.. NL-BIOMERO documentation master file

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

**NL-BIOMERO** is a containerized deployment of OMERO with BIOMERO for bioimage analysis workflows, 
featuring automated data import, workflow management, and enhanced web interfaces.

This platform provides a complete solution for bioimage data management and analysis, combining:

* **OMERO** - Image data management platform
* **BIOMERO** - BioImage analysis workflows with Slurm integration
* **OMERO.biomero** - Modern web interfaces for data import and analysis
* **OMERO.forms** - Flexible form-based interfaces for metadata annotation
* **Metabase** - Analytics and visualization dashboards
* **Docker Compose** - Easy deployment and scaling scenarios

.. 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.

Getting Started
===============

Choose your deployment scenario:

* **New Installation**: Start with :doc:`sysadmin/deployment` for fresh deployments
* **Existing OMERO**: See :doc:`sysadmin/hybrid-deployment` for integration options  
* **Development**: Use :doc:`developer/contributing` for local development setup

.. toctree::
   :caption: System Administration
   :maxdepth: 3

   sysadmin/index

.. toctree::
   :caption: Developer Guide  
   :maxdepth: 3

   developer/index

.. toctree::
   :caption: User Guide
   :maxdepth: 3

   user/index

Quick Links
===========

* :doc:`sysadmin/deployment` - Deployment scenarios and setup
* :doc:`sysadmin/backup-restore` - Backup and restore procedures
* :doc:`user/getting-started` - First steps with NL-BIOMERO
* :doc:`developer/architecture` - Technical architecture overview

.. note::
   This documentation covers containerized deployment scenarios. For non-containerized 
   installations, refer to the individual component documentation.

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`