A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation

Brown, Hamish G.; Pelz, Philipp M.; Hsu, Shang-Lin; Zhang, Zimeng; Ramesh, Ramamoorthy; Inzani, Katherine; Sheridan, Evan; Griffin, Sinéad M.; Schloz, Marcel; Pekin, Thomas C.; Koch, Christoph T.; Findlay, Scott D.; Allen, Leslie J.; Scott, Mary C.; Ophus, Colin; Ciston, Jim

doi:10.1017/S1431927622012090

Title: A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation

Abstract

Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. In this work, we present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data. We apply the approach to a lead iridate, Pb₂Ir₂O₇, and yttrium-stabilized zirconia, Y_0.095Zr_0.905O₂, heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction. We demonstrate that Pb-Ir atomic columns are visible in the uppermost layers of the reconstructed volume. We compare this approach to the alternative techniques of depth sectioning using differential phase contrast scanning transmission electron microscopy (DPC-STEM) and multislice ptychographic reconstruction.

Authors:

; Pelz, Philipp M.; Hsu, Shang-Lin; Zhang, Zimeng; Ramesh, Ramamoorthy; Inzani, Katherine; Sheridan, Evan; Griffin, Sinéad M.; Schloz, Marcel; Pekin, Thomas C.;

;

; Allen, Leslie J.; Scott, Mary C.; Ophus, Colin; Ciston, Jim

Publication Date:: Sat Oct 01 00:00:00 EDT 2022

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; USDOE Laboratory Directed Research and Development (LDRD) Program; US Air Force Office of Scientific Research (AFOSR); Australian Research Council; German Research Foundation (DFG)

OSTI Identifier:: 1914336

Alternate Identifier(s):: OSTI ID: 1894632

Grant/Contract Number:: Contract number DE-AC02-05CH11231; AC02-05CH11231; FA9550-18-1-0480; FT190100619; 414984028 - SFB 1404

Resource Type:: Published Article

Journal Name:: Microscopy and Microanalysis

Additional Journal Information:: Journal Name: Microscopy and Microanalysis Journal Volume: 28 Journal Issue: 5; Journal ID: ISSN 1431-9276

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Subject:: 47 OTHER INSTRUMENTATION; Scanning transmission electron microscopy; Image reconstruction; Ptychography; Differential phase contrast

Citation Formats


                    Brown, Hamish G., Pelz, Philipp M., Hsu, Shang-Lin, Zhang, Zimeng, Ramesh, Ramamoorthy, Inzani, Katherine, Sheridan, Evan, Griffin, Sinéad M., Schloz, Marcel, Pekin, Thomas C., Koch, Christoph T., Findlay, Scott D., Allen, Leslie J., Scott, Mary C., Ophus, Colin, and Ciston, Jim. A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation.  United States: N. p., 2022. 
Web.  doi:10.1017/S1431927622012090.

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                    Brown, Hamish G., Pelz, Philipp M., Hsu, Shang-Lin, Zhang, Zimeng, Ramesh, Ramamoorthy, Inzani, Katherine, Sheridan, Evan, Griffin, Sinéad M., Schloz, Marcel, Pekin, Thomas C., Koch, Christoph T., Findlay, Scott D., Allen, Leslie J., Scott, Mary C., Ophus, Colin, & Ciston, Jim. A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation.  United States.  https://doi.org/10.1017/S1431927622012090

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                    Brown, Hamish G., Pelz, Philipp M., Hsu, Shang-Lin, Zhang, Zimeng, Ramesh, Ramamoorthy, Inzani, Katherine, Sheridan, Evan, Griffin, Sinéad M., Schloz, Marcel, Pekin, Thomas C., Koch, Christoph T., Findlay, Scott D., Allen, Leslie J., Scott, Mary C., Ophus, Colin, and Ciston, Jim. Sat .  
"A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation".  United States.  https://doi.org/10.1017/S1431927622012090.

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@article{osti_1914336,

  title        = {A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation},

  author       = {Brown, Hamish G. and Pelz, Philipp M. and Hsu, Shang-Lin and Zhang, Zimeng and Ramesh, Ramamoorthy and Inzani, Katherine and Sheridan, Evan and Griffin, Sinéad M. and Schloz, Marcel and Pekin, Thomas C. and Koch, Christoph T. and Findlay, Scott D. and Allen, Leslie J. and Scott, Mary C. and Ophus, Colin and Ciston, Jim},

  abstractNote = {Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. In this work, we present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data. We apply the approach to a lead iridate, Pb2Ir2O7, and yttrium-stabilized zirconia, Y0.095Zr0.905O2, heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction. We demonstrate that Pb-Ir atomic columns are visible in the uppermost layers of the reconstructed volume. We compare this approach to the alternative techniques of depth sectioning using differential phase contrast scanning transmission electron microscopy (DPC-STEM) and multislice ptychographic reconstruction.},

  doi          = {10.1017/S1431927622012090},

  journal      = {Microscopy and Microanalysis},

  number       = 5,

  volume       = 28,

  place        = {United States},

  year         = {Sat Oct 01 00:00:00 EDT 2022},

  month        = {Sat Oct 01 00:00:00 EDT 2022}

}

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Title: A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation

Abstract

Citation Formats

Phase retrieval with transverse translation diversity: a nonlinear optimization approach journal, January 2008

Light-emitting diodes by band-structure engineering in van der Waals heterostructures journal, February 2015

Ptychographic transmission microscopy in three dimensions using a multi-slice approach journal, January 2012

A quantitative analysis of the cone-angle dependence in precession electron diffraction journal, May 2008

Maximum-likelihood refinement for coherent diffractive imaging journal, June 2012

Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization journal, January 2020

Observation of polar vortices in oxide superlattices journal, January 2016

Quantitative structure retrieval using scanning transmission electron microscopy journal, June 2005

Phase-contrast imaging of multiply-scattering extended objects at atomic resolution by reconstruction of the scattering matrix journal, May 2021

Electron ptychographic phase imaging of light elements in crystalline materials using Wigner distribution deconvolution journal, September 2017

Advanced Phase Reconstruction Methods Enabled by Four-Dimensional Scanning Transmission Electron Microscopy journal, August 2019

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

Direct Inversion of Dynamical Electron Diffraction Patterns to Structure Factors journal, January 1998

Three-dimensional ADF imaging of individual atoms by through-focal series scanning transmission electron microscopy journal, October 2006

Design and synthesis of multigrain nanocrystals via geometric misfit strain journal, January 2020

Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution journal, April 2015

Solving Systems of Random Quadratic Equations via Truncated Amplitude Flow journal, February 2018

Resolution beyond the 'information limit' in transmission electron microscopy journal, April 1995

Analysis of depth-sectioning STEM for thick samples and 3D imaging journal, December 2019

Breaking the Rayleigh Limit in Thick Samples with Multi-slice Ptychography journal, August 2018

Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting journal, February 2017

Practical aspects of diffractive imaging using an atomic-scale coherent electron probe journal, October 2016

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

Oxide pyrochlores — A review journal, January 1983

Electric field imaging of single atoms journal, May 2017

The Quantum Theory of Fields book, May 2013

Structure Retrieval at Atomic Resolution in the Presence of Multiple Scattering of the Electron Probe journal, December 2018

Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data journal, August 2020

The Calculation of Electron Diffraction Intensities journal, August 1962

Electron ptychographic microscopy for three-dimensional imaging journal, July 2017

Electron ptychography of 2D materials to deep sub-ångström resolution journal, July 2018

New area detector for atomic-resolution scanning transmission electron microscopy journal, April 2010

Experimental tests on double-resolution coherent imaging via STEM journal, March 1993

Inversion of dynamical electron diffraction data including absorption journal, March 2000

Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond journal, May 2019

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

Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons journal, December 2015

Aberration-corrected ADF-STEM depth sectioning and prospects for reliable 3D imaging in S/TEM journal, January 2009

Inelastic scattering of high-energy electrons in real space journal, October 1990

Fourier Images: II - The Out-of-focus Patterns journal, May 1957

Position averaged convergent beam electron diffraction: Theory and applications journal, January 2010

Phase retrieval with transverse translation diversity: a nonlinear optimization approach
journal, January 2008

Light-emitting diodes by band-structure engineering in van der Waals heterostructures
journal, February 2015

Ptychographic transmission microscopy in three dimensions using a multi-slice approach
journal, January 2012

A quantitative analysis of the cone-angle dependence in precession electron diffraction
journal, May 2008

Maximum-likelihood refinement for coherent diffractive imaging
journal, June 2012

Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization
journal, January 2020

Observation of polar vortices in oxide superlattices
journal, January 2016

Quantitative structure retrieval using scanning transmission electron microscopy
journal, June 2005

Phase-contrast imaging of multiply-scattering extended objects at atomic resolution by reconstruction of the scattering matrix
journal, May 2021

Electron ptychographic phase imaging of light elements in crystalline materials using Wigner distribution deconvolution
journal, September 2017

Advanced Phase Reconstruction Methods Enabled by Four-Dimensional Scanning Transmission Electron Microscopy
journal, August 2019

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

Direct Inversion of Dynamical Electron Diffraction Patterns to Structure Factors
journal, January 1998

Three-dimensional ADF imaging of individual atoms by through-focal series scanning transmission electron microscopy
journal, October 2006

Design and synthesis of multigrain nanocrystals via geometric misfit strain
journal, January 2020

Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution
journal, April 2015

Solving Systems of Random Quadratic Equations via Truncated Amplitude Flow
journal, February 2018

Resolution beyond the 'information limit' in transmission electron microscopy
journal, April 1995

Analysis of depth-sectioning STEM for thick samples and 3D imaging
journal, December 2019

Breaking the Rayleigh Limit in Thick Samples with Multi-slice Ptychography
journal, August 2018

Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting
journal, February 2017

Practical aspects of diffractive imaging using an atomic-scale coherent electron probe
journal, October 2016

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

Oxide pyrochlores — A review
journal, January 1983

Electric field imaging of single atoms
journal, May 2017

The Quantum Theory of Fields
book, May 2013

Structure Retrieval at Atomic Resolution in the Presence of Multiple Scattering of the Electron Probe
journal, December 2018

Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data
journal, August 2020

The Calculation of Electron Diffraction Intensities
journal, August 1962

Electron ptychographic microscopy for three-dimensional imaging
journal, July 2017

Electron ptychography of 2D materials to deep sub-ångström resolution
journal, July 2018

New area detector for atomic-resolution scanning transmission electron microscopy
journal, April 2010

Experimental tests on double-resolution coherent imaging via STEM
journal, March 1993

Inversion of dynamical electron diffraction data including absorption
journal, March 2000

Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond
journal, May 2019

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

Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons
journal, December 2015

Aberration-corrected ADF-STEM depth sectioning and prospects for reliable 3D imaging in S/TEM
journal, January 2009

Inelastic scattering of high-energy electrons in real space
journal, October 1990

Fourier Images: II - The Out-of-focus Patterns
journal, May 1957

Position averaged convergent beam electron diffraction: Theory and applications
journal, January 2010