New paper on how Galaxy can support FAIR bioimage analysis

A new paper published in the Journal of Microscopy brings together several years of community work around FAIR bioimage analysis in Galaxy.

“Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices” features contributions from researchers and developers across Europe and the US, including contributors from Euro-BioImaging Nodes. It provides an overview of the tools, workflows, data resources and training materials that support bioimage analysis in Galaxy.

The Euro-BioImaging FAIR Image Data Workflows Expert Group coordinated the work, bringing together complementary expertise from the bioimaging and Galaxy communities. The paper builds on a multi-year effort involving people with expertise in bioimage analysis, Galaxy development, research infrastructures, training and bioimage data management.

Bringing bioimage analysis into a FAIR workflow environment

Bioimage analysis combines image formats, metadata, software tools, computational methods and biological knowledge. While many powerful tools are available, researchers often find these resources across different platforms and repositories. This can make analyses difficult to reproduce and workflows difficult to reuse.

The paper describes how Galaxy brings these different components together in a common computational environment. Researchers can access, process and analyse image data while keeping track of the steps performed. Galaxy supports a broad range of image formats and can connect to public, institutional and private data repositories.

A central contribution of the paper is a reference structure for FAIR image analysis workflows. This approach makes analyses easier to understand, reproduce, share and adapt. It also shows how researchers can incorporate FAIR principles directly into executable workflows rather than treating them as an additional layer of documentation.

Connecting tools, workflows and community training

Making workflows FAIR is only useful if researchers can discover, understand and use them. The paper highlights the role of community resources and training alongside the technical infrastructure. 

Galaxy's imaging ecosystem connects tools and workflows with a dedicated section of training materials in the Galaxy Training Network. These resources provide researchers with practical, step-by-step guidance for image analysis.

Executable tutorials and shared workflows can also become reusable community resources. This connects training with FAIR practices and helps researchers learn reproducible approaches through practical examples.

A community effort coordinated by the Expert Group

The work grew out of discussions and activities within the Euro-BioImaging FAIR Image Data Workflows Expert Group. The group provides a forum for researchers and technical experts to coordinate work on FAIR bioimage analysis and connect activities across institutions and countries.

The paper draws on practical experience from both the Galaxy and bioimaging communities. Rather than focusing on individual tools, it looks at how tools, workflows, data resources and training can work together to support reproducible bioimage analysis.

Euro-BioImaging coordinated this work, with OSCARS-FIESTA providing partial support for the coordination activities.

Towards sustainable and reusable bioimage analysis

The paper also highlights the importance of sustainability. Reproducibility depends not only on individual software tools, but also on how researchers combine, document, maintain and teach them.

More broadly, the work shows how collaboration between research infrastructures, developers, researchers and training communities can support bioimage analysis methods that are easier to find, access, understand, reproduce and reuse.

Read the full paper: Kostrykin, L.,  Massei, R.,  Chiang, D.,  Wollmann, T.,  Burel, J.-M.,  Tabernero, D. L.,  Sun, Y.,  Gao, Q.,  Paul, M. W., Videm, P.,  Watson, C.,  Franco-Barranco, D.,  Kumar, A.,  Goué, N.,  Koopaei, R. T.,  Ulman, V.,  Jum'ah, K.,  Poterlowicz, K.,  Etzrodt, M., …  Serrano-Solano, B. (2026).  Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices. Journal of Microscopy,  1–15. https://doi.org/10.1111/jmi.70165