Tiatoolbox

Major Updates and Feature Improvements

- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449
- Adds Annotation Store Reader 476
- Adds [DFBR](https://arxiv.org/abs/2202.09971) 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

Major Updates and Feature Improvements

- Adds an AnnotationTileGenerator and AnnotationRenderer which allows serving of tiles rendered directly from an annotation store.
- Adds [DFBR](https://arxiv.org/abs/2202.09971) registration model and jupyter notebook example
- Adds DICE metric
- Adds [SCCNN](https://doi.org/10.1109/tmi.2016.2525803) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.sccnn.SCCNN.html)\]
- Adds [MapDe](https://arxiv.org/abs/1806.06970) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.mapde.MapDe.html)\]
- 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

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.

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](https://ngff.openmicroscopy.org/latest/).
- 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](https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression).

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.

Major Updates and Feature Improvements

- Adds DICOM Support.
- Updates license to more permissive BSD 3-clause.
- Adds `micronet` model.
- Improves support for `tiff` files.
- Adds a check for tiles in a TIFF file when opening.
- Uses OpenSlide to read a TIFF if it has tiles instead of OpenCV (VirtualWSIReader).
- Adds a fallback to tifffile if it is tiled but openslide cannot read it
(e.g. jp2k or jpegxl tiles).
- Adds support for multi-channel images (HxWxC).
- Fixes performance issues in `semantic_segmentor.py`.
- Performance gain measurement: 21.67s (new) vs 45.564 (old) using a 4k x 4k WSI.
- External Contribution from ByteHexler.
- Adds benchmark for Annotations Store.

Changes to API

- None

Bug Fixes and Other Changes

- Enhances the error messages to be more informative.
- Fixes Flake8 Errors, typos.
- Fixes patch predictor models based after fixing a typo.
- Bug fixes in Graph functions.
- Adds documentation for docker support.
- General tidying up of docstrings.
- Adds metrics to readthedocs/docstrings for pretrained models.

Development related changes

- Adds `pydicom` and `wsidicom` as dependency.
- Updates dependencies.
- Fixes Travis detection and makes improvements to run tests faster on Travis.
- Adds Dependabot to automatically update dependencies.
- Improves CLI definitions to make it easier to integrate new functions.
- Fixes compile options for test_annotation_stores.py

Major Updates and Feature Improvements

- Updates dependencies for conda recipe 262

Changes to API

- None

Bug Fixes and Other Changes

- Adds User Warning For Missing SQLite Functions
- Fixes Pixman version check errors
- Fixes empty query in instance segmentor

Development related changes

- Fixes flake8 linting issues and typos
- Conditional pytest.skipif to skip GPU tests on travis while running them locally or elsewhere