Healthcare AI Examples - Data Repository

Sample datasets and embeddings for microsoft/healthcareai-examples.

Prerequisites

This repository uses Git LFS (Large File Storage) to manage large medical imaging files and datasets.

Installing Git LFS

Windows:

Download installer from https://git-lfs.github.com/ or using Chocolatey:

choco install git-lfs

macOS:

Download installer from https://git-lfs.github.com/ or using Homebrew:

# Using Homebrew
brew install git-lfs

Linux (Ubuntu/Debian):

curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash
sudo apt-get install git-lfs

Linux (Fedora/RHEL):

curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh | sudo bash
sudo yum install git-lfs

After installation, initialize Git LFS:

git lfs install

Usage

Clone this repository alongside the main examples repository:

git clone https://github.com/microsoft/healthcareai-examples-data.git

The example notebooks in microsoft/healthcareai-examples reference these datasets.

Already Cloned Without Git LFS?

If you cloned the repository before installing Git LFS, you'll need to fetch the actual files:

cd healthcareai-examples-data
git lfs install
git lfs pull

This will download all the large files that were previously stored as LFS pointers.

Data Attribution

• TCGA-GBM
  Scarpace, L., Mikkelsen, T., Cha, S., Rao, S., Tekchandani, S., Gutman, D., Saltz, J. H., Erickson, B. J., Pedano, N., Flanders, A. E., Barnholtz-Sloan, J., Ostrom, Q., Barboriak, D., & Pierce, L. J. (2016). The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM) (Version 5) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.RNYFUYE9

• TCGA-LGG
  Pedano, N., Flanders, A. E., Scarpace, L., Mikkelsen, T., Eschbacher, J. M., Hermes, B., Sisneros, V., Barnholtz-Sloan, J., & Ostrom, Q. (2016). The Cancer Genome Atlas Low Grade Glioma Collection (TCGA-LGG) (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.L4LTD3TK

License

See LICENSE file for details.