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Systematic analysis of immune cell motility leveraging the open intravital microscopy database Immunemap.

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Title: Systematic analysis of immune cell motility leveraging the open intravital microscopy database Immunemap.
Authors: Pizzagalli, Diego Ulisse, Carrillo-Barberà, Pau, Bansal, Himanshu, Palladino, Elisa, Ceni, Kevin, Thelen, Benedikt, Pulfer, Alain, Moscatello, Enrico, Fiamma Cabini, Raffaella, Textor, Johannes, M N Wortel, Inge, Immunemap Consortium, Hickey, Michael, Norman, Ursula, Hidalgo, Andres, Crainiciuc, Georgiana, Adrover, Jose M, Palomino-Segura, Miguel, Marangoni, Francesco, Mempel, Thorsten R
Source: EMBO Journal; Jan2026, Vol. 45 Issue 1, p334-348, 15p
Subject Terms: CELL motility, CELL imaging, COMPUTER-assisted image analysis (Medicine), DATA integration, QUANTITATIVE research, CELLULAR mechanics, OPEN scholarship, DATA collection platforms
Abstract: Understanding the spatiotemporal dynamics of immune cells in living organisms is a major goal in bioimaging. Intravital microscopy enables direct observation of cellular behavior over time with tissue-to-subcellular resolution, making it essential for investigating immune responses across tissues, conditions, and disease contexts. However, most intravital microscopy data remain siloed in individual labs, limiting reuse, standardization, and large-scale analysis. To address these limitations, we present Immunemap, an open-data platform and interactive atlas of immune cell motility. Immunemap currently provides access to over 58,000 curated single-cell tracks and more than 1,049,000 cell-centroid annotations from 400 intravital microscopy videos in murine models, spanning diverse tissues and conditions. The platform supports both exploratory and quantitative research. We show here how unsupervised learning identifies distinct motility patterns, and how large-scale mapping enables comparisons across stimuli, imaging setups, and organs. Its cloud-based architecture offers an interactive web interface and public APIs for integration with computational pipelines. By adhering to FAIR principles (Findability, Accessibility, Interoperability, and Reuse) and fostering cross-disciplinary studies, Immunemap supports reproducible research and provides a benchmark for bioimage analysis and tool development in intravital imaging. Synopsis: Intravital microscopy enables researchers to study the dynamic behavior of immune cells over time in living organisms. Immunemap is an open-data platform that integrates curated cell-tracking datasets from intravital microscopy with interactive tools to support biological discovery, cross-disciplinary collaboration, and the development of new computational methods. Immunemap integrates immune cell motility data with experiment-associated metadata in a standardized format. It enables large-scale analyses of cellular dynamics across tissues, stimuli, and imaging conditions. It provides interactive visualization and programmable access for computational pipelines. It adheres to FAIR principles, ensuring transparency and reusability for both biological and computational research. Immunemap facilitates the identification of immune cell motility patterns across imaging setups, conditions, stimuli, and organs. [ABSTRACT FROM AUTHOR]
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Database: Complementary Index
Description
Abstract:Understanding the spatiotemporal dynamics of immune cells in living organisms is a major goal in bioimaging. Intravital microscopy enables direct observation of cellular behavior over time with tissue-to-subcellular resolution, making it essential for investigating immune responses across tissues, conditions, and disease contexts. However, most intravital microscopy data remain siloed in individual labs, limiting reuse, standardization, and large-scale analysis. To address these limitations, we present Immunemap, an open-data platform and interactive atlas of immune cell motility. Immunemap currently provides access to over 58,000 curated single-cell tracks and more than 1,049,000 cell-centroid annotations from 400 intravital microscopy videos in murine models, spanning diverse tissues and conditions. The platform supports both exploratory and quantitative research. We show here how unsupervised learning identifies distinct motility patterns, and how large-scale mapping enables comparisons across stimuli, imaging setups, and organs. Its cloud-based architecture offers an interactive web interface and public APIs for integration with computational pipelines. By adhering to FAIR principles (Findability, Accessibility, Interoperability, and Reuse) and fostering cross-disciplinary studies, Immunemap supports reproducible research and provides a benchmark for bioimage analysis and tool development in intravital imaging. Synopsis: Intravital microscopy enables researchers to study the dynamic behavior of immune cells over time in living organisms. Immunemap is an open-data platform that integrates curated cell-tracking datasets from intravital microscopy with interactive tools to support biological discovery, cross-disciplinary collaboration, and the development of new computational methods. Immunemap integrates immune cell motility data with experiment-associated metadata in a standardized format. It enables large-scale analyses of cellular dynamics across tissues, stimuli, and imaging conditions. It provides interactive visualization and programmable access for computational pipelines. It adheres to FAIR principles, ensuring transparency and reusability for both biological and computational research. Immunemap facilitates the identification of immune cell motility patterns across imaging setups, conditions, stimuli, and organs. [ABSTRACT FROM AUTHOR]
ISSN:02614189
DOI:10.1038/s44318-025-00629-4