ImmGenMaps, an open-source cartography of the immune system
Nature Immunology. 2025;26(5):637-638. DOI 10.1038/s41590-025-02119-5.
How to cite
AMA
Reina-Campos M, Farhi SL, Benoist C, et al. ImmGenMaps, an open-source cartography of the immune system. Nat Immunol. 2025;26(5):637-638. doi:10.1038/s41590-025-02119-5APA
Reina-Campos, M., Farhi, S. L., Benoist, C., et al. (2025). ImmGenMaps, an open-source cartography of the immune system. Nature Immunology, 26(5), 637-638. https://doi.org/10.1038/s41590-025-02119-5BibTeX
@article{reinacampos2025immgenmaps,
title = {ImmGenMaps, an open-source cartography of the immune system},
author = {Reina-Campos, Miguel and Farhi, Samouil L. and Benoist, Christophe and others},
journal = {Nature Immunology},
volume = {26},
number = {5},
pages = {637--638},
year = {2025},
doi = {10.1038/s41590-025-02119-5}
}Immunology has spent years cataloguing the genes that define every immune cell, but most of that work first grinds a tissue into a cell suspension. That step throws away where each cell actually sat and loses fragile cell types, such as granulocytes, altogether. Where every immune cell lives inside an intact organ, which neighbors surround it, and which local signals shape it there had not been mapped at scale.
The Immunological Genome Project (ImmGen), the consortium behind the long-running atlases of mouse immune-cell gene regulation, is launching ImmGenMaps — an open, community-built effort to spatially profile every immune cell across the whole mouse anatomy. Using spatial profiling technology, it reads immune cells within their natural tissue environments across all major organs, at baseline and under immune challenge, and also captures the non-immune stroma, epithelia and connective tissue that make up the surrounding structure.
The aim is a shared reference map: the immune cells (the pieces), the tissue they sit in (the board), and the chemokine and cytokine signals that govern them (the rules) — assembled openly with immunology and computational-biology labs beyond the core consortium.
Key findings
- ImmGenMaps sets out to spatially profile every immune cell across the whole mouse anatomy. The Immunological Genome Project consortium is extending its bulk and single-cell atlases into intact tissue, reading immune cells within their natural environments across all major organs, at baseline and under challenge.
- The map includes the tissue itself, not just the immune cells. Alongside immunocyte transcriptional profiles, the project profiles non-immune stroma, epithelia and connective tissue, and aims to recover cell types such as granulocytes that dissociation-based methods typically lose — then define discrete cellular niches, spatial domains and the sources of chemokine and cytokine signals in health and disease.
- Reading landmark protein markers in place, at single-cell resolution, is part of the plan. Beyond transcripts, ImmGenMaps captures a subset of landmark protein markers of immunocytes within intact tissue — the class of whole-slide, single-round multiplex spatial-proteomics readout that RareCyte's Orion, confirmed by RareCyte as part of the ImmGenMaps effort, is built to deliver.
Orion in the methods
This publication is a Comment announcing the ImmGenMaps consortium, not a methods paper, and the full article sits behind the Nature Immunology paywall — so there is no verbatim methods passage to quote here, and none is invented. RareCyte's Orion whole-slide spatial-proteomics platform is used within the ImmGenMaps spatial-profiling effort, involvement that RareCyte has directly confirmed. The specific acquisition settings, marker panels and per-organ protocols will appear in the project's forthcoming data releases and method papers rather than in this announcement.
Why it matters for Orion users
An atlas of the whole immune system only holds together if the readout keeps every cell where it actually sits. That is the demand a project like ImmGenMaps places on its imaging: profile immune and non-immune cells together, across an entire organ section, in enough colors to separate several cell types at once, without grinding the tissue into a suspension that discards spatial context and loses fragile cells such as granulocytes. This is the job a whole-slide, single-round multiplex spatial-proteomics platform is built for, and it is where RareCyte's Orion fits the effort. Because Orion stains and images a whole slide in a single round, each precious section is read once rather than carried through repeated stain-and-strip cycles — which matters when a map has to span many organs and conditions consistently. And because it resolves a high-plex marker panel together at single-cell resolution, it can support the questions the consortium set out to ask, which cells occupy which niche and where the chemokine and cytokine signals originate, that a dissociated or lower-plex readout cannot reach. For a prospective user the takeaway is concrete: the same properties that let Orion carry one section of a community-scale atlas are the ones that let you hold position, plex and tissue integrity together in your own study.
