NL-BIOMERO
1.8.0-beta.9

Overview

  • BIOMERO Videos
    • Conceptual introduction
      • BIOMERO explained: a conceptual introduction
    • Technical architecture clips
      • What NL-BIOMERO adds to OMERO
      • One format, flexible workflows
      • In-place importing
      • Provenance while the work happens
      • Adding an analysis workflow
    • Live demonstration
      • NL-BIOMERO in practice
  • Citing NL-BIOMERO and BIOMERO
    • Which paper should I cite?
    • BIOMERO 2.0 / NL-BIOMERO
    • BIOMERO analysis framework
    • Software citation metadata

System Administration

  • Development & Demo Setup
    • Quick Links to Other Guides
    • Windows Development Setup
      • Prerequisites
      • Quick Setup Steps
    • Container Management
    • Configuration Overview
    • BIOMERO 101 Installation Guide
  • Advanced 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
      • Upgrading BIOMERO Components
      • Next Steps
  • Docker Compose Scenarios
    • NL-BIOMERO Deployment Scenarios and Docker Compose Files
      • Overview
      • Important Usage Note
      • Scenario 0: Development & Demo
        • Scenario 0.1: Local Development Setup
        • Scenario 0.2: Default (Local Build)
      • Scenario 1: Fresh Deployment (no existing data)
        • Scenario 1.1: Standard Production Deployment
        • Scenario 1.2: Production with SSL (Ubuntu)
      • Scenario 2: Fresh Deployment with Existing Data
        • Scenario 2.1: Restore from OMERO Backup
      • Scenario 3: Hybrid Deployment with Existing OMERO Server
        • Scenario 3.1: BIOMERO Only (External OMERO)
        • Scenario 3.2: BIOMERO.importer Only (External OMERO)
      • Additional Configurations
        • Component Selection with Profiles
        • Toggle UI Modules (OMERO.biomero plugin)
        • Environment Customization
      • Creating a Custom Deployment
  • Linux/Ubuntu Deployment
    • NL‑BIOMERO (Ubuntu/Linux) 🚀
      • 🧰 Prerequisites
      • 🔧 Key Differences from Windows Docker Desktop
        • 1. PostgreSQL Image
        • 2. Privileged Access Needed
        • 3. SSH Permissions in biomero-worker
        • 4. Containerized Slurm Build
        • 5. Host Networking (host.docker.internal Replacement)
        • 6. Volume Permission Fixes
        • 7. Secrets & Metabase Setup
        • 8. HTTPS via Nginx Reverse Proxy
        • 9. Persistent Logs
      • ✅ Quick Start (Ubuntu)
      • 🛠️ Troubleshooting Tips
      • 🧠 Lessons Learned
      • 📋 TL;DR
      • 🔗 Additional Resources
  • BIOMERO.analyzer SLURM Integration for NL-BIOMERO
    • Overview
    • Architecture
    • SSH Key Management for Container Deployment
      • Development/Docker Compose Setup
      • Production/Podman Deployment with Secrets
    • Configuration Files
      • Container File Sharing Setup
      • Configuration Content Structure
      • SSH Configuration
    • SLURM Environment Setup
      • Web-Based Configuration (Recommended)
      • Manual SLURM Cluster Setup
    • Security Considerations
      • File Permissions
      • SSH Access Security
      • Database Access
      • Manual Verification
    • Network Security
      • Required Network Access
      • Firewall Configuration
    • Service Account Architecture
      • Single Service Account
      • Account Requirements
    • Deployment-Specific Examples
      • Local Development (docker-compose)
      • Production (Podman with Secrets)
    • Troubleshooting
      • SSH Connection Issues
      • SLURM Job Issues
      • Configuration Validation
    • Advanced: BIOMERO Environment Variable Overrides
    • Further Reading
  • OMERO.biomero Plugin Administration
    • Accessing Admin Interfaces
    • Importer Admin Configuration
      • Group Folder Mappings
      • Configuration File Management
    • Analyzer Admin Configuration
      • Overview
      • Configuration Management
      • Settings Interface Usage
    • Settings Categories
      • SSH Settings
      • SLURM Settings
      • Analytics Settings
      • Converters Settings
      • Workflows Settings
        • Adding New Workflows
        • Common SBATCH Parameters
        • Editing Existing Workflows
        • Required Follow-up Actions
      • Zarr and Plate Workflow Types
        • Zarr Workflow
        • Zarr Plate Workflow
        • BIAFLOWS descriptors and Zarr auto-detection
      • Slurm Check Setup Output
    • Interface Troubleshooting
    • Related Documentation
  • BIOMERO.analyzer + BIOMERO.importer Integration
    • Overview
    • Required configuration changes
      • .env
      • docker-compose.yml — biomeroworker service
    • Storage and file-system setup
      • Shared mount
      • Result folder structure
      • Group path resolution
      • Permissions
    • Non-Docker deployments
    • Validating the setup
    • Zarr Workflow Support
      • Shallow OME-Zarr Storage
    • Troubleshooting
    • Related documentation
  • Shallow OME-Zarr Storage
    • Lifecycle overview
    • Choosing local or remote shallowing
    • Requirements and enablement
    • Admin settings
    • Failure and observability
  • Detached BIOMERO Workflows
    • Overview
    • Configuration
    • Session and timeout settings
    • Operational behavior
    • Troubleshooting
    • See also
  • Resumable Web Uploader
    • Overview
    • Administrative Configuration
      • Uploader Settings
      • Storage Configuration
    • Infrastructure & Permission Requirements
      • Nginx Configuration
      • Cross-Container Permission Requirements
      • Deployment Options
    • Uploader Data Flow
    • Troubleshooting
      • Upload Hangs or Resets
      • Import Not Triggered
    • Related Documentation
  • OME-Zarr Viewer
    • Installation
      • Install the package
      • Register the plugin
      • Add the Nginx locations
    • Storage path mapping
    • Apply and verify
  • Metabase Administration
    • Overview
    • Initial Security Setup
      • After First Deployment
    • Database Connection Management
      • Adding Database Connections
      • Testing Connections
      • Database Connection Encryption
    • Dashboard Management
      • Standard Dashboards
      • Embedding Configuration
      • Editing Dashboards
    • User Account Management
      • Admin Account
      • Additional Users
    • Backup and Migration
      • Database File Management
      • Upgrading Dashboards
    • Environment Configuration
      • Docker Compose Setup
      • Integration with OMERO.web
    • Security Considerations
      • Network Access
      • Data Protection
    • Troubleshooting
      • Common Issues
      • Performance Issues
    • Related Documentation
  • UI Customization
    • Login Page Branding
  • Backup and Restore
    • NL-BIOMERO Backup & Restore Scripts
      • Key Features
      • Quick Start
        • Master Backup (Recommended)
        • Common Options
        • Typical Backup Workflow
        • Typical Restore Workflow
      • Individual Script Usage
        • Database Backup
        • Server Backup
        • Metabase Backup
      • Restore Scripts
      • OMERO Configuration Hierarchy
      • Example: Backup OMERO from Host Folder
      • Example: Backup Metabase from Host Folder
      • Requirements
      • Troubleshooting
      • Help
  • Workflow Metadata Refresh
    • Before starting
    • Options
    • Progress and results
    • Backups and incomplete updates

Developer Guide

  • Architecture Overview
    • System Architecture Diagram
    • Core Components
      • BIOMERO 2.0 Architecture Overview
    • Container Architecture
      • Core Infrastructure
      • BIOMERO Services
    • Data Flow Architecture
      • In-Place Import Pipeline
      • Analysis Pipeline
    • Network Architecture
      • Internal Communication
      • External Access Points
    • Storage Architecture
      • Persistent Storage
      • Remote Storage Integration
    • Compute Integration
      • Demo/Development Environment
      • HPC Integration (Production)
    • Security Architecture
      • Authentication & Authorization
      • Data Protection
    • Monitoring & Analytics
      • Workflow Monitoring
      • Data Analytics
    • Extensibility & Integration
      • Workflow Development
      • API Integration
    • Deployment Scenarios
    • Next Steps
  • Detached Workflow Supervisor
    • Components and responsibilities
    • Worker identity and OMERO access
    • Discovery and concurrency
    • Claim and recovery semantics
    • Startup, shutdown, and failures
    • Deployment compatibility
    • Metadata maintenance
    • Diagnostics
    • See also
  • Developer Getting Started
    • Quick Setup for Development
    • Development Features
    • Architecture Overview
    • Deployment Documentation
  • Adding Your Workflow to BIOMERO
    • Overview
    • Getting Started
      • Core Documentation
    • Workflow Types & Tutorials
      • CellProfiler Workflows
      • Python Workflows
    • FAIR Workflow Packaging
      • Workshop Materials
      • Real-World Example: Stardist Workflow
    • Additional Resources
      • BIAFLOWS Integration
      • Multiple Descriptors / Multiple UIs per Repository
      • Zarr Workflow Types (BIOMERO ≥ 2.4.0)
    • Development Workflow
    • Next Steps
    • Community Support
  • Bilayers Workflows in BIOMERO
    • Why Bilayers?
    • How BIOMERO Reads a Bilayers Descriptor
    • I/O Directory Handling
    • Parameter Choices (radio / dropdown)
    • Minimal Working Example
    • Adding a Bilayers Workflow to Your BIOMERO Instance
      • Pointing to a Specific Descriptor File
    • Bilayers Features Not Supported by BIOMERO
  • Developing OME-Zarr workflows
    • The workflow boundary
    • Returning results
    • Current compatibility
  • Working with shallow OME-Zarr results
    • What is stored?
    • What you see in OMERO
    • How BIOMERO checks that pixels are unchanged
    • Using results in another workflow
    • Exporting a standalone Zarr
    • Local, remote and detached processing
  • Container Development
    • OMERO Server Container
      • Overview
      • Key Customizations
        • Script Installation
        • Automated Configuration Restoration
      • Dockerfile Key Changes
      • Development Guidelines
        • Configuration Changes
        • Adding New Scripts
        • Testing Changes
      • Related Documentation
    • OMERO Web Container
      • Overview
      • Development Workflow
        • Development Mode
        • OMERO.biomero Plugin Development
      • Key Installed Plugins
        • Core OMERO Plugins
        • Supporting Libraries
      • Custom Interface Modifications
      • Dockerfile Key Sections
      • Development Guidelines
        • Starting Development
        • Making Changes
        • Customizing Login Page with Volume Mounts
        • Testing
      • Related Documentation
    • BIOMERO Worker Container
      • Overview
      • Key Features
      • Container Customizations
        • SSH Integration
        • Database Integration
        • Data Export Pipeline
        • BIOMERO Library Integration
        • Custom Processor Implementation
        • Detached Workflow Execution
      • Configuration Management
        • Slurm Configuration
        • Analytics Configuration
      • Worker Startup Process
        • Configuration Generation
      • Development Guidelines
        • BIOMERO Script Development
        • SSH Key Management
        • Configuration Testing
        • Eventsourcing
      • Troubleshooting
        • Common Issues
        • Performance Optimization
      • Upgrade Considerations
        • BIOMERO Library Updates
        • Processor.py Maintenance
      • 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
        • Access
        • Dashboards in use
        • Embedding in OMERO.web
        • Editing dashboards
        • Adding a new dashboard
        • Browse attached databases
        • Managing database connections
        • User account and password
        • Versioning and migration
        • Upgrading Metabase Dashboards
      • Troubleshooting
        • Common Issues and Solutions
      • 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
    • Analyzer → Importer Integration
      • Overview
      • How it works
        • Script selection
        • Permanent storage layout
        • Group base path resolution
        • Permission requirements
        • Upload order and in-place import
        • Progress tracking
      • Infrastructure requirements
        • Shared storage mount
        • Environment variables for biomeroworker
        • Volume mounts for biomeroworker
      • Docker Compose changes
      • Non-Docker deployments
      • Troubleshooting
        • Results end up on OMERO server storage instead of remote storage
        • Upload order created but import never completes
        • Files not found at expected path
        • PermissionError writing to .analyzed folder
        • Import polling times out
      • Related documentation
    • Container Releases
      • Release Overview
      • Release Workflow
        • Container Build Automation
        • Typical Release Process
      • Versioning Guidelines
        • Semantic Versioning
        • Pre-release Versions
        • Release Examples
      • Dependency Management
        • Library Updates
        • Example Dependency Update
      • OMERO ADI Submodule
        • Special Handling
      • Docker Hub Management
        • Container Registry
        • Repository Management
      • Communication & Announcements
        • Release Communication
        • Release Notes Template
      • Troubleshooting Releases
        • Common Issues
        • Emergency Releases
      • Best Practices
        • Release Checklist
        • Release Quality
      • Related Documentation

User Guide

  • Getting Started
    • Before You Start
    • Interface at a Glance
    • How Do I Add Data Already on Remote Storage?
    • How Do I Add Data Directly from the Web?
    • How Do I Run a Workflow on My Images?
    • How Do I Get a New Workflow into BIOMERO?
    • Frequently Asked Questions
      • I cannot find my folder on the remote disk
      • The Upload Images tab is missing
      • The workflow I need is missing
      • My import or workflow is not progressing
      • Where are my workflow results?
NL-BIOMERO
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  • NL-BioImaging/NL-BIOMERO

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