BioHackathon Europe 2025 - Project 9

_{CC BY 4.0 📸 Leonid Kostrykin}

Evolving FAIR Image Analysis in Galaxy for Cross-domain & AI-ready Applications

At this year’s BioHackathon Europe, Project 9 brought together a multidisciplinary, cross-RI team to advance FAIR image analysis in Galaxy, focusing on interoperability, reusability, and AI‑readiness. The project connected members of Euro‑BioImaging, ELIXIR, and beyond.

Why this project?

Image analysis is still fragmented between domains, infrastructures, repositories, and tools. Our goal? Simple but ambitious:
Make image analysis more interoperable, reusable, and scalable in Galaxy, while staying FAIR from data to results.

What we achieved

Concrete results from the hackathon:

• BioImage Archive → Galaxy integration
  • Added BioStudies upload support
  • Improved BIA retrieval tooling
• International Standard Content Code (ISCC) support in Galaxy
  • ISCC hash generator for generating content-based identifiers
  • Tools for hash verification and comparison (in development)
• Metadata & standards
  • Ongoing work on extended GeoJSON support
  • Roadmap towards advanced EDAM Bioimaging maturity
    • Tool and tutorial annotation
    • Domain-specific term enrichment

Together, these improvements strengthen provenance, traceability, and FAIRness across Galaxy image analysis workflows.

Work in progress (WIP)

Key efforts still evolving:

• OMERO → Galaxy integration for seamless image import
• ISCC tutorial to support adoption and good practices
• Galaxy Imaging Lab setup
• “Where to start” tutorial for new users
• Community paper
  • Authorship coordination
  • Outline and roadmap underway

➡️ Follow our progress on the project board

What’s next

We’re aiming to:

• Write a report
• Finalize and stabilize all WIPs
• Keep delivering ready-to-use workflows for image analysis in Galaxy
• Publish a community paper including tutorials and training materials
• Keep building an open, collaborative imaging community that makes image data science FAIR!

Get involved

Whether you’re into Galaxy or any kind of imaging, your input is welcome. We’re always looking for feedback, tool testers, tutorial contributors, and creative ideas.

If you’re passionate about open science and FAIR imaging, join us, we’re building this together.

Communication Channels

Join our Matrix channel for live discussions and updates.

Community Meetings

We meet monthly via the Euro-BioImaging Expert Group on “FAIR Image Data Workflows”.

• When: 3rd Wednesday of each month at 16:00 CET
• Duration: ~1 hour
• Agenda: Community updates, short talks, planning for grants/papers/events
• Meeting notes & open agenda

In-person Meetings

We’re active in conferences and hackathons—including the BioHackathons 2023 and 2024—where we shared new developments and collaborative outputs, like this preprint and community poster.

🙌 Meet the dream team of Project 9 @ BioHackathon Europe 2025

🎉 Hats off to Leonid Kostrykin, Diana Chiang Jurado, Beatriz Serrano‑Solano, Pavan Videm, David Lopez, Maarten Paul, and Martin Etzrodt!