Welcome to the Image Analysis Community in Galaxy!

Image analysis bridges multiple disciplines, and this community gathers researchers and developers from diverse scientific fields to share knowledge, tools, and workflows.

Community goals

Our primary goals are to:

• Coordinate efforts across the Galaxy ecosystem to reduce redundancy in tools, workflows, and training.
• Share our work — from within and outside Galaxy—to showcase our advancements.
• Support each other through knowledge-sharing, troubleshooting, and collaboration.

Additionally, we strive to:

• Develop and maintain image analysis tools within Galaxy.
• Implement FAIR principles to make workflows reproducible and reusable.
• Expand documentation and training resources for accessible learning and skill-building.

Who we are

We are a diverse group of users, developers, trainers, and image data enthusiasts, collaborating to expand Galaxy’s image analysis capabilities, bringing the latest tools, feedback, and beyond.

• Developers: Are you building image analysis tools in Galaxy, or thinking of starting a project here? Do you need users, testers, or just want to make sure you’re not duplicating tools that already exist? Join us to connect, share ideas, and get support for your development journey!

• Users: Do you use Galaxy’s image analysis tools for bioimaging, Earth observation, or other fields? Have feedback for us, or interested in testing new resources? Perhaps you have ideas or requests for new tools — your input can help shape future developments!

• Trainers: Are you using Galaxy to train others in image analysis? If you have suggestions or specific needs to better support your trainees, we'd love to hear from you. Your insights are invaluable in helping us create better learning experiences and share data image analysis knowledge.

Getting started: GTN tutorials

To dive into Galaxy, the Galaxy Training Network (GTN) offers a wealth of tutorials for beginners and experts alike. These tutorials cover basic and advanced workflows, guiding you through analyses step-by-step. They also include a curated selection of workflows to help you gain hands-on experience in Galaxy.

What is available?

Image analysis tools

The Galaxy ToolShed offers a variety of tools for image data analysis, freely available for installation on any Galaxy server. Our community maintains a curated list of available tools to keep users informed and up-to-date.

Are we missing some tools? Reach out to us to keep the list comprehensive.

Interactive tools

Image analysis often involves hands-on interaction, and Galaxy offers resources that make this possible. Check out our interactive tools to experience Galaxy's potential beyond traditional workflows.

Visualizations

The zarr format is becoming a standard for storing large image data. With various adaptations like OME-Zarr and GEOZarr, this interoperable format enhances data reusability across disciplines. Our community supports zarr-based visualization through tools like vizarr, helping bring this dream of cross-discipline interoperability to life.

A dedicated Galaxy interface

Our dedicated interface for image data analysis—imaging.usegalaxy.eu—provides a comprehensive suite of tools and workflows tailored specifically for imaging scientists.

How to get involved?

If you're interested in image analysis (within or outside Galaxy) and want to help ensure our tools represent the best, up-to-date practices, your feedback is needed! We’re constantly looking for ways to improve, whether in scientific fields already supported by Galaxy or in exploring new applications.

If you're passionate about shaping the future of image analysis in Galaxy and want to help build a strong, collaborative, and supportive community, you're in the right place!

Communication channels

Our community connects via our dedicated Matrix channel.

Online community meetings

We organize regular meetups as part of the Euro-BioImaging Expert Group "FAIR Image Data Workflows," chaired by Anne Fouilloux and Beatriz Serrano-Solano.

• Frequency: Monthly
• Duration: 1 hour
• Time: 3rd Wednesday of the month at 4 pm CET
• Meeting Agenda: Updates from the community (e.g., upcoming events), relevant talks or case studies, and coordination for activities such as grant writing, paper development, and event planning. View our open agenda and notes here.

In-person meetings and conferences

In-person meetups are also part of our community engagement. We recently participated in BioHackathon 2023 and 2024, where we collaborated on new projects and shared preprints.

Poster available in Zenodo.

Community calendar

Acknowledgments

Our community's success is made possible through partnerships and collaborations. We thank our partners for their support.

Partner projects

Community members actively pursue funding opportunities and contribute to various projects, such as: