Quick Start
Contents
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