OMERO in Jupyter

Run OMERO inside Jupyter!

Mybinder

Start OMERO.web by clicking the OMERO.web launcher icon. This will launch a new tab.

WARNING: mybinder.org limits the available memory to 2 GB which may prevent OMERO.server from running properly. mybinder.org also prevents outgoing network access on the standard OMERO ports so even if you configure OMERO.web to connect to an external server you will not be able to login to OMERO.web unless the OMERO.server is listening on a web port. If you get a timeout whilst launching OMERO.web refresh the page.

Quickstart

1. Launch the container.
2. Start a terminal. Run ./intialise.sh to start PostgreSQL and initialise OMERO.server. If you are running on mybinder.org run ./intialise.sh 2048 to configure OMERO to run with less memory.
3. Start OMERO.server: omero admin start
4. Start OMERO.web by clicking the OMERO.web launcher icon. This will launch a new tab. Login as user root password omero.

Configuration

omero is in the standard PATH so you can configure OMERO by running omero config in the terminal before starting OMERO.server or OMERO.web.