HuBMAP Data Portal: A Resource for Multimodal Spatial and Single-Cell Data of Healthy Human Tissues

Abstract

The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multimodal, multi-scale spatial and single-cell data from healthy human tissues. As of June 2026, the portal hosts 9,232 public datasets from 25 data types spanning 29 organ classes across 498 donors. Portal infrastructure and user interfaces support data search and discovery, visualization, and analysis directly in web browsers. These capabilities include metadata- and data-driven search, collaborative Workspaces with access to high-performance compute, and interactive Vitessce visualizations across non-spatial, 2D, and 3D spatial datasets. Data-type-specific uniform processing pipelines and rigorous quality control processes ensure comparability of results across laboratories, organs, and donors, while externally processed community-contributed datasets provide complementary perspectives. Here we describe portal functionality, infrastructure, and design, and highlight its role as a platform for large-scale spatial single-cell research across diverse data types, organs, and scales.