Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations

Abstract

Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the conventional multislice algorithm to perform these simulations can require extremely large calculation times, particularly for experiments with millions of probe positions as each probe position must be simulated independently. Recently, the plane-wave reciprocal-space interpolated scattering matrix (PRISM) algorithm was developed to reduce calculation times for large STEM simulations. Here, we introduce a new method for STEM simulation: partitioning of the STEM probe into “beamlets,” given by a natural neighbor interpolation of the parent beams. This idea is compatible with PRISM simulations and can lead to even larger improvements in simulation time, as well requiring significantly less computer random access memory (RAM). We have performed various simulations to demonstrate the advantages and disadvantages of partitioned PRISM STEM simulations. We find that this new algorithm is particularly useful for 4D-STEM simulations of large fields of view. We also provide a reference implementation of the multislice, PRISM, and partitioned PRISM algorithms.

Authors:
 [1];  [2]; ORCiD logo [1];  [2];  [1]; ORCiD logo [2]
+ Show Author Affiliations
  1. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for Electron Microscopy
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for Electron Microscopy
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1815403
Alternate Identifier(s):
OSTI ID: 1819865
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Microscopy and Microanalysis
Additional Journal Information:
Journal Volume: 27; Journal Issue: 4; Journal ID: ISSN 1431-9276
Publisher:
Microscopy Society of America (MSA)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; electron scattering; open source; scanning transmission electron microscopy; simulation; transmission electron microscopy

Citation Formats

Pelz, Philipp M., Rakowski, Alexander, Rangel DaCosta, Luis, Savitzky, Benjamin H., Scott, Mary C., and Ophus, Colin. A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations. United States: N. p., 2021. Web. doi:10.1017/s1431927621012083.
Copy to clipboard
Pelz, Philipp M., Rakowski, Alexander, Rangel DaCosta, Luis, Savitzky, Benjamin H., Scott, Mary C., & Ophus, Colin. A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations. United States. https://doi.org/10.1017/s1431927621012083
Copy to clipboard
Pelz, Philipp M., Rakowski, Alexander, Rangel DaCosta, Luis, Savitzky, Benjamin H., Scott, Mary C., and Ophus, Colin. Tue . "A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations". United States. https://doi.org/10.1017/s1431927621012083. https://www.osti.gov/servlets/purl/1815403.
Copy to clipboard
@article{osti_1815403,
title = {A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations},
author = {Pelz, Philipp M. and Rakowski, Alexander and Rangel DaCosta, Luis and Savitzky, Benjamin H. and Scott, Mary C. and Ophus, Colin},
abstractNote = {Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the conventional multislice algorithm to perform these simulations can require extremely large calculation times, particularly for experiments with millions of probe positions as each probe position must be simulated independently. Recently, the plane-wave reciprocal-space interpolated scattering matrix (PRISM) algorithm was developed to reduce calculation times for large STEM simulations. Here, we introduce a new method for STEM simulation: partitioning of the STEM probe into “beamlets,” given by a natural neighbor interpolation of the parent beams. This idea is compatible with PRISM simulations and can lead to even larger improvements in simulation time, as well requiring significantly less computer random access memory (RAM). We have performed various simulations to demonstrate the advantages and disadvantages of partitioned PRISM STEM simulations. We find that this new algorithm is particularly useful for 4D-STEM simulations of large fields of view. We also provide a reference implementation of the multislice, PRISM, and partitioned PRISM algorithms.},
doi = {10.1017/s1431927621012083},
journal = {Microscopy and Microanalysis},
number = 4,
volume = 27,
place = {United States},
year = {Tue Jul 06 00:00:00 EDT 2021},
month = {Tue Jul 06 00:00:00 EDT 2021}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1017/s1431927621012083
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Structure refinement from ‘digital’ large angle convergent beam electron diffraction patterns
journal, March 2019

Computation in electron microscopy
journal, January 2016

  • Kirkland, Earl J.
  • Acta Crystallographica Section A Foundations and Advances, Vol. 72, Issue 1
  • DOI: 10.1107/S205327331501757X

Scattered data interpolation methods for electronic imaging systems: a survey
journal, April 2002

  • Amidror, Isaac
  • Journal of Electronic Imaging, Vol. 11, Issue 2
  • DOI: 10.1117/1.1455013

Benchmark test of accelerated multi-slice simulation by GPGPU
journal, November 2015

Lattice-resolution contrast from a focused coherent electron probe. Part I
journal, July 2003

Random vs realistic amorphous carbon models for high resolution microscopy and electron diffraction
journal, December 2013

  • Ricolleau, C.; Le Bouar, Y.; Amara, H.
  • Journal of Applied Physics, Vol. 114, Issue 21
  • DOI: 10.1063/1.4831669

STEMcl–A multi-GPU multislice algorithm for simulation of large structure and imaging parameter series
journal, May 2018

Improving the Speed and Accuracy of Large-scale Scanning Transmission Electron Microscopy (STEM) Electron Scattering Simulations
journal, July 2020

  • Ophus, Colin; Brown, Hamish; Dacosta, Luis Rangel
  • Microscopy and Microanalysis, Vol. 26, Issue S2
  • DOI: 10.1017/S1431927620014725

Theorie der Beugung von Elektronen an Kristallen
journal, January 1928

Linear-scaling algorithm for rapid computation of inelastic transitions in the presence of multiple electron scattering
journal, December 2019

Strain mapping at nanometer resolution using advanced nano-beam electron diffraction
journal, June 2015

  • Ozdol, V. B.; Gammer, C.; Jin, X. G.
  • Applied Physics Letters, Vol. 106, Issue 25
  • DOI: 10.1063/1.4922994

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

Patterned probes for high precision 4D-STEM bragg measurements
journal, February 2020

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy
journal, October 2017

  • Pryor, Alan; Ophus, Colin; Miao, Jianwei
  • Advanced Structural and Chemical Imaging, Vol. 3, Issue 1
  • DOI: 10.1186/s40679-017-0048-z

Dr. Probe: A software for high-resolution STEM image simulation
journal, October 2018

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

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

A Python Based Open-source Multislice Simulation Package for Transmission Electron Microscopy
journal, July 2020

Scattering Matrix Determination in Crystalline Materials from 4D Scanning Transmission Electron Microscopy at a Single Defocus Value
journal, July 2021

  • Findlay, Scott D.; Brown, Hamish G.; Pelz, Philipp M.
  • Microscopy and Microanalysis, Vol. 27, Issue 4
  • DOI: 10.1017/S1431927621000490

cloudEMAPS: A Cloud Computing Environment for Electron Microscopy Application Simulations
journal, January 2021

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis
journal, May 2021

Transmission Electron Microscopy
book, January 2009

An efficient way of including thermal diffuse scattering in simulation of scanning transmission electron microscopic images
journal, August 2006

Using electron vortex beams to determine chirality of crystals in transmission electron microscopy
journal, March 2015

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

Modification of the multislice method for calculating coherent STEM images
journal, July 1995

  • Chen, J. H.; Van Dyck, D.; de Beeck, M. Op
  • Physica Status Solidi (a), Vol. 150, Issue 1
  • DOI: 10.1002/pssa.2211500103

Advanced Computing in Electron Microscopy
book, January 2020

Lattice-resolution contrast from a focused coherent electron probe. Part II
journal, July 2003

abTEM: ab Initio Transmission Electron Microscopy Image Simulation
journal, July 2020

Modelling the inelastic scattering of fast electrons
journal, April 2015

Optimizing disk registration algorithms for nanobeam electron diffraction strain mapping
journal, May 2017

Phase Contrast Imaging in Thick, Heterogeneous Samples via S-Matrix Phase Retrieval and Depth Sectioning
journal, July 2020

  • Pelz, Philipp; Brown, Hamish; Findlay, Scott
  • Microscopy and Microanalysis, Vol. 26, Issue S2
  • DOI: 10.1017/S1431927620014749

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

Diffraction imaging of nanocrystalline structures in organic semiconductor molecular thin films
journal, June 2019

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

Towards data-driven next-generation transmission electron microscopy
journal, October 2020

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

Electron ptychography achieves atomic-resolution limits set by lattice vibrations
journal, May 2021

    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: