Deployment Guide

NL-BIOMERO Deployment & Upgrade Guide

This document outlines several deployment scenarios for the NL-BIOMERO platform. Containers are available prebuilt and deployment is possible on Linux, Windows (via Docker Desktop), or Podman (e.g. RHEL/SELinux). Kubernetes setups should also be possible with shares between services.

Note: The scenarios in this document are examples for inspiration, not official recommendations or complete solutions. You should adapt them to your infrastructure, security posture, and operational requirements.

For detailed docker-compose configurations for each scenario, see Docker Compose Scenarios.

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Scenario 0: Development & Demo

• Development-focused deployments with source code access

• Suitable for testing, development, and demonstration purposes

• Builds containers from local source code

• Can include special configurations for easier development workflow

→ See Docker Compose Scenarios for specific configurations and usage details.

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Scenario 1: Fresh Deployment (no existing data)

• Deploy all containers using docker-compose (1 server) or across multiple VMs.

• Configuration files define all ports, mounts, and credentials.

  • You can change mounted Docker volumes to be on-disk mounts.

• No OMERO data required.

• Works on Windows (Docker Desktop), Linux (Docker or Podman).

• For Kubernetes, adjust disk mounts and configs accordingly; some data needs to be shared between services.

→ See Docker Compose Scenarios for specific deployment configurations.

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Scenario 2: Fresh Deployment with Existing Data

• Use this if restoring an existing OMERO backup.

• Requires OMERO backup (just follow the standard OMERO.server backup and restore):

  • PostgreSQL dump (pg_dump ...)

  • Config dump (omero config get), store in /OMERO/backup

  • /OMERO data backup

• Restore using scripts in backup_and_restore/:

  • restore/restore_db.sh/.ps1

  • restore/restore_server.sh/.ps1

  • The config dump is picked up by 00-restore-config.sh on server startup

• Supports upgrade to newer PostgreSQL too (e.g. dump from 11, restore into 16)

• OMERO.server version must match w/ container, upgrade locally first if it doesn’t.

→ See backup_and_restore/README.md for exact steps of such restore scripts. It also describes the opposite (backing up containers).

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Scenario 3: Hybrid Deployment with Existing OMERO Server

• Keep your existing OMERO.server + PostgreSQL.

• Deploy (perhaps on a separate VM) only a subset of containers, e.g.:

  • biomero, metabase, omeroweb, biomero-database, biomero-importer (BIOMERO.analyzer & BIOMERO.importer)

  • biomero, metabase, omeroweb, biomero-database (BIOMERO.analyzer only)

  • biomero-importer, metabase, omeroweb, biomero-database (BIOMERO.importer only)

• Connect these to the external OMERO server through the env/config variables.

  • Specifically, this would require an OMERO.grid connection between the 2 VMs. See for example the Micron Oxford setup and OMERO docs on multiple hosts for such a split.

• Still requires some minimal config/scripts additions to your OMERO server to make the rest work. For now, see the Dockerfile of server and its config in the deployment configurations.

→ Please contact us directly or on image.sc for help with such a scenario. We’d love to hear from you and see how we can help streamline such a deployment.

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Scenario 4: Full Non-Docker Install (Not Recommended)

• Manual install of OMERO + BIOMERO + Metabase on disk (e.g. with Ansible).

• Not officially supported — too many OS/env dependencies.

• Harder to upgrade with new versions or reproduce issues.

• But: All Dockerfiles are open source and all install steps can be followed if needed.

• Note that Windows is not supported by OMERO itself. And our dockerfiles only show installations on Linux too.

→ Use only if containerized deployment is not possible.

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Notes

• All mounts and port mappings are defined in the deployment configuration files.

• Environment files control ports, secrets, paths — adjust before deploy.

• Podman with SELinux is supported (e.g. on RHEL) with volume labels set.

• For restore/upgrade: follow OMERO docs: https://omero.readthedocs.io/en/stable/sysadmins/server-backup-and-restore.html

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Next Steps

• Want a quick install? → Start with Scenario 1.

• Migrating old data? → Use Scenario 2 and the restore scripts.

• Extending an existing OMERO setup? → Use Scenario 3.

• Avoiding containers? → Proceed with caution (Scenario 4).

Containers reduce complexity — you’re not stuck managing dependencies or OS quirks.

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