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

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; Hickey, Michael; Norman, Ursula; Hidalgo, Andres; Crainiciuc, Georgiana; Adrover, Jose M; Palomino-Segura, Miguel; Marangoni, Francesco; Mempel, Thorsten R; Xu, Chris; Choe, Kibaek; Lennon-Dumenil, Ana-Maria; Obino, Dorian; Bousso, Philippe; Moreau, Helene D; Halin, Cornelia; Hunter, Morgan Campbell; Stein, Jens V; Pfenninger, Petra; Abe, Jun; Murooka, Thomas T; Iannacone, Matteo; Ficht, Xenia; Moalli, Federica; Bénéchet, Alexandre P; Kastenmüller, Wolfgang; Eickhoff, Sarah; Sarris, Milka; Georgantzoglou, Antonios; Engelhardt, Britta; Vladymyrov, Mykhailo; Pareja, Javier; Jahromi, Neda Haghayegh; Cahalan, Michael D; Othy, Shivashankar; Farsakoglu, Yagmur; Simon, Hans-Uwe; Germic, Nina; Di Pilato, Mauro; Sintes, Jordi; Virgilio, Tommaso; Latino, Irene; Romero, Daniel Molina; Pizzichetti, Chiara; Cappucetti, Arianna; Chahine, Kamil; Caetano dos Santos, Florentino Luciano; Bordini, Joy; Krause, Rolf; Fernandez Gonzalez, Santiago

doi:10.1038/s44318-025-00629-4

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Pizzagalli_2025_SPringer_EMBO_s44318-025-00629-4

Journal article

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

Pizzagalli, Diego Ulisse ORCID Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland - Euler Institute (EUL), Università della Svizzera italiana, Switzerland - Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland
Carrillo-Barberà, Pau ORCID Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland - Departamento de Biologia Celular, Biologia Funcional y Antropologia Fisica, Universitat de Valencia, Spain - Instituto de Biotecnologia y Biomedicina (BioTecMed), Universitat de Valencia, Spain
Bansal, Himanshu ORCID Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland - Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland
Palladino, Elisa Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland
Ceni, Kevin Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland - Institute for Diagnostic and Interventional Neuroradiology, Inselspital, Bern University Hospital, Switzerland
Thelen, Benedikt Euler Institute (EUL), Università della Svizzera italiana, Switzerland
Pulfer, Alain Euler Institute (EUL), Università della Svizzera italiana, Switzerland - Department of Information Technology and Electrical Engineering, ETH Zurich, Switzerland
Moscatello, Enrico Euler Institute (EUL), Università della Svizzera italiana, Switzerland
Fiamma Cabini, Raffaella ORCID Euler Institute (EUL), Università della Svizzera italiana, Switzerland
Textor, Johannes Medical BioSciences, Radboud University, Nijmegen, Netherlands - Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, Netherlands
M N Wortel, Inge Medical BioSciences, Radboud University, Nijmegen, Netherlands - Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, Netherlands
Hickey, Michael Immunemap Consortium
Norman, Ursula Immunemap Consortium
Hidalgo, Andres Immunemap Consortium
Crainiciuc, Georgiana Immunemap Consortium
Adrover, Jose M Immunemap Consortium
Palomino-Segura, Miguel Immunemap Consortium
Marangoni, Francesco Immunemap Consortium
Mempel, Thorsten R Immunemap Consortium
Xu, Chris Immunemap Consortium
Choe, Kibaek Immunemap Consortium
Lennon-Dumenil, Ana-Maria Immunemap Consortium
Obino, Dorian Immunemap Consortium
Bousso, Philippe Immunemap Consortium
Moreau, Helene D Immunemap Consortium
Halin, Cornelia Immunemap Consortium
Hunter, Morgan Campbell Immunemap Consortium
Stein, Jens V Immunemap Consortium
Pfenninger, Petra Immunemap Consortium
Abe, Jun Immunemap Consortium
Murooka, Thomas T Immunemap Consortium
Iannacone, Matteo Immunemap Consortium
Ficht, Xenia Immunemap Consortium
Moalli, Federica Immunemap Consortium
Bénéchet, Alexandre P Immunemap Consortium
Kastenmüller, Wolfgang Immunemap Consortium
Eickhoff, Sarah Immunemap Consortium
Sarris, Milka Immunemap Consortium
Georgantzoglou, Antonios Immunemap Consortium
Engelhardt, Britta Immunemap Consortium
Vladymyrov, Mykhailo Immunemap Consortium
Pareja, Javier Immunemap Consortium
Jahromi, Neda Haghayegh Immunemap Consortium
Cahalan, Michael D Immunemap Consortium
Othy, Shivashankar Immunemap Consortium
Farsakoglu, Yagmur Immunemap Consortium
Simon, Hans-Uwe Immunemap Consortium
Germic, Nina Immunemap Consortium
Di Pilato, Mauro Immunemap Consortium
Sintes, Jordi Immunemap Consortium
Virgilio, Tommaso Immunemap Consortium
Latino, Irene Immunemap Consortium
Romero, Daniel Molina Immunemap Consortium
Pizzichetti, Chiara Immunemap Consortium
Cappucetti, Arianna Immunemap Consortium
Chahine, Kamil Immunemap Consortium
Caetano dos Santos, Florentino Luciano Immunemap Consortium
Bordini, Joy Immunemap Consortium
Krause, Rolf ORCID Euler Institute (EUL), Università della Svizzera italiana, Switzerland
Fernandez Gonzalez, Santiago ORCID Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland - Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland

2025

Published in:

The EMBO Journal. - 2025, vol. 45, no. 1, p. 334-348

English 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.

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