Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

Jesse, S.; Chi, M.; Belianinov, A.; Beekman, C.; Kalinin, S. V.; Borisevich, A. Y.; Lupini, A. R.

doi:10.1038/srep26348

Title: Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

Journal Article · Mon May 23 00:00:00 EDT 2016 · Scientific Reports

DOI:https://doi.org/10.1038/srep26348· OSTI ID:1261280

Jesse, S. ^[1]; Chi, M. ^[1]; Belianinov, A. ^[1]; Beekman, C. ^[2]; Kalinin, S. V. ^[1]; Borisevich, A. Y. ^[3]; Lupini, A. R. ^[3]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Inst. for Functional Imaging of Materials; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Sciences
Florida State Univ., Tallahassee, FL (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Inst. for Functional Imaging of Materials; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Sciences and Technology Division

Electron microscopy is undergoing a transition; from the model of producing only a few micrographs, through the current state where many images and spectra can be digitally recorded, to a new mode where very large volumes of data (movies, ptychographic and multi-dimensional series) can be rapidly obtained. In this paper, we discuss the application of so-called “big-data” methods to high dimensional microscopy data, using unsupervised multivariate statistical techniques, in order to explore salient image features in a specific example of BiFeO₃ domains. Remarkably, k-means clustering reveals domain differentiation despite the fact that the algorithm is purely statistical in nature and does not require any prior information regarding the material, any coexisting phases, or any differentiating structures. While this is a somewhat trivial case, this example signifies the extraction of useful physical and structural information without any prior bias regarding the sample or the instrumental modality. Further interpretation of these types of results may still require human intervention. Finally, however, the open nature of this algorithm and its wide availability, enable broad collaborations and exploratory work necessary to enable efficient data analysis in electron microscopy.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1261280

Journal Information:: Scientific Reports, Vol. 6; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 48 works

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References (49)

Mapping Octahedral Tilts and Polarization Across a Domain Wall in BiFeO ₃ from Z-Contrast Scanning Transmission Electron Microscopy Image Atomic Column Shape Analysis Borisevich, AlbinaY.; Ovchinnikov, Oleg S.; Chang, Hye Jung ACS Nano, Vol. 4, Issue 10 https://doi.org/10.1021/nn1011539	journal	October 2010
Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi APL Materials, Vol. 2, Issue 12 https://doi.org/10.1063/1.4902996	journal	December 2014
Multivariate statistical methods for the analysis of microscope image series: applications in materials science Bonnet, N. Journal of Microscopy, Vol. 190, Issue 1‐2 https://doi.org/10.1046/j.1365-2818.1998.3250876.x	journal	April 1998
Ptychographic microscope for three-dimensional imaging Godden, T. M.; Suman, R.; Humphry, M. J. Optics Express, Vol. 22, Issue 10 https://doi.org/10.1364/OE.22.012513	journal	January 2014
Principal component and spatial correlation analysis of spectroscopic-imaging data in scanning probe microscopy Jesse, Stephen; Kalinin, Sergei V. Nanotechnology, Vol. 20, Issue 8 https://doi.org/10.1088/0957-4484/20/8/085714	journal	February 2009
A Strain-Driven Morphotropic Phase Boundary in BiFeO₃ Zeches, R. J.; Rossell, M. D.; Zhang, J. X. Science, Vol. 326, Issue 5955, p. 977-980 https://doi.org/10.1126/science.1177046	journal	November 2009
Aberration measurement using the Ronchigram contrast transfer function Lupini, A. R.; Wang, P.; Nellist, P. D. Ultramicroscopy, Vol. 110, Issue 7 https://doi.org/10.1016/j.ultramic.2010.04.006	journal	June 2010
Mapping internal structure of coal by confocal micro-Raman spectroscopy and scanning microwave microscopy Tselev, Alexander; Ivanov, Ilia N.; Lavrik, Nickolay V. Fuel, Vol. 126 https://doi.org/10.1016/j.fuel.2014.02.029	journal	June 2014
Ptychography and Related Diffractive Imaging Methods Rodenburg, J. M. Advances in Imaging and Electron Physics https://doi.org/10.1016/S1076-5670(07)00003-1	book	May 2008
Interplay of Octahedral Tilts and Polar Order in BiFeO ₃ Films Kim, Young-Min; Kumar, Amit; Hatt, Alison Advanced Materials, Vol. 25, Issue 17 https://doi.org/10.1002/adma.201204584	journal	March 2013
Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging Humphry, M. J.; Kraus, B.; Hurst, A. C. Nature Communications, Vol. 3, Issue 1 https://doi.org/10.1038/ncomms1733	journal	January 2012
STEM imaging of 47-pm-separated atomic columns by a spherical aberration-corrected electron microscope with a 300-kV cold field emission gun Sawada, H.; Tanishiro, Y.; Ohashi, N. Journal of Electron Microscopy, Vol. 58, Issue 6 https://doi.org/10.1093/jmicro/dfp030	journal	June 2009
Big–deep–smart data in imaging for guiding materials design Kalinin, Sergei V.; Sumpter, Bobby G.; Archibald, Richard K. Nature Materials, Vol. 14, Issue 10 https://doi.org/10.1038/nmat4395	journal	September 2015
Mechanisms for microstructure enhancement in flux-assisted growth of barium titanate on sapphire Burch, Matthew J.; Li, Jing; Harris, David T. Journal of Materials Research, Vol. 29, Issue 7 https://doi.org/10.1557/jmr.2014.59	journal	March 2014
Suppression of Octahedral Tilts and Associated Changes in Electronic Properties at Epitaxial Oxide Heterostructure Interfaces Borisevich, A. Y.; Chang, H. J.; Huijben, M. Physical Review Letters, Vol. 105, Issue 8 https://doi.org/10.1103/PhysRevLett.105.087204	journal	August 2010
Complete information acquisition in dynamic force microscopy Belianinov, Alexei; Kalinin, Sergei V.; Jesse, Stephen Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7550	journal	March 2015
Letter to the Editor: Limitations to the Measurement of Oxygen Concentrations by HRTEM Imposed by Surface Roughness Lupini, Andrew R.; Chisholm, Matthew F.; van Benthem, Klaus Microscopy and Microanalysis, Vol. 11, Issue 2 https://doi.org/10.1017/S1431927605210309	journal	March 2005
Direct observation of ferroelectric field effect and vacancy-controlled screening at the BiFeO3/LaxSr1−xMnO3 interface Kim, Young-Min; Morozovska, Anna; Eliseev, Eugene Nature Materials, Vol. 13, Issue 11 https://doi.org/10.1038/nmat4058	journal	August 2014
Constraining Data Mining with Physical Models: Voltage- and Oxygen Pressure-Dependent Transport in Multiferroic Nanostructures Strelcov, Evgheni; Belianinov, Alexei; Hsieh, Ying-Hui Nano Letters, Vol. 15, Issue 10 https://doi.org/10.1021/acs.nanolett.5b02472	journal	August 2015
Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction Müller, Knut; Krause, Florian F.; Béché, Armand Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6653	journal	December 2014
Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series Dahmen, Tim; Baudoin, Jean-Pierre; Lupini, Andrew R. Microscopy and Microanalysis, Vol. 20, Issue 2 https://doi.org/10.1017/S1431927614000075	journal	February 2014
Direct Observation of Continuous Electric Dipole Rotation in Flux-Closure Domains in Ferroelectric Pb(Zr,Ti)O3 Jia, C. -L.; Urban, K. W.; Alexe, M. Science, Vol. 331, Issue 6023 https://doi.org/10.1126/science.1200605	journal	March 2011
Spontaneous Vortex Nanodomain Arrays at Ferroelectric Heterointerfaces Nelson, Christopher T.; Winchester, Benjamin; Zhang, Yi Nano Letters, Vol. 11, Issue 2 https://doi.org/10.1021/nl1041808	journal	February 2011
Artificial intelligence and pattern recognition techniques in microscope image processing and analysis Bonnet, Noël Advances in Imaging and Electron Physics https://doi.org/10.1016/S1076-5670(00)80020-8	book	January 2000
Oxygen octahedron reconstruction in the ${SrTiO}_{3} / {LaAlO}_{3}$ heterointerfaces investigated using aberration-corrected ultrahigh-resolution transmission electron microscopy Jia, C. L.; Mi, S. B.; Faley, M. Physical Review B, Vol. 79, Issue 8 https://doi.org/10.1103/PhysRevB.79.081405	journal	February 2009
Graphene engineering by neon ion beams Iberi, Vighter; Ievlev, Anton V.; Vlassiouk, Ivan Nanotechnology, Vol. 27, Issue 12 https://doi.org/10.1088/0957-4484/27/12/125302	journal	February 2016
Prominent electrochromism through vacancy-order melting in a complex oxide Seidel, J.; Luo, W.; Suresha, S. J. Nature Communications, Vol. 3, Issue 1 https://doi.org/10.1038/ncomms1799	journal	January 2012
3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography Midgley, P. A.; Weyland, M. Ultramicroscopy, Vol. 96, Issue 3-4 https://doi.org/10.1016/S0304-3991(03)00105-0	journal	September 2003
Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts Yankovich, Andrew B.; Berkels, Benjamin; Dahmen, W. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5155	journal	June 2014
Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution Pennycook, Timothy J.; Lupini, Andrew R.; Yang, Hao Ultramicroscopy, Vol. 151, p. 160-167 https://doi.org/10.1016/j.ultramic.2014.09.013	journal	April 2015
Mapping chemical and bonding information using multivariate analysis of electron energy-loss spectrum images Bosman, M.; Watanabe, M.; Alexander, D. T. L. Ultramicroscopy, Vol. 106, Issue 11-12, p. 1024-1032 https://doi.org/10.1016/j.ultramic.2006.04.016	journal	October 2006
Phase Transitions, Phase Coexistence, and Piezoelectric Switching Behavior in Highly Strained BiFeO ₃ Films Beekman, C.; Siemons, W.; Ward, T. Z. Advanced Materials, Vol. 25, Issue 39 https://doi.org/10.1002/adma.201302066	journal	July 2013
Full information acquisition in piezoresponse force microscopy Somnath, Suhas; Belianinov, Alexei; Kalinin, Sergei V. Applied Physics Letters, Vol. 107, Issue 26 https://doi.org/10.1063/1.4938482	journal	December 2015
Deep Data Analysis of Conductive Phenomena on Complex Oxide Interfaces: Physics from Data Mining Strelcov, Evgheni; Belianinov, Alexei; Hsieh, Ying-Hui ACS Nano, Vol. 8, Issue 6 https://doi.org/10.1021/nn502029b	journal	May 2014
Comment on "Single Crystals of Single-Walled Carbon Nanotubes Formed by Self-Assembly" Chisholm, M. F. Science, Vol. 300, Issue 5623 https://doi.org/10.1126/science.1080395	journal	May 2003
Algorithm AS 136: A K-Means Clustering Algorithm Hartigan, J. A.; Wong, M. A. Applied Statistics, Vol. 28, Issue 1 https://doi.org/10.2307/2346830	journal	January 1979
Control of Octahedral Tilts and Magnetic Properties of Perovskite Oxide Heterostructures by Substrate Symmetry He, Jun; Borisevich, Albina; Kalinin, Sergei V. Physical Review Letters, Vol. 105, Issue 22 https://doi.org/10.1103/PhysRevLett.105.227203	journal	November 2010
Identification of phases, symmetries and defects through local crystallography Belianinov, Alex; He, Qian; Kravchenko, Mikhail Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8801	journal	July 2015
Big data in reciprocal space: Sliding fast Fourier transforms for determining periodicity Vasudevan, Rama K.; Belianinov, Alex; Gianfrancesco, Anthony G. Applied Physics Letters, Vol. 106, Issue 9 https://doi.org/10.1063/1.4914016	journal	March 2015
Multifrequency spectrum analysis using fully digital G Mode-Kelvin probe force microscopy Collins, Liam; Belianinov, Alex; Somnath, Suhas Nanotechnology, Vol. 27, Issue 10 https://doi.org/10.1088/0957-4484/27/10/105706	journal	February 2016
Stress-induced $R - M_{A} - M_{C} - T$ symmetry changes in BiFeO $_{3}$ films Christen, H. M.; Nam, J. H.; Kim, H. S. Physical Review B, Vol. 83, Issue 14 https://doi.org/10.1103/PhysRevB.83.144107	journal	April 2011
Unit-cell scale mapping of ferroelectricity and tetragonality in epitaxial ultrathin ferroelectric films Jia, Chun-Lin; Nagarajan, Valanoor; He, Jia-Qing Nature Materials, Vol. 6, Issue 1 https://doi.org/10.1038/nmat1808	journal	December 2006
Big-Data Reflection High Energy Electron Diffraction Analysis for Understanding Epitaxial Film Growth Processes Vasudevan, Rama K.; Tselev, Alexander; Baddorf, Arthur P. ACS Nano, Vol. 8, Issue 10 https://doi.org/10.1021/nn504730n	journal	October 2014
Atomically Resolved Mapping of Polarization and Electric Fields Across Ferroelectric/Oxide Interfaces by Z-contrast Imaging Chang, Hye Jung; Kalinin, Sergei V.; Morozovska, Anna N. Advanced Materials, Vol. 23, Issue 21 https://doi.org/10.1002/adma.201004641	journal	April 2011
Blind analysis: Hide results to seek the truth MacCoun, Robert; Perlmutter, Saul Nature, Vol. 526, Issue 7572 https://doi.org/10.1038/526187a	journal	October 2015
Detection of Single Atoms and Buried Defects in Three Dimensions by Aberration-Corrected Electron Microscope with 0.5-Å Information Limit Kisielowski, C.; Freitag, B.; Bischoff, M. Microscopy and Microanalysis, Vol. 14, Issue 5 https://doi.org/10.1017/S1431927608080902	journal	September 2008
Probing oxygen vacancy concentration and homogeneity in solid-oxide fuel-cell cathode materials on the subunit-cell level Kim, Young-Min; He, Jun; Biegalski, Michael D. Nature Materials, Vol. 11, Issue 10 https://doi.org/10.1038/nmat3393	journal	August 2012
Single Crystals of Single-Walled Carbon Nanotubes Formed by Self-Assembly Schlittler, R. R. Science, Vol. 292, Issue 5519 https://doi.org/10.1126/science.1057823	journal	April 2001
Erratum: Big data and deep data in scanning and electron microscopies: deriving functionality from multidimensional data sets Belianinov, Alex; Vasudevan, Rama; Strelcov, Evgheni Advanced Structural and Chemical Imaging, Vol. 1, Issue 1 https://doi.org/10.1186/s40679-015-0011-9	journal	August 2015

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