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

TL;DR

The HuBMAP Data Portal is a comprehensive, user-friendly platform providing access to multi-modal spatial and single-cell datasets from healthy human tissues, supporting large-scale spatial atlas creation and analysis.

Contribution

This paper introduces a scalable, integrated data portal with standardized processing, visualization tools, and collaborative features for multi-modal human tissue data.

Findings

Hosts over 5,000 datasets across 27 organs

Enables visualization of spatial and single-cell data in web browsers

Supports collaborative analysis with Jupyter and Vitessce

Abstract

The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multi-modal spatial and single-cell data from healthy human tissues. This resource facilitates the NIH HuBMAP consortium's mission to create a widely accessible multi-scale spatial atlas of the healthy human body at single-cell resolution. As of October 2025, the portal hosts 5,032 datasets from 22 different data types spanning 27 organ classes across 310 donors. The portal's infrastructure and user interfaces enable efficient visualization and analysis directly in web browsers through integrated collaborative Jupyter workspaces and interactive Vitessce visualizations for over 1,500 non-spatial, 2D, and 3D spatial datasets. Uniform processing pipelines and rigorous quality control processes ensure comparability of results from different laboratories, organs, and donors for large-scale analyses, while externally processed, community-contributed datasets (EPICs) provide complementary perspectives. The portal interface supports both metadata- and data-driven search functionalities, bulk downloads, and integrated data collections, including supplementary data and visualizations for consortium publications.