Adding Your Workflow to BIOMERO
==================================

This guide is for **image analysts and workflow developers** who want to make their image analysis workflows available through the BIOMERO platform. Whether you're developing CellProfiler pipelines, Python-based analysis scripts, or other computational workflows, BIOMERO provides a standardized framework for packaging and deploying your work.

Overview
--------

BIOMERO enables you to:

* Package your analysis workflows as containerized, FAIR-compliant tools
* Make workflows discoverable and executable through OMERO.web
* Ensure reproducible analysis with proper provenance tracking
* Share workflows with the broader research community
* Run workflows on high-performance computing infrastructure via Slurm

Getting Started
---------------

Core Documentation
~~~~~~~~~~~~~~~~~~

The primary resource for workflow development is the **BIOMERO documentation**:

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   <h4 style="margin: 0 0 10px 0; color: #0066cc;">📚 Main BIOMERO Workflow Guide</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Comprehensive guide for adding custom workflows to BIOMERO</p>
   <a href="https://nl-bioimaging.github.io/biomero/readme_link.html#how-to-add-your-new-custom-workflow" target="_blank" style="background: #007bff; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📖 Read the Guide →</a>
   </div>

Workflow Types & Tutorials
---------------------------

BIOMERO supports various types of workflows. Here are specific tutorials for popular tools:

CellProfiler Workflows
~~~~~~~~~~~~~~~~~~~~~~

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   <h4 style="margin: 0 0 10px 0; color: #495057;">🧬 CellProfiler Integration</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Learn how to package CellProfiler pipelines for BIOMERO deployment</p>
   <a href="https://nl-bioimaging.github.io/biomero/tutorial_link.html#cellprofiler-tutorial" target="_blank" style="background: #6c757d; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📖 CellProfiler Tutorial →</a>
   </div>

Python Workflows
~~~~~~~~~~~~~~~~

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   <h4 style="margin: 0 0 10px 0; color: #495057;">🐍 Python Script Integration</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Package custom Python scripts as BIOMERO workflows, featuring CellExpansion example (simple mask expansion script similar to watershed)</p>
   <a href="https://nl-bioimaging.github.io/biomero/tutorial_link.html#cellexpansion-tutorial" target="_blank" style="background: #6c757d; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📖 Python Tutorial →</a>
   </div>

FAIR Workflow Packaging
------------------------

Workshop Materials
~~~~~~~~~~~~~~~~~~

**ELMI 2025 BIOMERO Workshop** provides hands-on guidance for creating workflow containers:

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   <div style="background: #fff3e0; border: 1px solid #ffcc80; padding: 20px; border-radius: 8px; margin: 20px 0;">
   <h4 style="margin: 0 0 10px 0; color: #e65100;">🎓 ELMI 2025 Workshop: Adding Workflow Containers to BIOMERO</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Complete workshop materials covering the creation of FAIR workflow containers, featuring the modern Stardist workflow example</p>
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   <a href="https://doi.org/10.5281/zenodo.15642506" target="_blank" style="background: #ff9800; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📦 Full Workshop Materials</a>
   <a href="https://zenodo.org/records/15642507/files/250604_ELMI_BIOMERO_workshop_SetupWorkflow.pdf?download=1" target="_blank" style="background: #f57c00; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📄 Setup Guide PDF</a>
   </div>
   </div>

Real-World Example: Stardist Workflow
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The workshop demonstrates the creation of a modern, FAIRly-packaged workflow container:

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   <h4 style="margin: 0 0 10px 0; color: #2e7d32;">🌟 W_NucleiSegmentation-Stardist5d Example</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Modern Stardist-based nuclei segmentation workflow, demonstrating best practices for FAIR workflow packaging</p>
   <a href="https://github.com/maartenpaul/W_NucleiSegmentation-Stardist5d" target="_blank" style="background: #4caf50; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">🔍 View Repository →</a>
   </div>

Additional Resources
--------------------

BIAFLOWS Integration
~~~~~~~~~~~~~~~~~~~~

For workflows that are part of the BIAFLOWS ecosystem:

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   <h4 style="margin: 0 0 10px 0; color: #7b1fa2;">🔗 BIAFLOWS Documentation</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Comprehensive documentation for BIAFLOWS workflow development and integration</p>
   <a href="http://biaflows-doc.neubias.org/" target="_blank" style="background: #9c27b0; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">📚 BIAFLOWS Docs →</a>
   </div>

Development Workflow
--------------------

Typical workflow development process:

1. **Design Your Workflow**
   
   * Define input/output specifications
   * Identify computational requirements
   * Plan parameter configurations

2. **Container Development**
   
   * Follow the ELMI workshop guide for containerization
   * Implement FAIR principles in your packaging
   * Test locally before deployment

3. **BIOMERO Integration**
   
   * Follow the main BIOMERO workflow guide
   * Ensure compatibility with OMERO data structures
   * Test integration with BIOMERO.analyzer

4. **Deployment & Sharing**
   
   * Deploy to your BIOMERO instance
   * Share with the community through appropriate channels
   * Document usage and cite appropriately

.. note::
   **Coming Soon:** A comprehensive new document detailing workflow development best practices is in development. Watch this space for updates!

Next Steps
----------

* **Start with the tutorials** above that match your workflow type
* **Review the ELMI workshop materials** for hands-on examples
* **Examine the Stardist example** for modern best practices
* **Consult the BIOMERO documentation** for technical details
* **Engage with the community** for support and collaboration

Community Support
-----------------

Get help and connect with the BIOMERO community:

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   <h4 style="margin: 0 0 10px 0; color: #0066cc;">💬 Community Forum</h4>
   <p style="margin: 0 0 15px 0; font-size: 14px;">Join discussions, ask questions, and share your experiences with the bioimage analysis community</p>
   <div style="display: flex; gap: 10px; flex-wrap: wrap;">
   <a href="https://forum.image.sc/tag/biomero" target="_blank" style="background: #007bff; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">#biomero</a>
   <a href="https://forum.image.sc/tag/biaflows" target="_blank" style="background: #6f42c1; color: white; padding: 8px 16px; text-decoration: none; border-radius: 4px; font-weight: bold;">#biaflows</a>
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.. tip::
   Consider starting with a simple workflow to understand the process before tackling more complex analysis pipelines. The community is available to help guide you through the development process.