TIA Toolbox

Computational Pathology Toolbox developed by TIA Lab

Getting Started

First, install

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

Git

1.Create the virtual environment

conda env create -f requirements.conda.yml

or (on Windows)

conda env create -f requirements.win64.conda.yml

or

pip install -r requirements.txt

2.Clone the tiatoolbox

git clone https://github.com/TIA-Lab/tiatoolbox.git

3.Please try

python -m tiatoolbox -h

pip

pip install tiatoolbox

conda

conda env create -n tiatoolbox python=3.{6,7,8}
conda activate tiatoolbox
pip install tiatoolbox

tiatoolbox --help

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

positional arguments:
  {slide_info}

read-bounds         usage: tiatoolbox read-bounds -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 (tialab@dcs.warwick.ac.uk).