.. NL-BIOMERO documentation master file

Welcome to NL-BIOMERO's documentation!
======================================

|biomero_badge| |biomero_importer_badge| |omero_biomero_badge| |omero_forms_badge|

**NL-BIOMERO** delivers a complete FAIR-oriented bioimaging infrastructure built on OMERO and BIOMERO 2.0.

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   <h4 style="margin: 0 0 10px 0; color: #007bff;">🔬 What is BIOMERO 2.0?</h4>
   <p style="margin: 0; font-size: 14px;">An end-to-end platform that transforms OMERO into a provenance-aware system for bioimage data import, analysis, and sharing. <a href="https://arxiv.org/abs/2511.13611" target="_blank">📄 Read our preprint</a></p>
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   <h4 style="margin: 0 0 10px 0; color: #28a745;">🚀 Why use NL-BIOMERO?</h4>
   <p style="margin: 0; font-size: 14px;">Get a unified environment where raw data flows seamlessly through automated import, preprocessing, analysis workflows, and results—all with complete provenance tracking and FAIR compliance.</p>
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   <h4 style="margin: 0 0 10px 0; color: #6366f1;">🎥 Introduction Video</h4>
   <p style="margin: 0; font-size: 14px;">New to BIOMERO? Watch our overview explaining FAIR challenges, OMERO data management, and how BIOMERO transforms your workflow. <a href="overview.html">Watch Now →</a></p>
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🚀 **Get Started Now!**
========================

Choose your path forward:

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   <h4 style="margin: 0 0 10px 0; color: #0066cc;">🆕 New Installation</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Fresh deployment on your infrastructure</p>
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   <a href="sysadmin/development-setup.html" style="background: #28a745; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📒 Dev/Demo Setup →</a>
   <a href="sysadmin/deployment.html#scenario-1-fresh-deployment-no-existing-data" target="_blank" style="background: #007bff; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">🚀 Production →</a>
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   <h4 style="margin: 0 0 10px 0; color: #e65100;">🔧 Existing OMERO</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Integrate with current OMERO setup</p>
   <a href="sysadmin/deployment.html#scenario-3-hybrid-deployment-with-existing-omero-server" target="_blank" style="background: #ff9800; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">Integration Guide →</a>
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   <h4 style="margin: 0 0 10px 0; color: #7b1fa2;">⚡ Development</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Extend the platform or add your workflows</p>
   <div style="display: flex; gap: 8px; justify-content: center; flex-wrap: wrap;">
   <a href="developer/architecture.html" style="background: #673ab7; color: white; padding: 6px 12px; text-decoration: none; border-radius: 4px; font-weight: bold; font-size: 12px;">🏗️ Architecture</a>
   <a href="developer/getting-started.html" target="_blank" style="background: #9c27b0; color: white; padding: 6px 12px; text-decoration: none; border-radius: 4px; font-weight: bold; font-size: 12px;">Dev Setup</a>
   <a href="developer/workflow-development.html" target="_blank" style="background: #4caf50; color: white; padding: 6px 12px; text-decoration: none; border-radius: 4px; font-weight: bold; font-size: 12px;">Add Workflows</a>
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   <h4 style="margin: 0 0 10px 0; color: #424242;">📚 Browse Components</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Explore individual platform components</p>
   <a href="#core-platform-components" style="background: #616161; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">Continue Reading ↓</a>
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Core Platform Components
=========================

This documentation serves as your **main gateway** to the BIOMERO 2.0 ecosystem. Each component below links to both external documentation and local integration guides:

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   <h3 style="margin: 0; font-size: 18px;">⚡ BIOMERO.analyzer</h3>
   <div style="display: flex; gap: 8px; align-items: center;">
   <a href="https://hub.docker.com/r/cellularimagingcf/biomero" target="_blank" style="background: rgba(255,255,255,0.2); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/NL-BioImaging/biomero" target="_blank" style="background: rgba(0,0,0,0.3); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(255,255,255,0.2); padding: 4px 8px; border-radius: 15px; font-size: 11px;">Apache-2.0</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px; opacity: 0.9;">Remote high-performance computing workflow management for FAIR image analysis</p>
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   <a href="https://nl-bioimaging.github.io/biomero/" target="_blank" style="background: #007bff; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(0,123,255,0.3);">📚 Documentation</a>
   <a href="https://github.com/NL-BioImaging/biomero?tab=readme-ov-file#readme" target="_blank" style="background: #6c757d; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(108,117,125,0.3);">📖 README</a>
   <a href="developer/workflow-development.html" target="_blank" style="background: #17a2b8; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(23,162,184,0.3);">👨‍💻 Dev Guide</a>
   <a href="sysadmin/slurm-integration.html" target="_blank" style="background: #28a745; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: bold; box-shadow: 0 2px 6px rgba(40,167,69,0.4);">⚙️ Admin Guide</a>
   <a href="sysadmin/analyzer-importer-admin.html" target="_blank" style="background: #6f42c1; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: bold; box-shadow: 0 2px 6px rgba(111,66,193,0.4);">🔗 Analyzer+Importer</a>
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   <h3 style="margin: 0; font-size: 18px;">🛠️ BIOMERO.scripts</h3>
   <div style="display: flex; gap: 8px; align-items: center;">
   <a href="https://hub.docker.com/r/cellularimagingcf/omeroserver" target="_blank" style="background: rgba(255,255,255,0.2); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/NL-BioImaging/biomero-scripts" target="_blank" style="background: rgba(0,0,0,0.3); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(255,255,255,0.2); padding: 4px 8px; border-radius: 15px; font-size: 11px;">GPL-2.0</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px; opacity: 0.9;">Run BIOMERO.analyzer directly from OMERO.web via these BIOMERO.scripts</p>
   <div style="display: flex; gap: 8px; flex-wrap: wrap;">
   <a href="https://github.com/NL-BioImaging/biomero-scripts?tab=readme-ov-file#readme" target="_blank" style="background: #6c757d; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(108,117,125,0.3);">📖 README</a>
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   <h3 style="margin: 0; font-size: 18px;">📥 BIOMERO.importer</h3>
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   <a href="https://hub.docker.com/r/cellularimagingcf/biomero-importer" target="_blank" style="background: rgba(255,255,255,0.2); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/NL-BioImaging/BIOMERO.importer" target="_blank" style="background: rgba(0,0,0,0.3); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
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   <p style="margin: 0 0 15px 0; font-size: 14px; opacity: 0.9;">User-friendly data import workflows for in-place importing - keep your raw data where it belongs!</p>
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   <a href="https://github.com/NL-BioImaging/BIOMERO.importer?tab=readme-ov-file#readme" target="_blank" style="background: #6c757d; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(108,117,125,0.3);">📖 README</a>
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   <h3 style="margin: 0; font-size: 18px;">📝 OMERO.forms</h3>
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   <a href="https://hub.docker.com/r/cellularimagingcf/omeroweb" target="_blank" style="background: rgba(255,255,255,0.2); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/NL-BioImaging/OMERO.forms" target="_blank" style="background: rgba(0,0,0,0.3); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(255,255,255,0.2); padding: 4px 8px; border-radius: 15px; font-size: 11px;">AGPL-3.0</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px; opacity: 0.9;">Flexible metadata annotation interfaces</p>
   <div style="display: flex; gap: 8px; flex-wrap: wrap;">
   <a href="https://github.com/NL-BioImaging/OMERO.forms?tab=readme-ov-file#readme" target="_blank" style="background: #6c757d; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(108,117,125,0.3);">📖 README</a>
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   <a href="https://hub.docker.com/r/cellularimagingcf/omeroweb" target="_blank" style="background: rgba(0,0,0,0.1); color: #333; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/NL-BioImaging/OMERO.biomero" target="_blank" style="background: rgba(0,0,0,0.2); color: #333; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(0,0,0,0.1); padding: 4px 8px; border-radius: 15px; font-size: 11px;">AGPL-3.0</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px;">Modern web interfaces for BIOMERO.importer and BIOMERO.analyzer</p>
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   <a href="https://github.com/NL-BioImaging/OMERO.biomero?tab=readme-ov-file#readme" target="_blank" style="background: #6c757d; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(108,117,125,0.3);">📖 README</a>
   <a href="sysadmin/omero-biomero-admin.html" target="_blank" style="background: #28a745; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: bold; box-shadow: 0 2px 6px rgba(40,167,69,0.4);">⚙️ Admin Guide</a>
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   <h3 style="margin: 0; font-size: 18px;">📊 Metabase</h3>
   <div style="display: flex; gap: 8px; align-items: center;">
   <a href="https://hub.docker.com/r/metabase/metabase" target="_blank" style="background: rgba(0,0,0,0.1); color: #333; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/metabase/metabase" target="_blank" style="background: rgba(0,0,0,0.2); color: #333; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(0,0,0,0.1); padding: 4px 8px; border-radius: 15px; font-size: 11px;" title="AGPL-3.0 + Embedding License">Dual License</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px;">Analytics and visualization dashboards for live progress tracking</p>
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   <a href="https://www.metabase.com/docs/" target="_blank" style="background: #007bff; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(0,123,255,0.3);">📚 Documentation</a>
   <a href="https://www.metabase.com/license/" target="_blank" style="background: #ffc107; color: #212529; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(255,193,7,0.3);">📄 Licensing</a>
   <a href="sysadmin/metabase-admin.html" target="_blank" style="background: #28a745; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: bold; box-shadow: 0 2px 6px rgba(40,167,69,0.4);">⚙️ Admin Guide</a>
   <a href="developer/containers/metabase.html" target="_blank" style="background: #17a2b8; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(23,162,184,0.3);">👨‍💻 Dev Guide</a>
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   <span style="background: white; padding: 0 20px; color: #8b5cf6; font-weight: 600; font-size: 14px; text-transform: uppercase; letter-spacing: 1px;">Infrastructure</span>
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   <h3 style="margin: 0; font-size: 18px;">🔬 OMERO</h3>
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   <a href="https://hub.docker.com/r/cellularimagingcf/omeroserver" target="_blank" style="background: rgba(0,0,0,0.1); color: #333; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/ome/openmicroscopy" target="_blank" style="background: rgba(0,0,0,0.2); color: #333; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(0,0,0,0.1); padding: 4px 8px; border-radius: 15px; font-size: 11px;">GPL-2.0</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px;">Renowned image data management platform for microscopy data</p>
   <div style="display: flex; gap: 8px; flex-wrap: wrap;">
   <a href="https://omero.readthedocs.io/" target="_blank" style="background: #007bff; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(0,123,255,0.3);">📚 Documentation</a>
   <a href="sysadmin/deployment.html" target="_blank" style="background: #28a745; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: bold; box-shadow: 0 2px 6px rgba(40,167,69,0.4);">⚙️ Setup Guide</a>
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   <div style="background: linear-gradient(135deg, #89f7fe 0%, #66a6ff 100%); color: white; padding: 25px; border-radius: 12px; position: relative; box-shadow: 0 4px 15px rgba(0,0,0,0.1);">
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   <h3 style="margin: 0; font-size: 18px;">🐳 Docker</h3>
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   <a href="https://hub.docker.com/u/cellularimagingcf" target="_blank" style="background: rgba(255,255,255,0.2); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🐳 DockerHub</a>
   <a href="https://github.com/moby/moby" target="_blank" style="background: rgba(0,0,0,0.3); color: white; padding: 4px 8px; text-decoration: none; border-radius: 4px; font-size: 11px;">🔍 Repository</a>
   <div style="background: rgba(255,255,255,0.2); padding: 4px 8px; border-radius: 15px; font-size: 11px;" title="Apache-2.0 (CE/Engine) + Commercial (Desktop for enterprise)">Mixed License</div>
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   <p style="margin: 0 0 15px 0; font-size: 14px; opacity: 0.9;">Easy deployment and scaling scenarios</p>
   <div style="display: flex; gap: 8px; flex-wrap: wrap;">
   <a href="https://docs.docker.com/compose/" target="_blank" style="background: #007bff; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(0,123,255,0.3);">📚 Documentation</a>
   <a href="https://docs.docker.com/engine/#licensing" target="_blank" style="background: #ffc107; color: #212529; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(108,117,125,0.3);">📄 Licensing</a>
   <a href="sysadmin/docker-compose-scenarios.html" target="_blank" style="background: #28a745; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: bold; box-shadow: 0 2px 6px rgba(40,167,69,0.4);">⚙️ Setup Guide</a>
   <a href="developer/containers/index.html" target="_blank" style="background: #17a2b8; color: white; padding: 6px 12px; text-decoration: none; border-radius: 6px; font-size: 12px; font-weight: 500; box-shadow: 0 2px 4px rgba(23,162,184,0.3);">📋 Our Containers</a>
   </div>
   </div>
   
   </div>

.. note::
   Deployment, migration, and backup procedures shown in this documentation are examples for inspiration. They are not prescriptive recommendations and may not address all environments. Always adapt and validate them for your organization's security, compliance, and operational requirements.

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   <div style="margin: 40px 0; padding: 20px; background: linear-gradient(135deg, #f5f7fa 0%, #c3cfe2 100%); border-radius: 8px; border-left: 4px solid #667eea; text-align: center; color: #4a5568;">
   <p style="font-size: 14px; margin: 0; opacity: 0.8;">💡 This documentation covers containerized deployment scenarios. For non-containerized installations, refer to the individual component documentation.</p>
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