To launch Jupyter from XNAT, navigate to a project, subject, or experiment of your choice. If your administrator has enabled Jupyter for your user account, a new action called Start Jupyter will be available in the actions panel.
Clicking on "Start Jupyter" will prompt you to select a Jupyter Environment and a Hardware configuration. The Jupyter environment you choose determines the available software packages within your Jupyter server, while the hardware selection determines the allocated memory, CPU, and other hardware resources for your Jupyter server. By making these selections, you can customize your Jupyter environment according to your specific needs and requirements.
When you start the Jupyter server, it will run as a background process. You can monitor the status of the Jupyter process by locating the background processes activity tab at the bottom right of your screen. Expand this tab to view the details and status of your Jupyter notebook server.
When the Jupyter server starts successfully, you will see a notebook icon in this activity tab. Clicking on this icon will take you directly to your Jupyter server, where you can begin working with your notebooks.
Please note that our testing indicates an average start time of less than 60 seconds for launching a Jupyter server. However, the duration may vary on your specific XNAT setup. During the startup phase of your Jupyter server, feel free to navigate to other pages within XNAT without any interruption.
If Jupyter failed to start, expand the dialog for more details.
If you are asked to login to JupyterHub, use your XNAT username and password. JupyterHub will authenticate your credentials by verifying the information with XNAT.
Please note that your Jupyter notebook server is associated with your XNAT user account, and logging out of XNAT does not automatically log you out of JupyterHub. To ensure a complete logout, you will need to log out of Jupyter separately from XNAT.
To log out of Jupyter, navigate to File → Log Out within your Jupyter interface. This action will successfully log you out of Jupyter, but it will not immediately stop your Jupyter container. To stop the Jupyter server and release the associated resources, you can use the Stop Jupyter option available in XNAT's top navigation menu.
Furthermore, there is an inactivity timeout plugin setting that can automatically stop an inactive Jupyter server. This feature helps optimize resource utilization by automatically terminating idle Jupyter servers after a certain period of inactivity. Your administrator may or may not have this feature enabled.