Getting Started with OMERO

The Basics

Before You Begin

Read through the documentation listed here:

https://www.openmicroscopy.org/omero/institution/getting-started.html https://omero-guides.readthedocs.io/en/latest/

https://docs.alliancecan.ca/wiki/Technical_documentation

https://github.com/WU-BIMAC/W-IDM_OmeroImporter

What You Will Need

  1. Compute Canada account

    1. PI needs to sponsor you to get this

  2. Submit a request to get associated with the rpp-steveogg project

    1. This will allow you to login to the Arbutus open stack dashboard here. The dashboard is where we can manage instances, volumes, etc.

  3. Before you can ssh into the VMs, you need to whitelist your IP on the dashboard. Do so by adding your IP to the ssh group with the appropriate labels.

  4. Someone will make an admin account for you for each of the OMERO instances so that you can manage groups/users.

  5. In order to ssh into the servers, you need the identity key (arbutus-key, omero-dev) associated with the server. It will be provided to you.

Managing Groups/Users

Rule of Thumb:

  • A PI or Lab gets their own group

  • Anybody working under the PI or in the Lab becomes a member of the lab (there is no difference between an undergraduate student vs a postdoc in roles)

  • Each publication gets its own public group with the Public user as a member and the authors as the owners

All of this management can be done through your admin account on OMERO.web through the Admin tab.

It is also possible to send out emails to users from the Admin tab. The email will be sent out from omero.notifications@gmail.com to the specified users. Use this feature to let the users know when the server may be down for updates, etc.

Logging into an Instance

Any installations or config updates can be done by logging in directly into the server, or through ansible playbooks here. All of the playbooks are forked from the OME playbooks here and here.

Use command ssh -i [PATH TO KEY] ubuntu@[IP] to login.

The available instances are:

Description

Key

Production (National_OMERO)

arbutus_key, omero_dev

Training (Replica of Dundee’s training with already uploaded data)

Daily Backup

Grafana

If you ever need to add a new key to an instance, append the public key to .ssh/authorized_keys

Any OMERO configuration changes that need to be made through the CLI can be done with /opt/omero/server/OMERO.server/bin/omero or /opt/omero/web/OMERO.web/bin/omero as the omero command shown on the official OMERO docs.