The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality

Abstract

The Human Reference Atlas (HRA, https://humanatlas.io) funded by the NIH Human Biomolecular Atlas Program (HuBMAP, https://commonfund.nih.gov/hubmap) and other projects engages 17 international consortia to create a spatial reference of the healthy adult human body at single-cell resolution. The specimen, biological structure, and spatial data that define the HRA are disparate in nature and benefit from a visually explicit method of data integration. Virtual reality (VR) offers unique means to enable users to explore complex data structures in a three-dimensional (3D) immersive environment. On a 2D desktop application, the 3D spatiality and real-world size of the 3D reference organs of the atlas is hard to understand. If viewed in VR, the spatiality of the organs and tissue blocks mapped to the HRA can be explored in their true size and in a way that goes beyond traditional 2D user interfaces. Added 2D and 3D visualizations can then provide data-rich context. In this paper, we present the HRA Organ Gallery, a VR application to explore the atlas in an integrated VR environment. Presently, the HRA Organ Gallery features 55 3D reference organs,1,203 mapped tissue blocks from 292 demographically diverse donors and 15 providers that link to 5,000+ datasets; it also features prototype visualizations of cell type distributions and 3D protein structures. We outline our plans to support two biological use cases: on-ramping novice and expert users to HuBMAP data available via the Data Portal (https://portal.hubmapconsortium.org), and quality assurance/quality control (QA/QC) for HRA data providers. Code and onboarding materials are available at https://github.com/cns-iu/ccf-organ-vr-gallery#readme.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

“…The HRA Organ Gallery 68,69 (https://github.com/cns-iu/hra-organ-gallery-in-vr, see Supplemental Figure 11) supports the multi-scale exploration of 1,218 anatomical structures in the 65 3D Reference Objects of the HRA 2.0. Using a Meta Quest VR device, users select the male or female reference body; they can then select a specific organ and explore it with both hands.…”

Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

“…The VR setup makes it possible to explore the HRA data across different scales—from encountering a whole body in real size (see Fig. 5d ), zooming into single organs and studying their many anatomical structures, or examining cell-type populations within specific anatomical structures 11 . The HRA Organ Gallery utilizes the CCF API to retrieve all 53 reference organs published in the third HRA release and 350 HuBMAP tissue blocks publicly available on August 25, 2022 (see Zenodo Table 3 27 ).…”

“…Figure 1a depicts how Visible Human Project data (VHP) 10 (a high-quality, whole-body dataset published by the National Library of Medicine) is used to create reference organs (different anatomical structures of a kidney are shown) and how resulting data is uniformly represented using the spatial and specimen information. All reference organs can be interactively examined in the Exploration User Interface (EUI, https://github.com/hubmapconsortium/ccf-ui ) and the HRA Organ Gallery in virtual reality (VR) 11 , both of which are detailed in the CCF Ontology Applications section. The spatial size, shape, location, and rotation of experimental tissue data is captured relative to the organs in the 3D Reference Object Library.…”