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:

πŸ“š Main BIOMERO Workflow Guide

Comprehensive guide for adding custom workflows to BIOMERO

πŸ“– Read the Guide β†’

Workflow Types & Tutorials

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

CellProfiler Workflows

🧬 CellProfiler Integration

Learn how to package CellProfiler pipelines for BIOMERO deployment

πŸ“– CellProfiler Tutorial β†’

Python Workflows

🐍 Python Script Integration

Package custom Python scripts as BIOMERO workflows, featuring CellExpansion example (simple mask expansion script similar to watershed)

πŸ“– Python Tutorial β†’

FAIR Workflow Packaging

Workshop Materials

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

πŸŽ“ ELMI 2025 Workshop: Adding Workflow Containers to BIOMERO

Complete workshop materials covering the creation of FAIR workflow containers, featuring the modern Stardist workflow example

Real-World Example: Stardist Workflow

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

🌟 W_NucleiSegmentation-Stardist5d Example

Modern Stardist-based nuclei segmentation workflow, demonstrating best practices for FAIR workflow packaging

πŸ” View Repository β†’

Additional Resources

BIAFLOWS Integration

For workflows that are part of the BIAFLOWS ecosystem:

πŸ”— BIAFLOWS Documentation

Comprehensive documentation for BIAFLOWS workflow development and integration

πŸ“š BIAFLOWS Docs β†’

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:

πŸ’¬ Community Forum

Join discussions, ask questions, and share your experiences with the bioimage analysis community

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.