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†’

Zarr Workflow Types (BIOMERO β‰₯ 2.4.0)

From BIOMERO v2.4.0 / NL-BIOMERO v1.5.0 onward, workflows can be configured to receive Zarr input instead of the default flat folder of TIFF images. This is set by a system administrator in the Analyzer Admin UI β€” it is not part of the workflow descriptor itself.

Two modes exist:

Zarr Workflow

The workflow receives a single Zarr file exported from OMERO. BIOMERO skips the TIFF conversion step and passes the Zarr directly to the SLURM job.

Zarr Plate Workflow

The workflow receives an entire plate packaged as a single Zarr, preserving well and acquisition structure. Only plates can be submitted as input. These workflows appear under the dedicated Plate Workflows tab in the analyzer UI.

Important

Standard BIAFLOWS workflows β€” which read a flat folder of TIFF images β€” are not compatible with either Zarr mode. A workflow must be specifically written to read Zarr input (or Zarr plate structure) in order to work with these options.

For the full explanation of how this interacts with the BIAFLOWS descriptor format, why auto-detection is not currently possible, and plans for CWL-based descriptor support, see BIAFLOWS descriptors and Zarr auto-detection in OMERO.biomero Plugin Administration.

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.