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Title: A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

Abstract

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.

Authors:
 [1];  [2];  [1]
  1. Univ. of California, Los Angeles, CA (United States). Dept. of Physics and Astronomy and California NanoSystems Inst.
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for Electron Microscopy and Molecular Foundry
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
SC-22.3 USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division; National Science Foundation (NSF)
OSTI Identifier:
1404737
Alternate Identifier(s):
OSTI ID: 1440955
Grant/Contract Number:  
AC02-05CH11231; DMR 1548924; SC0010378; DMR-1437263
Resource Type:
Published Article
Journal Name:
Advanced Structural and Chemical Imaging
Additional Journal Information:
Journal Name: Advanced Structural and Chemical Imaging Journal Volume: 3 Journal Issue: 1; Journal ID: ISSN 2198-0926
Publisher:
Springer
Country of Publication:
Germany
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Scanning transmission electron microscopy; PRISM; Multislice; GPU; CUDA; Electron scattering; Imaging simulation; High performance computing; Atomic electron tomography

Citation Formats

Pryor, Alan, Ophus, Colin, and Miao, Jianwei. A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy. Germany: N. p., 2017. Web. doi:10.1186/s40679-017-0048-z.
Pryor, Alan, Ophus, Colin, & Miao, Jianwei. A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy. Germany. doi:10.1186/s40679-017-0048-z.
Pryor, Alan, Ophus, Colin, and Miao, Jianwei. Wed . "A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy". Germany. doi:10.1186/s40679-017-0048-z.
@article{osti_1404737,
title = {A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy},
author = {Pryor, Alan and Ophus, Colin and Miao, Jianwei},
abstractNote = {Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.},
doi = {10.1186/s40679-017-0048-z},
journal = {Advanced Structural and Chemical Imaging},
number = 1,
volume = 3,
place = {Germany},
year = {2017},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s40679-017-0048-z

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Works referenced in this record:

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography
journal, September 2015

  • Xu, Rui; Chen, Chien-Chun; Wu, Li
  • Nature Materials, Vol. 14, Issue 11
  • DOI: 10.1038/nmat4426

The impact of STEM aberration correction on materials science
journal, September 2017


Quantum mechanical model for phonon excitation in electron diffraction and imaging using a Born-Oppenheimer approximation
journal, September 2010


Electron tomography at 2.4-ångström resolution
journal, March 2012

  • Scott, M. C.; Chen, Chien-Chun; Mecklenburg, Matthew
  • Nature, Vol. 483, Issue 7390
  • DOI: 10.1038/nature10934

STEM_CELL: A software tool for electron microscopy: Part I—simulations
journal, February 2013


GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging
journal, September 2017


Atomic-scale imaging of nanoengineered oxygen vacancy profiles in SrTiO3
journal, August 2004

  • Muller, David A.; Nakagawa, Naoyuki; Ohtomo, Akira
  • Nature, Vol. 430, Issue 7000
  • DOI: 10.1038/nature02756

Image analysis and simulation software in transmission electron microscopy
journal, September 2003


Atomic scale imaging of competing polar states in a Ruddlesden–Popper layered oxide
journal, August 2016

  • Stone, Greg; Ophus, Colin; Birol, Turan
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12572

STEM image simulation with hybrid CPU/GPU programming
journal, July 2016


Dynamics of annular bright field imaging in scanning transmission electron microscopy
journal, June 2010


Method for Retrieval of the Three-Dimensional Object Potential by Inversion of Dynamical Electron Scattering
journal, December 2012


Direct Imaging of Single Au Atoms Within GaAs Nanowires
journal, April 2012

  • Bar-Sadan, Maya; Barthel, Juri; Shtrikman, Hadas
  • Nano Letters, Vol. 12, Issue 5
  • DOI: 10.1021/nl300314k

Benchmarking GPUs to tune dense linear algebra
conference, November 2008

  • Volkov, V.; Demmel, J. W.
  • 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis
  • DOI: 10.1109/SC.2008.5214359

Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures
journal, August 2016

  • Yang, H.; Rutte, R. N.; Jones, L.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12532

Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts
journal, June 2014

  • Yankovich, Andrew B.; Berkels, Benjamin; Dahmen, W.
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5155

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry
journal, February 2016

  • Ophus, Colin; Ciston, Jim; Pierce, Jordan
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10719

Origin of atomic displacement in HAADF image of the tilted specimen
journal, November 2017


Web-Based Electron Microscopy Application Software: Web-EMAPS
journal, August 2004


FDES, a GPU-based multislice algorithm with increased efficiency of the computation of the projected potential
journal, November 2015


A fast image simulation algorithm for scanning transmission electron microscopy
journal, May 2017


Deciphering chemical order/disorder and material properties at the single-atom level
journal, February 2017

  • Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.
  • Nature, Vol. 542, Issue 7639
  • DOI: 10.1038/nature21042

Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution
journal, March 2013

  • Chen, Chien-Chun; Zhu, Chun; White, Edward R.
  • Nature, Vol. 496, Issue 7443
  • DOI: 10.1038/nature12009

Simulation of annular dark field stem images using a modified multislice method
journal, January 1987


Low-dose cryo electron ptychography via non-convex Bayesian optimization
journal, August 2017


A practical approach for STEM image simulation based on the FFT multislice method
journal, February 2002


The Implementation of the 65nm Dual-Core 64b Merom Processor
conference, February 2007

  • Sakran, Nabeel; Yuffe, Marcelo; Mehalel, Moty
  • 2007 IEEE International Solid-State Circuits Conference. Digest of Technical Papers
  • DOI: 10.1109/ISSCC.2007.373610

Quantitative Atomic Resolution Scanning Transmission Electron Microscopy
journal, May 2008


Atomic electron tomography: 3D structures without crystals
journal, September 2016


Unscrambling Mixed Elements using High Angle Annular Dark Field Scanning Transmission Electron Microscopy
journal, June 2016


Progress and new advances in simulating electron microscopy datasets using MULTEM
journal, September 2016


Poisson noise removal from high-resolution STEM images based on periodic block matching
journal, March 2015

  • Mevenkamp, Niklas; Binev, Peter; Dahmen, Wolfgang
  • Advanced Structural and Chemical Imaging, Vol. 1, Issue 1
  • DOI: 10.1186/s40679-015-0004-8

The scattering of electrons by atoms and crystals. I. A new theoretical approach
journal, October 1957


Three-dimensional imaging in double aberration-corrected scanning confocal electron microscopy, Part I:
journal, November 2008


A new theoretical and practical approach to the multislice method
journal, September 1977


The Design and Implementation of FFTW3
journal, February 2005


Sub-ångstrom resolution using aberration corrected electron optics
journal, August 2002

  • Batson, P. E.; Dellby, N.; Krivanek, O. L.
  • Nature, Vol. 418, Issue 6898
  • DOI: 10.1038/nature00972

Scanning transmission electron microscopy*
journal, April 1974


Structure and bonding at the atomic scale by scanning transmission electron microscopy
journal, April 2009


Direct measurement of electron channeling in a crystal using scanning transmission electron microscopy
journal, August 2011