Manifold learning of four-dimensional scanning transmission electron microscopy

Li, Xin; Dyck, Ondrej E.; Oxley, Mark P.; Lupini, Andrew R.; McInnes, Leland; Healy, John; Jesse, Stephen; Kalinin, Sergei V.

doi:10.1038/s41524-018-0139-y

Title: Manifold learning of four-dimensional scanning transmission electron microscopy

Journal Article · Mon Jan 07 00:00:00 EST 2019 · npj Computational Materials

DOI:https://doi.org/10.1038/s41524-018-0139-y· OSTI ID:1491307

Li, Xin ^[1]; Dyck, Ondrej E. ^[1]; Oxley, Mark P. ^[1]; Lupini, Andrew R. ^[1];

^[2]; Healy, John ^[3]; Jesse, Stephen ^[1]; Kalinin, Sergei V. ^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Inst. for Functional Imaging of Materials
Tutte Inst. for Mathematics and Computing, Ottawa (Canada)
Tutte Inst. for Mathematics and Computing, Ottawa (Canada

Four-dimensional scanning transmission electron microscopy (4D-STEM) of local atomic diffraction patterns is emerging as a powerful technique for probing intricate details of atomic structure and atomic electric fields. However, efficient processing and interpretation of large volumes of data remain challenging, especially for two-dimensional or light materials because the diffraction signal recorded on the pixelated arrays is weak. Here we employ data-driven manifold leaning approaches for straightforward visualization and exploration analysis of 4D-STEM datasets, distilling real-space neighboring effects on atomically resolved deflection patterns from single-layer graphene, with single dopant atoms, as recorded on a pixelated detector. These extracted patterns relate to both individual atom sites and sublattice structures, effectively discriminating single dopant anomalies via multi-mode views. We believe manifold learning analysis will accelerate physics discoveries coupled between data-rich imaging mechanisms and materials such as ferroelectric, topological spin, and van der Waals heterostructures.

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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)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1491307

Journal Information:: npj Computational Materials, Vol. 5, Issue 1; ISSN 2057-3960

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 29 works

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References (40)

Nonstandard imaging methods in electron microscopy Rose, H. Ultramicroscopy, Vol. 2 https://doi.org/10.1016/S0304-3991(76)91538-2	journal	January 1976
Modified differential phase contrast Lorentz microscopy for improved imaging of magnetic structures Chapman, J. N.; McFadyen, I. R.; McVitie, S. IEEE Transactions on Magnetics, Vol. 26, Issue 5 https://doi.org/10.1109/20.104427	journal	January 1990
Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography Jesse, S.; Chi, M.; Belianinov, A. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep26348	journal	May 2016
Placing single atoms in graphene with a scanning transmission electron microscope Dyck, Ondrej; Kim, Songkil; Kalinin, Sergei V. Applied Physics Letters, Vol. 111, Issue 11 https://doi.org/10.1063/1.4998599	journal	September 2017
Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback Jesse, Stephen; Hudak, Bethany M.; Zarkadoula, Eva Nanotechnology, Vol. 29, Issue 25 https://doi.org/10.1088/1361-6528/aabb79	journal	April 2018
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
Directed Atom-by-Atom Assembly of Dopants in Silicon Hudak, Bethany M.; Song, Jiaming; Sims, Hunter ACS Nano, Vol. 12, Issue 6 https://doi.org/10.1021/acsnano.8b02001	journal	May 2018
Multiclass spectral clustering ICCV 2003: 9th International Conference on Computer Vision, Proceedings Ninth IEEE International Conference on Computer Vision https://doi.org/10.1109/ICCV.2003.1238361	conference	January 2003
Hierarchical Density Estimates for Data Clustering, Visualization, and Outlier Detection Campello, Ricardo J. G. B.; Moulavi, Davoud; Zimek, Arthur ACM Transactions on Knowledge Discovery from Data, Vol. 10, Issue 1 https://doi.org/10.1145/2733381	journal	July 2015
Visualizing Large-scale and High-dimensional Data Tang, Jian; Liu, Jingzhou; Zhang, Ming Proceedings of the 25th International Conference on World Wide Web - WWW '16 https://doi.org/10.1145/2872427.2883041	conference	January 2016
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
Convergent beam electron holography for analysis of van der Waals heterostructures Latychevskaia, Tatiana; Woods, Colin Robert; Wang, Yi Bo Proceedings of the National Academy of Sciences, Vol. 115, Issue 29 https://doi.org/10.1073/pnas.1722523115	journal	July 2018
Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures Yang, H.; Rutte, R. N.; Jones, L. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12532	journal	August 2016
E-beam manipulation of Si atoms on graphene edges with an aberration-corrected scanning transmission electron microscope Dyck, Ondrej; Kim, Songkil; Kalinin, Sergei V. Nano Research, Vol. 11, Issue 12 https://doi.org/10.1007/s12274-018-2141-6	journal	July 2018
Modelling the inelastic scattering of fast electrons Allen, L. J.; D׳Alfonso, A. J.; Findlay, S. D. Ultramicroscopy, Vol. 151 https://doi.org/10.1016/j.ultramic.2014.10.011	journal	April 2015
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
Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry Ophus, Colin; Ciston, Jim; Pierce, Jordan Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10719	journal	February 2016
Local and transient nanoscale strain mapping during in situ deformation Gammer, C.; Kacher, J.; Czarnik, C. Applied Physics Letters, Vol. 109, Issue 8 https://doi.org/10.1063/1.4961683	journal	August 2016
Differential phase contrast 2.0—Opening new “fields” for an established technique Lohr, Matthias; Schregle, Ralph; Jetter, Michael Ultramicroscopy, Vol. 117 https://doi.org/10.1016/j.ultramic.2012.03.020	journal	June 2012
Manipulating low-dimensional materials down to the level of single atoms with electron irradiation Susi, Toma; Meyer, Jannik C.; Kotakoski, Jani Ultramicroscopy, Vol. 180 https://doi.org/10.1016/j.ultramic.2017.03.005	journal	September 2017
Fire up the atom forge Kalinin, Sergei V.; Borisevich, Albina; Jesse, Stephen Nature, Vol. 539, Issue 7630 https://doi.org/10.1038/539485a	journal	November 2016
Deciphering chemical order/disorder and material properties at the single-atom level Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C. Nature, Vol. 542, Issue 7639 https://doi.org/10.1038/nature21042	journal	February 2017
Mitigating e-beam-induced hydrocarbon deposition on graphene for atomic-scale scanning transmission electron microscopy studies Dyck, Ondrej; Kim, Songkil; Kalinin, Sergei V. Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena, Vol. 36, Issue 1 https://doi.org/10.1116/1.5003034	journal	January 2018
Electron-Beam Manipulation of Silicon Dopants in Graphene Tripathi, Mukesh; Mittelberger, Andreas; Pike, Nicholas A. Nano Letters, Vol. 18, Issue 8 https://doi.org/10.1021/acs.nanolett.8b02406	journal	June 2018
hdbscan: Hierarchical density based clustering McInnes, Leland; Healy, John; Astels, Steve The Journal of Open Source Software, Vol. 2, Issue 11 https://doi.org/10.21105/joss.00205	journal	March 2017
Three-dimensional surface topography of graphene by divergent beam electron diffraction Latychevskaia, Tatiana; Hsu, Wei-Hao; Chang, Wei-Tse Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms14440	journal	February 2017
Differential phase-contrast microscopy at atomic resolution Shibata, Naoya; Findlay, Scott D.; Kohno, Yuji Nature Physics, Vol. 8, Issue 8 https://doi.org/10.1038/nphys2337	journal	June 2012
New area detector for atomic-resolution scanning transmission electron microscopy Shibata, N.; Kohno, Y.; Findlay, S. D. Journal of Electron Microscopy, Vol. 59, Issue 6 https://doi.org/10.1093/jmicro/dfq014	journal	April 2010
The investigation of magnetic domain structures in thin foils by electron microscopy Chapman, J. N. Journal of Physics D: Applied Physics, Vol. 17, Issue 4 https://doi.org/10.1088/0022-3727/17/4/003	journal	April 1984
Direct observation of Σ7 domain boundary core structure in magnetic skyrmion lattice Matsumoto, Takao; So, Yeong-Gi; Kohno, Yuji Science Advances, Vol. 2, Issue 2 https://doi.org/10.1126/sciadv.1501280	journal	February 2016
Random projection trees and low dimensional manifolds Dasgupta, Sanjoy; Freund, Yoav the 40th annual ACM symposium, Proceedings of the fourtieth annual ACM symposium on Theory of computing - STOC 08 https://doi.org/10.1145/1374376.1374452	conference	January 2008
Electric field imaging of single atoms Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15631	journal	May 2017
Electron ptychographic microscopy for three-dimensional imaging Gao, Si; Wang, Peng; Zhang, Fucai Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00150-1	journal	July 2017
High-veracity functional imaging in scanning probe microscopy via Graph-Bootstrapping Li, Xin; Collins, Liam; Miyazawa, Keisuke Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04887-1	journal	June 2018
Imaging of built-in electric field at a p-n junction by scanning transmission electron microscopy Shibata, Naoya; Findlay, Scott D.; Sasaki, Hirokazu Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep10040	journal	June 2015
Efficient k-nearest neighbor graph construction for generic similarity measures Dong, Wei; Moses, Charikar; Li, Kai Proceedings of the 20th international conference on World wide web - WWW '11 https://doi.org/10.1145/1963405.1963487	conference	January 2011
UMAP: Uniform Manifold Approximation and Projection McInnes, Leland; Healy, John; Saul, Nathaniel Journal of Open Source Software, Vol. 3, Issue 29 https://doi.org/10.21105/joss.00861	journal	September 2018
IL-33 expression in response to SARS-CoV-2 correlates with seropositivity in COVID-19 convalescent individuals Stanczak, Michal A.; Sanin, David E.; Apostolova, Petya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22449-w	journal	April 2021
Modified differential phase contrast Lorentz Microscopy for improved imaging of magnetic structures Chapman, J. N.; McFadyen, I. R.; McVitie, S. International Conference on Magnetics https://doi.org/10.1109/intmag.1990.734268	conference	January 1990
Convergent beam electron holography for analysis of van der Waals heterostructures Latychevskaia, Tatiana; Woods, Colin Robert; Wang, Yi Bo arXiv https://doi.org/10.48550/arxiv.1807.01927	text	January 2018

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