Distributed global digital volume correlation by optimal transport

John Michael L. MacNeil, Dmitriy Morozov, Francesco Panerai, Dilworth Parkinson, Harold Barnard, Daniela Ushizima

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Because of the speed and data rates of time-resolved experiments at facilities such as synchrotron beamlines, automation is critical during time-resolved experiments. In 3D imaging experiments like microCT (CT), this includes recognizing features of interest and 'zooming in' spatially and temporally to those features; ideally without requiring advanced information about which features are being imaged. Digital Volume Correlation (DVC) can achieve this by measuring the deformation field between images, but has not been used during autonomous experiments because of the scalability of the codes. In this work, we propose a model for global DVC and a parallel algorithm for solving it for large-scale images, suitable for giving feedback for autonomous experiments at synchrotron-based microCT beamlines. In particular, we leverage recent advancements in entropy-regularized optimal transport to develop efficient, simple-to-implement, parallel algorithms which scale linearly (O(N)) in space and time, where N is the number of voxels, and well with an increasing number of processors. As a demonstration, we compute the deformation field for every voxel from a CT volume with dimensions 2560x2560x2160. We discuss implementation details, drawbacks and future directions.

Original languageEnglish (US)
Title of host publicationProceedings of XLOOP 2019
Subtitle of host publication1st Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, Held in conjunction with SC 2019: The International Conference for High Performance Computing, Networking, Storage and Analysis
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages14-19
Number of pages6
ISBN (Electronic)9781728159836
DOIs
StatePublished - Nov 2019
Event1st IEEE/ACM Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, XLOOP 2019 - Denver, United States
Duration: Nov 18 2019 → …

Publication series

NameProceedings of XLOOP 2019: 1st Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, Held in conjunction with SC 2019: The International Conference for High Performance Computing, Networking, Storage and Analysis

Conference

Conference1st IEEE/ACM Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, XLOOP 2019
CountryUnited States
CityDenver
Period11/18/19 → …

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Information Systems and Management

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  • Cite this

    MacNeil, J. M. L., Morozov, D., Panerai, F., Parkinson, D., Barnard, H., & Ushizima, D. (2019). Distributed global digital volume correlation by optimal transport. In Proceedings of XLOOP 2019: 1st Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, Held in conjunction with SC 2019: The International Conference for High Performance Computing, Networking, Storage and Analysis (pp. 14-19). [8943546] (Proceedings of XLOOP 2019: 1st Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, Held in conjunction with SC 2019: The International Conference for High Performance Computing, Networking, Storage and Analysis). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/XLOOP49562.2019.00008