TIAToolbox 0.4.0

Major and Feature Improvements

• Adds OpenSlideWSIReader to read Openslide image formats
• Adds support to read Omnyx jp2 images using OmnyxJP2WSIReader.
• New feature added to perform stain normalisation using Ruifork, Reinhard, Vahadane, Macenko methods and using custom stain matrices.
• Adds example notebook to read whole slide images via tiatoolbox.
• Adds WSIMeta class to save meta data for whole slide images. WSIMeta casts properties to python types. Properties from OpenSlide are returned as string. raw values can always be accessed via slide.raw. Adds data validation e.g., checking that level_count matches up with the length of the level_dimensions and level_downsamples. Adds type hints to WSIMeta.
• Adds exceptions FileNotSupported and MethodNotSupported

Changes to API

• Restructures WSIReader as parent class to allow support to read whole slide images in other formats.
• Adds slide_info as a property of WSIReader
• Updates slide_info type to WSIMeta from dict
• Depreciates support for multiprocessing from within the toolbox. The toolbox is focused on processing single whole slide and standard images. External libraries can be used to run using multi processing on multiple files.

Bug Fixes and Other Changes

• Adds scikit-learn, glymur as a dependency
• Adds licence information
• Removes pathos as a dependency
• Updates openslide-python requirement to 1.1.2

Co-authored-by: Shan E Ahmed @shaneahmed, John Pocock @John-P, Simon Graham @simongraham, Dang Vu @vqdang, Srijay Deshpande @Srijay-lab, Saad Bashir @rajasaad