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
OMERO.biomero Plugin Administration
Accessing Admin Interfaces
Importer Admin Configuration
Group Folder Mappings
Configuration File Management
Analyzer Admin Configuration
Overview
Configuration File Sharing
Settings Interface Usage
Settings Categories
1. SSH Settings
2. Slurm Settings
3. Analytics Settings
4. Converters Settings
5. Models Settings (Workflows)
Slurm Check Setup Output
Security Considerations
Troubleshooting
Related Documentation
SLURM Integration
Overview
Architecture
Configuration
Basic Configuration
Container Environment Configuration
Workflow Definitions
Analytics and Monitoring
Deployment Considerations
SSH Configuration
Directory Structure
Permissions and Access
Troubleshooting
Common Issues
Debug Commands
Performance Tuning
Resource Allocation
Queue Management
Monitoring and Analytics
Security Considerations
Further Reading
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
Troubleshooting
Related Documentation
BIOMERO.importer 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
NL-BIOMERO
Index
Index