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

Description
Britta Engelhardt, Mykhailo Vladymyrov, Javier Pareja, Neda Haghayegh Jahromi (Theodor Kocher Institute) are Members of Immunemap Consortium
Hans-Uwe Simon, Nina Germic (Institute of Pharmacology) are Members of Immunemap Consortium
Kamil Chahine (Graduate School for Cellular and Biomedical Sciences) is Member of Immunemap Consortium
DOI
Publisher DOI
PubMed ID
41266653
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.
Date Issued
2026-01
Publication Type
Article
Subject(s)
Subjects
Bioimage Data Analysis
•
Cell Tracking
•
Immune Response
•
Intravital Microscopy
•
Spatiotemporal Dynamics
Language(s)
en
Author(s)
Carrillo-Barberà, Pau
Bansal, Himanshu
Palladino, Elisa
Ceni, Kevin
Pulfer, Alain
Moscatello, Enrico
Fiamma Cabini, Raffaella
Textor, Johannes
M N Wortel, Inge
Krause, Rolf
Fernandez Gonzalez, Santiago
Additional Credits
Journal
The Embo Journal
Publisher
Nature Publishing Group
ISSN
1460-2075
Access(Rights)
open.access
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