NL-BIOMERO

System Administration

  • System Administration Guide
    • Deployment Guide
      • NL-BIOMERO Deployment & Upgrade Guide
        • Scenario 0: Development & Demo
        • Scenario 1: Fresh Deployment (no existing data)
        • Scenario 2: Fresh Deployment with Existing Data
        • Scenario 3: Hybrid Deployment with Existing OMERO Server
        • Scenario 4: Full Non-Docker Install (Not Recommended)
        • Notes
        • Next Steps
    • Docker Compose Scenarios
      • NL-BIOMERO Deployment Scenarios and Docker Compose Files
        • Overview
        • Important Usage Note
        • Scenario 0: Development & Demo
        • Scenario 1: Fresh Deployment (no existing data)
        • Scenario 2: Fresh Deployment with Existing Data
        • Scenario 3: Hybrid Deployment with Existing OMERO Server
        • Additional Configurations
        • Creating a Custom Deployment
        • Detailed Deployment Guides
    • Linux/Ubuntu Deployment
      • NL‑BIOMERO (Ubuntu/Linux) 🚀
        • 🧰 Prerequisites
        • 🔧 Key Differences from Windows Docker Desktop
        • ✅ Quick Start (Ubuntu)
        • 🛠️ Troubleshooting Tips
        • 🧠 Lessons Learned
        • 📋 TL;DR
        • 🔗 Additional Resources
    • Development & Demo Setup
      • BIOMERO 101 Installation Guide
    • Backup and Restore
      • NL-BIOMERO Backup & Restore Scripts
        • Key Features
        • Quick Start
        • Individual Script Usage
        • Restore Scripts
        • OMERO Configuration Hierarchy
        • Example: Backup OMERO from Host Folder
        • Example: Backup Metabase from Host Folder
        • Requirements
        • Troubleshooting
        • Help

Developer Guide

  • Developer Guide
    • Developer Getting Started
      • Quick Setup for Development
      • Development Features
        • Containerized OMERO with BIOMERO
    • Architecture Overview
      • Container Architecture
      • Network Architecture
      • Storage Architecture
      • Integration Points
    • Container Development
      • OMERO Server Container
        • Overview
        • Key Customizations
        • Dockerfile Key Changes
        • Development Guidelines
        • Related Documentation
      • OMERO Web Container
        • Overview
        • Development Workflow
        • Key Installed Plugins
        • Custom Interface Modifications
        • Dockerfile Key Sections
        • Development Guidelines
        • Related Documentation
      • BIOMERO Worker Container
        • Overview
        • Key Features
        • Container Customizations
        • Configuration Management
        • Worker Startup Process
        • Development Guidelines
        • Troubleshooting
        • Upgrade Considerations
        • Related Documentation
        • External Resources
      • Database Containers
        • Overview
        • Key Components
        • Schema customization
        • Migration
        • Performance tuning
        • Backup automation
        • Accessing PostgreSQL
        • Related Documentation
      • Metabase Container
        • Why Metabase?
        • Dashboard Development
        • Related Documentation
      • OMERO ADI Container
        • Overview
        • Import Workflow
        • Import order creation and management
        • File system monitoring and processing
        • Configuration
        • Integration with OMERO server
        • Custom import pipeline development
        • Error handling and retry mechanisms
        • Testing
        • Security and runtime requirements
        • Related Documentation
      • Container Releases
        • Release Overview
        • Release Workflow
        • Versioning Guidelines
        • Dependency Management
        • OMERO ADI Submodule
        • Docker Hub Management
        • Communication & Announcements
        • Troubleshooting Releases
        • Best Practices
        • Related Documentation

User Guide

  • User Guide
    • Getting Started
      • First Steps with NL-BIOMERO
        • Access the Platform
        • Default Login
        • Next Steps
      • Platform Overview
        • 🧬 BIOMERO - BioImage Analysis
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