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 6,000+ 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/hra-organ-gallery-in-vr.

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.…”

A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps

“…There are a few examples of researchers in the 3D tissue map community exploring applications of fully immersive VR. For example, Bueckle et al [8] visualize the positions of 3D tissue blocks relative to a reference human body plan. However, this is a very different application than the one discussed here as it does not visualize the 3D tissue map data itself but only the position and size of tissue blocks.…”