research-article

Real-time spatial registration for 3D human atlas

Authors:

Bruce W. Herr, II,

Andreas Bueckle,

Fusheng WangAuthors Info & Claims

BigSpatial '22: Proceedings of the 10th ACM SIGSPATIAL International Workshop on Analytics for Big Geospatial Data

Pages 27 - 35

https://doi.org/10.1145/3557917.3567618

Published: 03 November 2022 Publication History

Abstract

The human body is made up of about 37 trillion cells (adults). Each cell has its own unique role and is affected by its neighboring cells and environment. The NIH Human BioMolecular Atlas Program (HuBMAP) aims at developing a 3D atlas of human body consisting of organs, vessels, tissues to singe cells with all 3D spatially registered in a single 3D human atlas using tissues obtained from normal individuals across a wide range of ages. A critical step of building the atlas is to register 3D tissue blocks in real-time to the right location of a human organ, which itself consists of complex 3D sub-structures. The complexity of the 3D organ model, e.g., 35 meshes for a typical kidney, poses a significant computational challenge for the registration. In this paper, we propose a comprehensive framework TICKET (TIssue bloCK rEgisTration) to support tissue block registration for 3D human atlas, including (1) 3D mesh pre-processing, (2) spatial queries on intersection relationship and (3) intersection volume computation between organs and tissue blocks. To minimize search space and computation cost, we develop multi-level indexing at both the anatomical structure level and mesh level, and utilize OpenMP for parallel computing. Considering cuboid based shape of the tissue block, we propose an efficient voxelization-based method to estimate the intersection volume. Our experiments demonstrate that the proposed framework is efficient and practical. TICKET is being integrated into the HuBMAP CCF registration portal [1].

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Cited By

Wang FLee RTeng DZhang XSaltz J(2024)High-Performance Spatial Data Analytics: Systematic R&D for Scale-Out and Scale-Up Solutions from the Past to NowProceedings of the VLDB Endowment10.14778/3685800.368591217:12(4507-4520)Online publication date: 1-Aug-2024
https://dl.acm.org/doi/10.14778/3685800.3685912
Shashidharan AGadiraju KVatsavai RChandola V(2023)The 10th ACM SIGSPATIAL International Workshop on Analytics for Big Spatial Data (BigSpatial 2022)SIGSPATIAL Special10.1145/3632268.363228114:1(43-44)Online publication date: 7-Nov-2023
https://dl.acm.org/doi/10.1145/3632268.3632281
Herr BHardi JQuardokus EBueckle AChen LWang FCaron AOsumi-Sutherland DMusen MBörner K(2023)Specimen, biological structure, and spatial ontologies in support of a Human Reference AtlasScientific Data10.1038/s41597-023-01993-810:1Online publication date: 27-Mar-2023
https://doi.org/10.1038/s41597-023-01993-8

Index Terms

Real-time spatial registration for 3D human atlas
1. Information systems
  1. Data management systems

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cover image ACM Conferences

BigSpatial '22: Proceedings of the 10th ACM SIGSPATIAL International Workshop on Analytics for Big Geospatial Data

November 2022

53 pages

ISBN:9781450395311

DOI:10.1145/3557917

Editors:
Ashwin Shashidharan
Esri, CA
,
Krishna Karthik Gadiraju
Juniper Networks, CA
,
Varun Chandola
State University of New York at Buffalo, NY
,
Ranga Raju Vatsavai
North Carolina State University, NC

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SIGSPATIAL: ACM Special Interest Group on Spatial Information

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Published: 03 November 2022

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NIH (National Institutes of Health)

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SIGSPATIAL '22: The 30th International Conference on Advances in Geographic Information Systems

November 1, 2022

Washington, Seattle

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BigSpatial '22 Paper Acceptance Rate 5 of 14 submissions, 36%;

Overall Acceptance Rate 32 of 58 submissions, 55%

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Cited By

Wang FLee RTeng DZhang XSaltz J(2024)High-Performance Spatial Data Analytics: Systematic R&D for Scale-Out and Scale-Up Solutions from the Past to NowProceedings of the VLDB Endowment10.14778/3685800.368591217:12(4507-4520)Online publication date: 1-Aug-2024
https://dl.acm.org/doi/10.14778/3685800.3685912
Shashidharan AGadiraju KVatsavai RChandola V(2023)The 10th ACM SIGSPATIAL International Workshop on Analytics for Big Spatial Data (BigSpatial 2022)SIGSPATIAL Special10.1145/3632268.363228114:1(43-44)Online publication date: 7-Nov-2023
https://dl.acm.org/doi/10.1145/3632268.3632281
Herr BHardi JQuardokus EBueckle AChen LWang FCaron AOsumi-Sutherland DMusen MBörner K(2023)Specimen, biological structure, and spatial ontologies in support of a Human Reference AtlasScientific Data10.1038/s41597-023-01993-810:1Online publication date: 27-Mar-2023
https://doi.org/10.1038/s41597-023-01993-8

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