Architecture Overview

NL-BIOMERO consists of several interconnected components:

Container Architecture

The platform uses Docker Compose to orchestrate multiple services:

  • omeroserver - Core OMERO server with BIOMERO.scripts

  • omeroweb - Web interface with custom plugins

  • biomeroworker - BIOMERO.analyzer processor

  • metabase - Analytics and visualization dashboard (BIOMERO.db)

  • database - PostgreSQL for OMERO data

  • database-biomero - PostgreSQL for BIOMERO workflows (BIOMERO.db)

  • biomero-importer - BIOMERO.importer service

Network Architecture

Services communicate through Docker networks:

  • Internal network for database connections

  • Exposed ports for web access (4080, 3000)

  • OMERO ports for client connections (4063, 4064)

Storage Architecture

Persistent data is managed through mounted or Docker volumes:

  • OMERO data volume for image metadata storage

  • Database volumes for persistent data

  • Configuration mounts for customization

Integration Points

  • Slurm Integration - BIOMERO connects to HPC clusters

  • SSH Configuration - Secure connections to compute resources

  • Shared Storage - Common data access across services