# Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas

> **NIH NIH OT2** · HARVARD MEDICAL SCHOOL · 2022 · $1,308,559

## Abstract

To enable the Human BioMolecular Atlas Program (HuBMAP) Consortium production phase, we 
will develop several new and improved spatial single cell and bioimaging data visualization 
features. These include Vitessce support for large volume 3D data combined with 2D 
maps, spatial queries in 2D maps via HuBMAP Data Portal UI and Vitessce, user workspaces 
with support for co-analysis of community and HuBMAP data, “datahubs” for external data that 
can be displayed in context of Human Reference Atlas and HuBMAP data, new file formats for 
3D spatial data, deployment of generalized “cell x gene” matrix format across HuBMAP Data 
Portal, ability to store and share analyses of data conducted with analysis workspaces, 
integration of Vitessce with Common Coordinate Framework navigation tools, UI enhancements 
to scale to growing body of HuBMAP data (both in terms of volume and richness of the data and 
analysis results), seamless integration between evolving Human Reference Atlas UI and Data 
Portal UI. Furthermore, we will research solutions for (1) Seamless navigation through HuBMAP 
and integrated community data through visual interfaces that combine data portal UI, human 
reference atlas UI, and interactive visualization tools, e.g., Vitessce. (2) Extension of Vitessce 
to support interpretation of functional single-cell and tissue data through network and pathway 
visualizations that support 2D and 3D spatial information. (3) Rollout of “data hubs”, i.e., formats 
and annotation standards for spatial single-cell and tissue data that can be viewed in the context 
of the Human Reference Atlas (similar to “track hubs” for genome browsers). (4) UI-based 
analysis workspaces to assemble execution pipelines for data processing and visualization.

## Key facts

- **NIH application ID:** 10534328
- **Project number:** 1OT2OD033758-01
- **Recipient organization:** HARVARD MEDICAL SCHOOL
- **Principal Investigator:** Nils Gehlenborg
- **Activity code:** OT2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $1,308,559
- **Award type:** 1
- **Project period:** 2022-08-01 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10534328

## Citation

> US National Institutes of Health, RePORTER application 10534328, Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas (1OT2OD033758-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10534328. Licensed CC0.

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