Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights
- 1Indiana University
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.
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BibTeX
@misc{bueckle2026multiscale,
title = {{Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights}},
author = {A. Bueckle and C. Zhu and A. Y. H. Wong and A. Enninful and Y. Miao and N. Farzad and M. Pedersen and C. Mattison and N. Sloan and J. Mares and C. Xing and B. W. Herr and J. Khare and Y. R. Kumar and K. Parekh and S. Chavan and P. Luby and U. Patel and Y. Jain and J. W. Hickey and G. D. Bader and H. Phatnani and V. Menon and R. Fan and P. Sorger and M. Snyder and K. Börner},
howpublished = {bioRxiv},
year = {2026},
month = jul,
doi = {10.64898/2026.07.07.737090},
url = {https://www.biorxiv.org/content/10.64898/2026.07.07.737090v3},
note = {CC BY},
}
RIS
TY - UNPB
TI - Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights
AU - A. Bueckle
AU - C. Zhu
AU - A. Y. H. Wong
AU - A. Enninful
AU - Y. Miao
AU - N. Farzad
AU - M. Pedersen
AU - C. Mattison
AU - N. Sloan
AU - J. Mares
AU - C. Xing
AU - B. W. Herr
AU - J. Khare
AU - Y. R. Kumar
AU - K. Parekh
AU - S. Chavan
AU - P. Luby
AU - U. Patel
AU - Y. Jain
AU - J. W. Hickey
AU - G. D. Bader
AU - H. Phatnani
AU - V. Menon
AU - R. Fan
AU - P. Sorger
AU - M. Snyder
AU - K. Börner
PY - 2026
DA - 2026/07/07
PB - bioRxiv
DO - 10.64898/2026.07.07.737090
UR - https://www.biorxiv.org/content/10.64898/2026.07.07.737090v3
AB - 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.
ER -