OMERO Server Container

The OMERO server container serves as the master node for the entire platform, handling core OMERO functionality with minimal but important customizations.

Overview

Based on the official openmicroscopy/omero-server image, this container acts as the central coordination point for:

Core OMERO server functionality
Script execution coordination
Database management
Ice grid management for distributed processing

Key Customizations

Script Installation

The container automatically installs three sets of scripts during build:

1. BIOMERO.scripts

Source: NL-BioImaging/biomero-scripts
Location: /opt/omero/server/OMERO.server/lib/scripts/biomero/
Purpose: Slurm-based image analysis workflows

2. OMERO.figure Script

Source: ome/omero-figure
Location: /opt/omero/server/OMERO.server/lib/scripts/omero/figure_scripts/
Purpose: PDF export functionality for figures

3. Labels2ROIs Script

Source: Cellular-Imaging-Amsterdam-UMC/label2rois
Location: /opt/omero/server/OMERO.server/lib/scripts/omero/util_scripts/
Purpose: Convert BIOMERO label images to OMERO ROIs

Automated Configuration Restoration

Configuration Backup/Restore System

Script: 00-restore-config.sh
Purpose: Enables stateless container redeployments by automatically restoring OMERO configuration from backup
Location: /OMERO/backup/omero.config
Benefit: No manual configuration needed after container (re)creation

LDAP Integration Ready

Config: 01-ldap-config.omero
Purpose: Pre-configured LDAP settings for enterprise authentication
Customizable via environment variables. Placeholder for now.

Dockerfile Key Changes

# Install required scripts for analysis workflows
RUN cd /opt/omero/server/OMERO.server/lib/scripts/ && \
    git clone --depth 1 --branch ${BIOMERO_VERSION} \
    https://github.com/NL-BioImaging/biomero-scripts.git biomero

# Configuration restoration on startup
ADD server/00-restore-config.sh* /startup/
ADD server/01-ldap-config.omero /opt/omero/server/config/

Development Guidelines

Configuration Changes

Programmatic Configuration: Always make configuration changes through scripts or environment variables to maintain stateless deployments:

# Example: Add new configuration via startup script
echo "config set -- omero.my.setting 'value'" >> /opt/omero/server/config/02-my-config.omero

Environment Variables: Use docker-compose environment variables for dynamic configuration:

environment:
  CONFIG_omero_db_host: "${POSTGRES_HOST}"
  CONFIG_omero_db_name: "${POSTGRES_DB}"

Adding New Scripts

To add additional OMERO scripts:

Via Git Repository (recommended for script collections):

RUN cd /opt/omero/server/OMERO.server/lib/scripts/ && \
    git clone https://github.com/your-org/your-scripts.git

Via Direct Download (for individual scripts):

RUN curl -o /opt/omero/server/OMERO.server/lib/scripts/path/script.py \
    https://raw.githubusercontent.com/your-org/repo/main/script.py

Testing Changes

Build and test locally:

docker-compose -f docker-compose-dev.yml build omeroserver
docker-compose -f docker-compose-dev.yml up -d omeroserver

Verify script installation:

docker-compose exec omeroserver omero script list

Check configuration:

docker-compose exec omeroserver omero config get