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ImmGenMaps, an open-source cartography of the immune system

Nature Immunology volume 26, pages 637–638 (2025)Cite this article

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The Immunological Genome Project Consortium (ImmGen) is announcing the launch of ImmGenMaps (https://www.immgen.org/ImmGenMaps/), a project designed to spatially profile every immune cell across the mouse anatomy. This community project builds upon the bulk and single-cell profiling efforts of ImmGen to characterize the genetic regulation of all cells of the mouse immune system. Using state-of-the-art spatial transcriptomics technology, ImmGenMaps goes one step further by profiling immune cells within their natural environments across all major organs, at baseline or under challenge. In addition to capturing transcriptional profiles and a subset of landmark protein markers of immunocytes, ImmGenMaps will also profile non-immune cells (stroma, epithelia, connective tissue), whose key roles in orchestrating immune function is increasingly recognized. By capturing the pieces of the immune game (immune cells) and the playing board (tissue structures and non-immune cells), and determining the rules that govern the immune game (environmental signals and cellular interactions), we expect to provide a key resource to the scientific community. In line with ImmGen’s previous ‘OpenSource’ projects1,2, the intent is to leverage the broader community’s expertise by welcoming the participation of immunology and computational biology labs beyond the core ImmGen membership.

ImmGenMaps aims to broach several initial questions aimed at deepening our understanding of cellular dynamics across tissues. It seeks to profile the frequency of all immune and non-immune cell types, including those, like granulocytes, that are typically lost during tissue dissociation-based profiling. In addition, the project aims to define discrete cellular niches, spatial domains and the relevant gradients of organ function, while also unraveling the connectivity between immune cells and their surrounding cells. Further objectives include mapping the sources of key signals — such as chemokines and cytokines — in both health and disease, assessing the link between cellular location and phenotype, and conducting a rigorous evaluation of how cell types and phenotypes correlate with tissue type and location.

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Author notes

  1. A full list of members appears in the Supplementary Information.

Authors and Affiliations

  1. La Jolla Institute for Immunology, La Jolla, CA, USA

    Miguel Reina-Campos

  2. Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Samouil L. Farhi

  3. Department of Immunology, Harvard Medical School, Boston, MA, USA

    Christophe Benoist

Authors
  1. Miguel Reina-Campos
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  2. Samouil L. Farhi
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  3. Christophe Benoist
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Consortia

on behalf of ImmGenMaps Group

  • Miguel Reina-Campos
  • , Samouil L. Farhi
  •  & Christophe Benoist

Corresponding authors

Correspondence to Miguel Reina-Campos or Christophe Benoist.

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The authors declare no competing interests.

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Reina-Campos, M., Farhi, S.L., Benoist, C. et al. ImmGenMaps, an open-source cartography of the immune system. Nat Immunol 26, 637–638 (2025). https://doi.org/10.1038/s41590-025-02119-5

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