diff --git a/README.md b/README.md index e214cb0..5af5892 100644 --- a/README.md +++ b/README.md @@ -8,3 +8,49 @@ This repository will contain the code for the paper ## Dataset The medical imaging dataset, CheXpert, used in this study is publicly available and can be downloaded from https://stanfordmlgroup.github.io/competitions/chexpert/. + +## Code + +For running the code, we recommend setting up a dedicated Python environment. + +### Setup Python environment using conda + +Create and activate a Python 3 conda environment: + + ```shell + conda create -n pymira python=3 + conda activate chexploration + ``` + +Install PyTorch using conda: + + ```shell + conda install pytorch torchvision cudatoolkit=10.1 -c pytorch + ``` + +### Setup Python environment using virtualenv + +Create and activate a Python 3 virtual environment: + + ```shell + virtualenv -p python3 /chexploration + source /chexploration/bin/activate + ``` + +Install PyTorch using pip: + + ```shell + pip install torch torchvision + ``` + +### Install additional Python packages: + + ```shell + pip install matplotlib jupyter pandas seaborn pytorch-lightning scikit-learn scikit-image tensorboard tqdm openpyxl + ``` + +## Funding sources +This work is supported through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 757173, [Project MIRA](https://www.project-mira.eu), ERC-2017-STG) and by the [UKRI London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare](https://www.aicentre.co.uk/). + +## License +This project is licensed under the [Apache License 2.0](LICENSE).