Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel
Abstract:
Single-cell atlassing efforts like the Human BioMolecular Atlas Program (HuBMAP) and Cellular Senescence Network (SenNet) produce multiscale datasets across the healthy, adult, human body but are typically explored on 2D screens with limited 3D affordances, even though understanding cell location within tissue, organ, and body requires spatial reasoning across many orders of magnitude. The Human Reference Atlas (HRA) provides standard terminologies and a Common Coordinate Framework (CCF) for harmonizing this data spatially and semantically. Building on the HRA Organ Gallery in virtual reality (VR), we present "HRA: Powers of Ten," which integrates, harmonizes, and visualizes biological data from these efforts in VR using a Multiscale Elevator System that lets users descend, like riding an elevator through an inverted skyscraper, from a whole body view of 81 reference organs to datasets across 5 organs (lymph node, brain, large intestine, small intestine, liver), 5 assay types (CODEX, Visium, v-CyCIF, Xenium, SBF-SEM), and 4 spatial scales. Shared by Data Providers, these VR scenes enable biological insights into senescence patterns, cellular neighborhoods, 3D tissue reconstruction, and subcellular liver architecture. A standard operating procedure supports adding further datasets. Freely available on the Meta Store to over 20 million headsets, the application, data, code are open-source.
