This repository currently contains sample notebooks for use in the XNAT/Jupyter integrated environment. Head to xnat-docker-compose/features/jupyterhub for information on setting that up.
You will also find notebooks used for the Jupyter demonstration during the XNAT Workshop in London 2022.
After you Start Jupyter from XNAT, start a terminal from within JupyterLab.
Your workspace directory is available at /workspace/{username}.
cd $JUPYTERHUB_ROOT_DIRThis is where you should store any Jupyter notebooks. Notebooks stored here will persist between Jupyter sessions. Git repositories should also be stored here.
git clone https://github.com/NrgXnat/xnat-jupyter-notebooks.gitAfter cloning checkout the sample notebook for a overview of the XNAT/Jupyter environmental variables, naviagting the XNAT file system, and converting stored searches to pandas DataFrames. There is also a introductory MONAI image classification tutorial using the MedNIST dataset.
The dashboards directory contains a few simple dashboards for use with Dash, Panel, Streamlit, and Voila. They can be deployed with the XNAT JupyterHub integration plugin and the xnat/datascience-notebook image.