Quick Start#

Luna docker images are available to help you get started with Luna. Before running these images, be sure to install Docker on your workspace.

Running Luna Pathology Tutorials on Docker#

We provide a docker image to help you get started with pathology analysis using Luna workflows. This image includes:

  • Luna pathology library

  • Luna notebook tutorials with sample data

Along with web applications:

  • JupyterLab for running notebooks

  • Digital Slide Archive (girder and mongodb) for viewing the slides and annotations

These set of notebook tutorials walk you through analysis workflows. A static version of the notebook Tutorials is also available on the documentation site for your reference.

1. Clone the git repository#

git clone https://github.com/msk-mind/docker.git

2. Run the docker-compose#

  • Build the docker image

cd docker/luna_tutorial
make build

  • Run the docker image

make run

Copy paste the Jupyter URL printed in luna_tutorial/vmount/logs/tutorial.log, and you will see a set of ipynb notebooks for exploring end-to-end Luna pathology analysis workflow.

To login to DSA, go to http://localhost:8080 and login with admin/password. After login, you can navigate to the TCGA Collection, and explore images on HistomicsUI. For details on using DSA, please refer to DSA documentation