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Systematic analysis of immune cell motility leveraging the open intravital microscopy database Immunemap
Diego Ulisse Pizzagalli1,2,3, Pau Carrillo-Barberà4,5,6, Himanshu Bansal4,7
1Institute for Research in Biomedicine, USI, Bellinzona, Switzerland. pizzad@usi.ch.
Insights
Immunemap is a new open-data platform and atlas for immune cell motility, offering over 58,000 cell tracks from intravital microscopy. This resource enhances large-scale analysis and reproducible research in bioimaging.
Area of Science:
- Bioimaging
- Immunology
- Computational Biology
Background:
- Intravital microscopy is crucial for observing immune cell dynamics in vivo.
- Current data sharing limitations hinder large-scale analysis and standardization of immune cell motility studies.
- A centralized platform is needed to consolidate and analyze intravital microscopy data.
Purpose of the Study:
- To introduce Immunemap, an open-data platform and interactive atlas for immune cell motility.
- To provide a comprehensive resource for analyzing and sharing intravital microscopy data.
- To facilitate reproducible research and advance bioimage analysis in immunology.
Main Methods:
- Development of a cloud-based platform with an interactive web interface and public APIs.
- Curation of over 58,000 single-cell tracks and 1,049,000 cell-centroid annotations from 400 intravital microscopy videos.
- Application of unsupervised learning to identify immune cell motility patterns.
Main Results:
- Immunemap provides access to a large, curated dataset of immune cell tracks and annotations from murine models.
- Unsupervised learning successfully identified distinct immune cell motility patterns.
- The platform enables comparisons of immune cell behavior across different tissues, conditions, and experimental setups.
Conclusions:
- Immunemap addresses data silos in intravital microscopy, promoting data reuse and standardization.
- The platform supports both exploratory and quantitative research, fostering cross-disciplinary studies.
- Immunemap serves as a valuable benchmark for bioimage analysis and tool development in intravital imaging, adhering to FAIR principles.
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.
