Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices
Abstract
Image analysis in the life sciences is constrained by fragmented software ecosystems, heterogeneous data formats, and limited reproducibility. These barriers hinder the reuse of image analysis methods and the sustainability of tools. In this article, we describe how the Galaxy platform enables FAIR (Findable, Accessible, Interoperable, and Reusable) image analysis by providing an integrated environment for data access, workflow execution, provenance tracing, and training. We present Galaxy as a computational workbench that supports diverse image formats and integrates with public, institutional, and private repositories. We describe a reference structure for FAIR image analysis workflows and illustrate how this pattern supports reproducibility, interoperability, and reuse. We also describe community-driven training and sustainability practices that embed FAIR principles directly into executable tutorials and shared workflows. Together, these foundations position Galaxy as a reproducible, scalable, and community-maintained platform for FAIR image analysis across the life sciences and beyond.
Authors 26
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Affiliation as printed
Biomedical Computer Vision Group Heidelberg University, BioQuant, IPMB Heidelberg Germany
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Helmholtz Centre for Environmental Research · German Centre for Integrative Biodiversity Research
Affiliation as printed
Department of Monitoring and Environmental Technology (Research Data Management Team) Helmholtz Centre for Environmental Research GmbH (UFZ) Leipzig Germany
Department of Physiological Diversity, Working Group Imaging Flow Cytometry German Centre for Integrative Biodiversity Research Halle‐Jena‐Leipzig (iDiv) Leipzig Germany
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Affiliation as printed
Bioinformatics Group, Department of Computer Science University of Freiburg Freiburg Germany
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Affiliation as printed
Biomedical Computer Vision Group Heidelberg University, BioQuant, IPMB Heidelberg Germany
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Affiliation as printed
College of Life Sciences University of Dundee Dundee Scotland UK
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Affiliation as printed
Bioinformatics Group, Department of Computer Science University of Freiburg Freiburg Germany
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European Molecular Biology Laboratory
Affiliation as printed
Data Science Centre European Molecular Biology Laboratory (EMBL) Heidelberg Heidelberg Germany
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Heidelberg University · Medizinische Fakultät Mannheim
Affiliation as printed
Biomedical Computer Vision Group Heidelberg University, BioQuant, IPMB Heidelberg Germany
Core Facility Platform Mannheim, Medical Faculty Mannheim Heidelberg University Mannheim Germany
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Affiliation as printed
Division of Cell Systems and Drug Safety (CDS), Leiden Academic Centre for Drug Research (LACDR) Leiden Universiteit Leiden The Netherlands
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Affiliation as printed
Bioinformatics Group, Department of Computer Science University of Freiburg Freiburg Germany
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Oregon Health & Science University · OHSU Knight Cancer Institute
Affiliation as printed
Department of Biomedical Engineering and Knight Cancer Institute Oregon Health & Science University Portland Oregon USA
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MRC Laboratory of Molecular Biology · University of Cambridge · Donostia International Physics Center
Affiliation as printed
Department of Physiology, Development and Neuroscience University of Cambridge Cambridge England UK
Donostia International Physics Center San Sebastián Spain
Neurobiology division MRC Laboratory of Molecular Biology Cambridge England UK
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Affiliation as printed
Bioinformatics Group, Department of Computer Science University of Freiburg Freiburg Germany
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Centre National de la Recherche Scientifique · Inserm · Université Clermont Auvergne · Commissariat à l'Énergie Atomique et aux Énergies Alternatives · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Institut Français de Bioinformatique
Affiliation as printed
AuBi Platform Université Clermont Auvergne Clermont‐Ferrand France
IFB‐core Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA Villejuif France
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Affiliation as printed
Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology University of Isfahan Isfahan Iran
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VSB - Technical University of Ostrava
Affiliation as printed
IT4Innovations, VSB – Technical University of Ostrava Ostrava Czech Republic
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Affiliation as printed
Faculty of Health and Social Care University of Bradford Bradfort England UK
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Affiliation as printed
Faculty of Health and Social Care University of Bradford Bradfort England UK
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Affiliation as printed
ISCC Foundation Hengelo The Netherlands
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Universidad Carlos III de Madrid
Affiliation as printed
Neuroscience and Life Sciences Department Universidad Carlos III de Madrid Madrid Spain
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Affiliation as printed
Division of Cell Systems and Drug Safety (CDS), Leiden Academic Centre for Drug Research (LACDR) Leiden Universiteit Leiden The Netherlands
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German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse
Affiliation as printed
RSE Unit German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse e.V. (GerBI‐GMB) Konstanz Germany
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Affiliation as printed
Department of Machine Learning Moffitt Cancer Center Tampa Florida USA
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Affiliation as printed
Bioinformatics Group, Department of Computer Science University of Freiburg Freiburg Germany
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Affiliation as printed
Biomedical Computer Vision Group Heidelberg University, BioQuant, IPMB Heidelberg Germany
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European Molecular Biology Laboratory
Affiliation as printed
Euro‐BioImaging ERIC Bio‐Hub European Molecular Biology Laboratory (EMBL) Heidelberg Heidelberg Germany
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