Computational pathology toolbox developed by TIA Lab.
Project description
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
0.1.0 (2020-05-28)
- First release on PyPI.
Project details
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