Kubernetes templates for OMERO as run at The Jackson Laboratory

The Jackson Laboratory hosts a public image repository using OMERO on Google Cloud at images.jax.org. These templates are made to mimic that OMERO deployment and related testing environments as closely as possible.

As a lightweight template repository, the current goal is to only require kubectl and either a local Kubernetes cluster or Google Cloud Project (GCP). Kustomize is used to provide multiple optional deployment configurations in the GCP yamls, run as kubectl apply -k.

Deployment overview

• One read-write OMERO server is run as an ephemeral Kubernetes pod and used for OMERO setup, data imports, and admin tasks
  • The read-write OMERO server has read-write access to the database and the NFS server with the OMERO directories. All data is imported in-place with --transfer ln_s, so image data (either on NFS or object storage) can be mounted read-only.
• One (or more) read-only OMERO servers use a read-only database user and mount both the data and OMERO directories as read-only
• One (or more) OMERO web deployment runs both OMERO web and Nginx and connects to the read-only OMERO server

Other relevant repositories

We are not involved with these repositories, but they are doing similar things:

• IDR Ansible deployment (IDR/deployment)
• Helm charts for OMERO (manics/kubernetes-omero)
• OMERO on AWS (aws-samples/digital-pathology-on-aws)