tiatoolbox 0.3.0

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. Then, create and activate the conda environment:

pip

pip install -r requirements.txt

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,
                  }
                 ...

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

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

History

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

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0.1.0 (2020-05-28)

• First release on PyPI.