About HuBMAP Data

The focus of HuBMAP is understanding the intrinsic intra-, inter-, and extra- cellular biomolecular distribution in human tissue. HuBMAP will focus on fresh, fixed, or frozen healthy human tissue using in situ and dissociative techniques that have high-spatial resolution.

The HuBMAP Data Portal aims to be an open map of the human body at the cellular level. These tools and maps are openly available, to accelerate understanding of the relationships between cell and tissue organization and function and human health.


Explore the Data

HuBMAP-developed tools Vitessce, the Common Coordinate Framework, and Azimuth allow visual exploration of HuBMAP tissues and cells. You can also search the data in the Data Portal directly, and download data for your use.


Vitessce enables the exploration of spatially-resolved, integrated single-cell datasets. An interactive visualization tool, Vitessce is available for datasets that have been processed through HuBMAP HIVE computing hardware and pipelines.

The HuBMAP Mapping effort is developing a Common Coordinate Framework (CCF) for the healthy human body. This framework will support cataloging different types of individual cells, understanding the functions of and relationships between those cell types, and modeling their individual and collective function.

Elements of the CCF already in use include the ASCT+B Reporter, the Exploration User Interface, and the Registration User Interface.

The CCF ASCT+B Reporter is a visualization tool for displaying anatomical structures, cell types, and biomarkers (ASCT+B) authored by domain experts for different human organs. The tables are used to develop a Common Coordinate Framework of the healthy human body.

The CCF Exploration User Interface (EUI) supports exploration of semantically and spatially explicit data—from the whole body to the single cell level.

The CCF Registration User Interface (RUI) supports uniform tissue data registration across organs and labs.

Azimuth is a web application that uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis.


Anyone can access the Data Portal without logging in to browse, download metadata, and visualize public data.

Viewers can browse by donors, samples, datasets, and collections, and refine their search by organ type, specimen type, assay type, donor information, affiliation (who produced the data), and more.


While an account is not necessary to access and view datasets within the Data Portal, viewers who log in are able to download processed data.

Login to the Data Portal is handled through Globus. Login with your institutional or eRACommons credentials for anonymous access to file downloads.


About the Data

HuBMAP is transparent about the origin of its data, how the data is processed, and the quality control processes used to ensure its integrity.

HuBMAP Data comprises healthy (normal, non-diseased) tissue from over 80 donors. The data for sex, race, and ethnicity provided are those pulled from the electronic medical records available and do not reflect the breadth of human identity and experience. We hope to expand the diversity of our donors in future data releases.



The HuBMAP data portal encompasses over 1200 data sets spanning more than 30 organs, including: bladder, brain, eye, fallopian tube, heart, kidney, knee, large intestine, liver, lung, lymph nodes, ovary, pancreas, pelvis, prostate, skin, spleen, thymus, ureter, uterus, and vasculature. Specimen types (fresh frozen tissue section, FFPE, single cell cryopreserved, etc.) are associated with the organs and can be used to filter during exploration.

Additional organs will be part of future releases.

Click on an organ to see its data in our data portal.



HuBMAP data was generated using three modalities: mass spectrometry, microscopy, and sequencing, with a variety of assay types used in each.



Data available through the Data Portal are linked directly to the protocols used in sample handling and assays. All protocols are available on protocols.io.

Go to the HuBMAP workspace in protocols.io.

Quality Control Reports

All data submitted to HuBMAP goes through a quality control process before being released to the Data Portal. Links to quality control reports are included in the Portal with the dataset information.