OMERO Server Extended

Custom OMERO.server image based on the official openmicroscopy/omero-server:5.6.16 that bundles extra OMERO scripts and useful tooling. The image:

• Installs jq, curl-minimal, and CA certificates for scripting inside the container
• Installs the Python package omero-metadata in the OMERO server venv
• Copies all scripts from scripts/ into OMERO.server/lib/scripts/omero/ so they are available in OMERO clients (OMERO.web/Insight).

What’s in this repo

• Dockerfile: Builds on top of the official OMERO server image, adds packages and Python deps, and copies scripts into the server
• scripts/: Collection of OMERO scripts grouped by purpose
  • analysis_scripts/
  • annotation_scripts/
  • export_scripts/
  • figure_scripts/
  • import_scripts/
  • util_scripts/

NOTE: The core scripts are available in OMERO clients under the omero-scripts git repository except Figure_To_Pdf.py which is available in the omero-figure git repository.

Requirements

• Docker 20.10+ (or compatible)
• A running PostgreSQL instance accessible by the OMERO server (or use your existing DB setup; see the base image docs for environment variables)

Image

Prebuilt image:

docker pull ghcr.io/scilifelabdatacentre/omero-server-extended:latest

Run (basic example)

Expose OMERO ports and configure DB connection via environment variables understood by the base image:

docker run -d --name omero-server \
  -p 4063:4063 -p 4064:4064 \
  -e OMERO_DB_HOST=postgres \
  -e OMERO_DB_NAME=omero \
  -e OMERO_DB_USER=omero \
  -e OMERO_DB_PASS=omero \
  -e OMERO_ROOT_PASSWORD=change-me \
  ghcr.io/scilifelabdatacentre/omero-server-extended:latest

• To iterate on scripts without rebuilding the image, you can bind-mount your local scripts/ into the container:

docker run -d --name omero-dev \
  -p 4063:4063 -p 4064:4064 \
  -v "$(pwd)/scripts:/opt/omero/server/OMERO.server/lib/scripts/omero:ro" \
  -e OMERO_DB_HOST=postgres -e OMERO_DB_NAME=omero -e OMERO_DB_USER=omero -e OMERO_DB_PASS=omero \
  -e OMERO_ROOT_PASSWORD=change-me \
  ghcr.io/scilifelabdatacentre/omero-server-extended:latest

• To add Python dependencies for the scripts, update the Dockerfile to pip install them inside /opt/omero/server/venv3
• To update the OMERO base version, change the tag on the FROM openmicroscopy/omero-server:<tag> line

Kubernetes (manifests example)

Below is a minimal example showing how to deploy this image on Kubernetes.

Deployment and Service:

apiVersion: apps/v1
kind: Deployment
metadata:
  name: omero-server
spec:
  replicas: 1
  selector:
    matchLabels:
      app: omero-server
  template:
    metadata:
      labels:
        app: omero-server
    spec:
      containers:
        - name: omero-server
          image: ghcr.io/scilifelabdatacentre/omero-server-extended:latest
          imagePullPolicy: IfNotPresent
# the rest of the manifest...