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.
- Collections
- Language
-
- English
- Classification
- Medicine
- License
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CC BY
- Open access status
- gold
- Identifiers
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- ISSN 1460-2075
- DOI 10.1038/s44318-025-00629-4
- RICERCO 67799
- ARK ark:/12658/srd1335518
- Persistent URL
- https://n2t.net/ark:/12658/srd1335518
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