What if we could explore the human body like a detailed map, zooming from whole organs down to individual cells, and even the molecules within them? That’s the ambitious goal behind the 3D Human Reference Atlas (HRA), a powerful new resource developed by researchers in the NIH Common Fund Human BioMolecular Atlas Program (HuBMAP). The atlas offers a comprehensive, spatial view of a healthy adult human body, combining detailed anatomical models with biological data to show where different cell types and molecular markers are located. Understanding where different cells and molecules are located helps researchers uncover how they interact, driving new discoveries in human health.
In a new publication, led by HuBMAP researcher Katy Börner, Ph.D., at Indiana University Bloomington, the team presents the latest version of the Human Reference Atlas. The update integrates multiple types of biological data to provide a comprehensive spatial framework to better understand how the human body is organized—and how that organization can shift with disease, aging, or injury.
The atlas combines different 3D models that cover 4,499 unique anatomical structures in the body, including organs, tissues, cells, even genes and proteins. Experts from more than 20 research groups collaborated to develop a shared spatial framework that enables meaningful comparisons across models and datasets. This standardized, openly accessible resource allows scientists to map their own data onto a common reference, making it easier to detect abnormalities, understand disease progression, and support precision medicine efforts.
The paper also highlights practical tools, standardized data formats, and user stories that guide researchers in using the HRA, facilitating collaboration and comparison across studies and laboratories.
The Human Reference Atlas is publicly available and continuously updated. Researchers and developers can access the atlas and related tools at https://hubmapconsortium.org.
Reference: Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber GJ, Misra RS, Purkerson JM, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber GM, Jain Y, Qaurooni D, Kong Y; HRA Team; Bueckle A, Herr BW. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nat Methods. 2025 Apr;22(4):845-860. doi: 10.1038/s41592-024-02563-5
