tiatoolbox 0.4.0

Computational pathology toolbox developed by TIA Lab.

TIA Toolbox

Computational Pathology Toolbox developed by TIA Lab

Please try

python -m tiatoolbox -h

Getting Started

First, install

• OpenSlide here.
• OpenJPEG here, using conda install -c conda-forge openjpeg>=2.3.0.

Then, create and activate the conda environment:

pip

pip install tiatoolbox

conda

conda env create --name tiatoolbox --file requirements.conda.yml
conda activate tiatoolbox

tiatoolbox --help

usage: tiatoolbox [-h] [--version] [--verbose VERBOSE]
                 {read-region,
                  save-tiles,
                  slide_info,
                  slide-thumbnail,
                  stainnorm,
                  }
                 ...

positional arguments:
  {slide_info}

read-region         usage: tiatoolbox read-region -h
save-tiles          usage: tiatoolbox save-tiles -h
slide-info          usage: tiatoolbox slide-info -h
slide-thumbnail     usage: tiatoolbox slide-thumbnail -h
stainnorm           usage: tiatoolbox stainnorm -h

optional arguments:
  -h, --help            show this help message and exit
  --version             show program`s version number and exit
  --verbose             VERBOSE

License

The source code TIA Toolbox (tiatoolbox) as hosted on GitHub is released under the GNU General Public License (Version 3).

The full text of the licence is included in LICENSE.md.

Auxiliary Files

Auxiliary files, such as pre-trained model weights downloaded from the TIA Lab webpage (https://warwick.ac.uk/fac/sci/dcs/research/tia/tiatoolbox), are provided under the Creative Commons Attribution-NonCommercial-ShareAlike Version 4 (CC BY-NC-SA 4.0) license.

Dual License

If you would like to use any of the source code or auxiliary files (e.g. pre-trained model weights) under a different license agreement please contact the Tissue Image Analytics (TIA) Lab at the University of Warwick ([e-mail]).

History

0.4.0 (2020-10-25)

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 the toolbox.
• 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
• Depericiates support for multiprocessing from within the toolbox. The toolbox is focussed 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

0.3.0 (2020-07-19)

Major and Feature Improvements

• Adds feature read_region to read a small region from whole slide images
• Adds feature save_tiles to save image tiles from whole slide images
• Adds feature imresize to resize images
• Adds feature transforms.background_composite to avoid creation of black tiles from whole slide images.

Changes to API

• None

Bug Fixes and Other Changes

• Adds pandas as dependency

---

0.2.2 (2020-07-12)

Major and Feature Improvements

• None

Changes to API

• None

Bug Fixes and Other Changes

• Fix command line interface for slide-info feature and travis pypi deployment

---

0.2.1 (2020-07-10)

Major and Feature Improvements

• None

Changes to API

• None

Bug Fixes and Other Changes

• Minor changes to configuration files.

---

0.2.0 (2020-07-10)

Major and Feature Improvements

• Adds feature slide_info to read whole slide images and display meta data information
• Adds multiprocessing decorator TIAMultiProcess to allow running toolbox functions using multiprocessing.

Changes to API

• None

Bug Fixes and Other Changes

• Adds Sphinx Readthedocs support https://readthedocs.org/projects/tia-toolbox/ for stable and develop branches
• Adds code coverage tools to test the pytest coverage of the package
• Adds deepsource integration to highlight and fix bug risks, performance issues etc.
• Adds README to allow users to setup the environment.
• Adds conda and pip requirements instructions

---

0.1.0 (2020-05-28)

• First release on PyPI.