Fixes and Other Changes

• TIFFWSIReader Bound Reading Adjustment (#777)
  • Fixed read_bound to use adjusted bounds.
  • Reduced code complexity in WSIReader (#814).
• Annotation Rendering Fixes (#813)
  • Corrected rendering of annotations with holes.
• Non-Tiled TIFF Support in WSIReader (#807, contributed by @GeorgeBatch)
• HoVer-Net Documentation Update (#751)
  • Corrected class output information.
• Citation File Fix for cffconvert (#869, contributed by @Alon-Alexander)
• Bokeh Compatibility Updates
  • Updated bokeh_app for compatibility with bokeh>=3.5.0.
  • Switched from size to radius for bokeh>3.4.0 compatibility (#796).
• JSON Extraction Fixes (#772)
  • Restructured SQL expression construction for JSON properties with dots in keys.
• VahadaneExtractor Warning (#871)
  • Added warning due to changes in scikit-learn>0.23.0 dictionary learning (#382).
• PatchExtractor Error Message Refinement (#883)
• Immutable Output Fix in WSIReader (#850)

Development-Related Changes

• Mypy Checks Added
  • Applied to utils, tools, data, annotation, and cli/common.
• ReadTheDocs PDF Build Deprecation
• Formatter Update
  • Replaced black with ruff-format.
• Dependency Removal
  • Removed jinja2.
• Test Environment Update
  • Updated to Ubuntu 24.04.
• Conda Environment Workflow Update
  • Implemented micromamba setup.
• Codecov Reporting Fix (#811)
  Full Changelog: v1.5.1...v1.6.0

TIAToolbox 1.5.1

1.5.1 (2023-12-16)

Development related changes

• Specifies compatible Python versions
  • Fixes tiatoolbox-feedstock build for conda-forge release #763

Full Changelog: v1.5.0...v1.5.1

TIAToolbox 1.5.0

1.5.0 (2023-12-15)

Major Updates and Feature Improvements

• Adds the bokeh visualization tool. #684
  • The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines.
  • This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/.
• Extends Annotation to Support Init from WKB #639
• Adds IOConfig for NuClick in pretrained_model.yaml #709
• Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724
• Adds Support for QuPath Annotation Imports #721

Changes to API

• Adds model.to(device) and model.load_model_from_file() functionality to make it compatible with PyTorch API. #733
• Replaces pretrained with weights to make the engines compatible with the new PyTorch API. #621
• Adds support for high-level imports for various utility functions and classes such as WSIReader, PatchPredictor and imread #606, #607,
• Adds tiatoolbox.typing for type hints. #619
• Fixes incorrect file size saved by save_tiles, issue with certain WSIs raised by @TomastpPereira
• TissueMasker transform now returns mask instead of a list. #748
  • Fixes #732

Bug Fixes and Other Changes

• Fixes pixman incompability error on Colab #601
• Removes shapely.speedups. The module no longer has any affect in Shapely >=2.0. #622
• Fixes errors in the slidegraph example notebook #608
• Fixes bugs in WSI Registration #645, #670, #693
• Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712
  • Fixes #710
• Fixes #738 raised by @xiachenrui

Development related changes

• Replaces flake8 and isort with ruff #625, #666
• Adds mypy checks to root and utils package. This will be rolled out in phases to other modules. #723
• Adds a module to detect file types using magic number/signatures #616
• Uses poetry for version updates instead of bump2version. #638
• Removes setup.cfg and uses pyproject.toml for project configurations.
• Reduces runtime for some unit tests e.g., #627, #630, #631, #629
• Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644
• Set up parallel tests locally #671

Full Changelog: v1.4.0...v1.5.0

TIAToolbox 1.4.1

Bug Fixes and Other Changes

• Fix dictionary changed size Error #626 (#605)

Full Changelog: v1.4.0...v1.4.1

TIAToolbox 1.4.0

1.4.0 (2023-04-24)

Major Updates and Feature Improvements

• Adds Python 3.11 support [experimental] #500
  • Python 3.11 is not fully supported by pytorch pytorch/pytorch#86566 and openslide openslide/openslide-python#188
• 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.

Full Changelog: v1.3.3...v1.4.0

TIAToolbox 1.3.3

Major Updates and Feature Improvements

• Restricts dependency versions for long term stability of the current version

Changes to API

None

Bug Fixes and Other Changes

• Fix bug related to reading scikit-image

Development related changes

• Restricts dependency versions for compatibility

TIAToolbox 1.3.2

Major Updates and Feature Improvements

• None

Changes to API

• None

Bug Fixes and Other Changes

• Fix bug related to reading DICOM files

Development related changes

• Restricts wsidicom version to <0.7.0 for compatibility

TIAToolbox 1.3.1

Major Updates and Feature Improvements

• Adds NuClick architecture #449
• Adds Annotation Store Reader #476
• Adds DFBR method for registering pair of images #510

Changes to API

• Adds a sample SVS loading function tiatoolbox.data.small_svs() to the data module #517

Bug Fixes and Other Changes

• Simplifies example notebook for image reading for better readability
• Restricts Shapely version to <2.0.0 for compatibility

Development related changes

• Adds GitHub workflow for automatic generation of docker image
• Updates dependencies
• Updates bump2version config
• Enables flake8 E800 checks for commented codes.
• Fixes several errors generated by DeepSource.
• Prevent test dumping file to root
• Removes duplicate functions to generate parameterized test scenarios

Note: Please note that Python 3.7 support will be removed after this release. We plan to add support for Python 3.11 in the next release.

TIAToolbox 1.3.0

Major Updates and Feature Improvements

• Adds an AnnotationTileGenerator and AnnotationRenderer which allows serving of tiles rendered directly from an annotation store.
• Adds DFBR registration model and Jupyter notebook example
  • Adds DICE metric
• Adds SCCNN architecture. [read the docs]
• Adds MapDe architecture. [read the docs]
• Adds support for reading MPP metadata from NGFF v0.4
• Adds enhancements to tiatoolbox.annotation.storage that are useful when using an AnnotationStore for visualization purposes.

Changes to API

• None

Bug Fixes and Other Changes

• Fixes colorbar_params #410
• Fixes Jupyter notebooks for better read the docs rendering
  • Fixes typos, metadata and links
• Fixes nucleus_segmentor_engine for boundary artefacts
• Fixes the colorbar cropping in tests
• Adds citation in README.md and CITATION.cff to Nature Communications Medicine paper
• Fixes a bug #452 raised by @rogertrullo where only the numerator of the TIFF resolution tags was being read.
• Fixes HoVer-Net+ post-processing to be inline with original work.
• Fixes a bug where an exception would be raised if the OME XML is missing objective power.

Development related changes

• Uses Furo theme for readthedocs
• Replaces nbgallery and nbsphinx with myst-nb for jupyter notebook rendering
• Uses myst for markdown parsing
• Uses requirements.txt to define dependencies for requirements consistency
• Adds notebook AST pre-commit hook
• Adds check to validate python examples in the code
• Adds check to resolve imports
• Fixes an error in a docstring which triggered the failing test.
• Adds pre-commit hooks to format markdown and notebook markdown
• Adds pip install workflow to resolve dependencies when requirements file is updated
• Improves TIAToolbox import using LazyLoader

TIAToolbox 1.2.1

Major Updates and Feature Improvements

• None

Changes to API

• None

Bug Fixes and Other Changes

• Fixes issues with dependencies
  • Adds flask to dependencies.
• Fixes missing file in the python package
• Clarifies help string for show-wsi option

Development related changes

• Removes Travis CI
  • GitHub Actions will be used instead.
• Adds pre-commit hooks to check requirements consistency.
• Adds GitHub Action to resolve conda environment checks on Windows and Ubuntu.