TIAToolbox 0.5.0

Major and Feature Improvements

• Adds get_wsireader() to return appropriate WSIReader.
• Adds new functions to allow reading of regions using WSIReader at different resolutions given in units of:
  • microns per-pixel (mpp)
  • objective lens power (power)
  • pixels-per baseline (baseline)
  • resolution level (level)
• Adds functions for reading regions are read_bounds and read_rect.
  • read_bounds takes a tuple (left, top, right, bottom) of coordinates in baseline (level 0) reference frame and returns a region bounded by those.
  • read_rect takes one coordinate in baseline reference frame and an output size in pixels.
• Adds VirtualWSIReader as a subclass of WSIReader which can be used to read visual fields (tiles).
  • VirtualWSIReader accepts ndarray or image path as input.
• Adds MPP fall back to standard TIFF resolution tags with warning.
  • If OpenSlide cannot determine microns per pixel (mpp) from the metadata, checks the TIFF resolution units (TIFF tags: ResolutionUnit, XResolution and YResolution) to calculate MPP. Additionally, add function to estimate missing objective power if MPP is known of derived from TIFF resolution tags.
• Estimates missing objective power from MPP with warning.
• Adds example notebooks for stain normalisation and WSI reader.
• Adds caching to slide info property. This is done by checking if a private self._m_info exists and returning it if so, otherwise self._info is called to create the info for the first time (or to force regenerating) and the result is assigned to self._m_info. This could in future be made much simpler with the functools.cached_property decorator in Python 3.8+.
• Adds pre processing step to stain normalisation where stain matrix encodes colour information from tissue region only.

Changes to API

• read_region refactored to be backwards compatible with openslide arguments.
• slide_info changed to info
• Updates WSIReader which only takes one input
• WSIReader input_path variable changed to input_img
• Adds tile_read_size, tile_objective_value and output_dir to WSIReader.save_tiles()
• Adds tile_read_size as a tuple
• transforms.imresize takes additional arguments output_size and interpolation method 'optimise' which selects cv2.INTER_AREA for scale_factor<1 and cv2.INTER_CUBIC for scale_factor>1

Bug Fixes and Other Changes

• Refactors glymur code to use index slicing instead of deprecated read function.
• Refactors thumbnail code to use read_bounds and be a member of the WSIReader base class.
• Updates README.md to clarify installation instructions.
• Fixes slide_info.py for changes in WSIReader API.
• Fixes save_tiles.py for changes in WSIReader API.
• Updates example_wsiread.ipynb to reflect the changes in WSIReader.
• Adds Google Colab and Kaggle links to allow user to run notebooks directly on colab or kaggle.
• Fixes a bug in taking directory input for stainnorm operation for command line interface.
• Pins numpy<=1.19.3 to avoid compatibility issues with opencv.
• Adds scikit-image or jupyterlab as a dependency.

Development related changes

• Moved test_wsireader_jp2_save_tiles to test_wsireader.py.
• Change recipe in Makefile for coverage to use pytest-cov instead of coverage.
• Runs travis only on PR.
• Adds pre-commit for easy setup of client-side git hooks for black code formatting and flake8 linting.
• Adds flake8-bugbear to pre-commit for catching potential deepsource errors.
• Adds constants for test regions in test_wsireader.py.
• Rearranges usage.rst for better readability.
• Adds pre-commit, flake8, flake8-bugbear, black, pytest-cov and recommonmark as dependency.

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