Systematic analysis of immune cell motility leveraging the open intravital microscopy database Immunemap
Additional information
Authors
Pizzagalli D. U.,
Carrillo-Barberà P.,
Bansal H.,
Palladino E.,
Ceni K.,
Thelen B.,
Pulfer A.,
Moscatello E.,
Fiamma Cabini R.,
Textor J.,
M N Wortel I.,
Hickey M.,
Norman U.,
Hidalgo A.,
Crainiciuc G.,
Adrover J. M.,
Palomino-Segura M.,
Marangoni F.,
Mempel T. R.,
Xu C.,
Choe K.,
Lennon-Dumenil A. M.,
Obino D.,
Bousso P.,
Moreau H. D.,
Halin C.,
Hunter M. C.,
Stein J. V.,
Pfenninger P.,
Abe J.,
Murooka T. T.,
Iannacone M.,
Ficht X.,
Moalli F.,
Bénéchet A. P.,
Kastenmüller W.,
Eickhoff S.,
Sarris M.,
Georgantzoglou A.,
Engelhardt B.,
Vladymyrov M.,
Pareja J.,
Jahromi N. H.,
Cahalan M. D.,
Othy S.,
Farsakoglu Y.,
Simon H. U.,
Germic N.,
Di Pilato M.,
Sintes J.,
Virgilio T.,
Latino I.,
Romero D. M.,
Pizzichetti C.,
Cappucetti A.,
Chahine K.,
Caetano dos Santos F. L.,
Bordini J.,
Krause R.,
Fernandez Gonzalez S.
Type
Journal Article
Year
2025
Language
English
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.
Keywords
Intravital microscopy, Cell tracking, Spatiotemporal dynamics, Immune response, Bioimage data analysis
Journal
The EMBO Journal
Volume
45
Number ( Month )
1
Pages (or article number)
334-348
ISSN
1460-2075
Diffusion
License
CC BY
Visibility
Public
Status open access
Gold
