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