Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition
Abstract
Tensor singular value decomposition (SVD) is a method to find a low-dimensional representation of data with meaningful structure in three or more dimensions. Here, tensor SVD has been applied to denoise atomic-resolution 4D scanning transmission electron microscopy (4D STEM) data. On data simulated from a SrTiO3 [100] perfect crystal and a Si [110] edge dislocation, tensor SVD achieved an average peak signal-to-noise ratio (PSNR) of ~40 dB, which matches or exceeds the performance of other denoising methods, with processing times at least 100 times shorter. On experimental data from SrTiO3 [100] and LiZnSb [11 0]/GaSb [110] samples, tensor SVD denoises multiple GB 4D STEM data sets in ten minutes on a typical personal computer. Denoising with tensor SVD improves both convergent beam electron diffraction patterns and virtual-aperture annular dark field images.
- Authors:
-
- Univ. of Wisconsin, Madison, WI (United States). Dept. of Materials Science and Engineering
- Univ. of Wisconsin, Madison, WI (United States). Dept. of Statistics
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institutes of Health (NIH)
- OSTI Identifier:
- 1849893
- Alternate Identifier(s):
- OSTI ID: 1809538
- Grant/Contract Number:
- FG02-08ER46547; DMS-1811868; CAREER-1944904; DMR-1720415; R01-GM131399
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Ultramicroscopy
- Additional Journal Information:
- Journal Volume: 219; Journal Issue: C; Journal ID: ISSN 0304-3991
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 42 ENGINEERING; 36 MATERIALS SCIENCE; microscopy; scanning transmission electron microscopy; convergent beam electron diffraction; image denoising; low-rank tensor
Citation Formats
Zhang, Chenyu, Han, Rungang, Zhang, Anru R., and Voyles, Paul. M. Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition. United States: N. p., 2020.
Web. doi:10.1016/j.ultramic.2020.113123.
Zhang, Chenyu, Han, Rungang, Zhang, Anru R., & Voyles, Paul. M. Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition. United States. https://doi.org/10.1016/j.ultramic.2020.113123
Zhang, Chenyu, Han, Rungang, Zhang, Anru R., and Voyles, Paul. M. Mon .
"Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition". United States. https://doi.org/10.1016/j.ultramic.2020.113123. https://www.osti.gov/servlets/purl/1849893.
@article{osti_1849893,
title = {Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition},
author = {Zhang, Chenyu and Han, Rungang and Zhang, Anru R. and Voyles, Paul. M.},
abstractNote = {Tensor singular value decomposition (SVD) is a method to find a low-dimensional representation of data with meaningful structure in three or more dimensions. Here, tensor SVD has been applied to denoise atomic-resolution 4D scanning transmission electron microscopy (4D STEM) data. On data simulated from a SrTiO3 [100] perfect crystal and a Si [110] edge dislocation, tensor SVD achieved an average peak signal-to-noise ratio (PSNR) of ~40 dB, which matches or exceeds the performance of other denoising methods, with processing times at least 100 times shorter. On experimental data from SrTiO3 [100] and LiZnSb [112¯0]/GaSb [110] samples, tensor SVD denoises multiple GB 4D STEM data sets in ten minutes on a typical personal computer. Denoising with tensor SVD improves both convergent beam electron diffraction patterns and virtual-aperture annular dark field images.},
doi = {10.1016/j.ultramic.2020.113123},
journal = {Ultramicroscopy},
number = C,
volume = 219,
place = {United States},
year = {Mon Oct 05 00:00:00 EDT 2020},
month = {Mon Oct 05 00:00:00 EDT 2020}
}
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Works referenced in this record:
Multitask Sparse Nonnegative Matrix Factorization for Joint Spectral–Spatial Hyperspectral Imagery Denoising
journal, May 2015
- Ye, Minchao; Qian, Yuntao; Zhou, Jun
- IEEE Transactions on Geoscience and Remote Sensing, Vol. 53, Issue 5
Atomic resolution convergent beam electron diffraction analysis using convolutional neural networks
journal, March 2020
- Zhang, Chenyu; Feng, Jie; DaCosta, Luis Rangel
- Ultramicroscopy, Vol. 210
Method to measure spatial coherence of subangstrom electron beams
journal, July 2008
- Dwyer, Christian; Erni, Rolf; Etheridge, Joanne
- Applied Physics Letters, Vol. 93, Issue 2
Quantitative characterization of nanoprecipitates in irradiated low-alloy steels: advances in the application of FEG-STEM quantitative microanalysis to real materials
journal, July 2006
- Burke, M. G.; Watanabe, M.; Williams, D. B.
- Journal of Materials Science, Vol. 41, Issue 14
Tensor SVD: Statistical and Computational Limits
journal, November 2018
- Zhang, Anru; Xia, Dong
- IEEE Transactions on Information Theory, Vol. 64, Issue 11
Total Variation Regularized Reweighted Sparse Nonnegative Matrix Factorization for Hyperspectral Unmixing
journal, July 2017
- He, Wei; Zhang, Hongyan; Zhang, Liangpei
- IEEE Transactions on Geoscience and Remote Sensing, Vol. 55, Issue 7
Chemical mapping of a block copolymer electrolyte by low-loss EFTEM spectrum-imaging and principal component analysis
journal, February 2011
- Allen, F. I.; Watanabe, M.; Lee, Z.
- Ultramicroscopy, Vol. 111, Issue 3
Hyperspectral image restoration using framelet-regularized low-rank nonnegative matrix factorization
journal, November 2018
- Chen, Yong; Huang, Ting-Zhu; Zhao, Xi-Le
- Applied Mathematical Modelling, Vol. 63
Principal component analysis
journal, August 1987
- Wold, Svante; Esbensen, Kim; Geladi, Paul
- Chemometrics and Intelligent Laboratory Systems, Vol. 2, Issue 1-3
The global k-means clustering algorithm
journal, February 2003
- Likas, Aristidis; Vlassis, Nikos; J. Verbeek, Jakob
- Pattern Recognition, Vol. 36, Issue 2
Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
journal, May 2013
- Li, Xueming; Mooney, Paul; Zheng, Shawn
- Nature Methods, Vol. 10, Issue 6
Phase reconstruction using fast binary 4D STEM data
journal, March 2020
- O'Leary, C. M.; Allen, C. S.; Huang, C.
- Applied Physics Letters, Vol. 116, Issue 12
Noise Reduction of Hyperspectral Images Using Kernel Non-Negative Tucker Decomposition
journal, June 2011
- Karami, A.; Yazdi, M.; Zolghadre Asli, Alireza
- IEEE Journal of Selected Topics in Signal Processing, Vol. 5, Issue 3
Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering
journal, August 2007
- Dabov, Kostadin; Foi, Alessandro; Katkovnik, Vladimir
- IEEE Transactions on Image Processing, Vol. 16, Issue 8
An adaptive rank-sparsity K-SVD algorithm for image sequence denoising
journal, August 2014
- Kuang, Yin; Zhang, Lei; Yi, Zhang
- Pattern Recognition Letters, Vol. 45
Optimal Sparse Singular Value Decomposition for High-Dimensional High-Order Data
journal, March 2019
- Zhang, Anru; Han, Rungang
- Journal of the American Statistical Association, Vol. 114, Issue 528
Control of polymorphism during epitaxial growth of hyperferroelectric candidate LiZnSb on GaSb (111)B
journal, March 2020
- Du, Dongxue; Strohbeen, Patrick J.; Paik, Hanjong
- Journal of Vacuum Science & Technology B, Vol. 38, Issue 2
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
Structure change of Ca 1− x Sr x TiO 3 perovskite with composition and pressure
journal, August 2002
- Yamanaka, Takamitsu; Hirai, Noriyuki; Komatsu, Yutaka
- American Mineralogist, Vol. 87, Issue 8-9
High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy
journal, January 2016
- Tate, Mark W.; Purohit, Prafull; Chamberlain, Darol
- Microscopy and Microanalysis, Vol. 22, Issue 1
On the Best Rank-1 and Rank-( R 1 , R 2 ,. . ., R N ) Approximation of Higher-Order Tensors
journal, January 2000
- De Lathauwer, Lieven; De Moor, Bart; Vandewalle, Joos
- SIAM Journal on Matrix Analysis and Applications, Vol. 21, Issue 4
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
Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond
journal, May 2019
- Ophus, Colin
- Microscopy and Microanalysis, Vol. 25, Issue 3
Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction
journal, December 2014
- Müller, Knut; Krause, Florian F.; Béché, Armand
- Nature Communications, Vol. 5, Issue 1
EELS elemental mapping with unconventional methods I. Theoretical basis: Image analysis with multivariate statistics and entropy concepts
journal, December 1990
- Trebbia, Pierre; Bonnet, Noël
- Ultramicroscopy, Vol. 34, Issue 3
Denoising time-resolved microscopy image sequences with singular value thresholding
journal, July 2017
- Furnival, Tom; Leary, Rowan K.; Midgley, Paul A.
- Ultramicroscopy, Vol. 178
Direct observation of Σ7 domain boundary core structure in magnetic skyrmion lattice
journal, February 2016
- Matsumoto, Takao; So, Yeong-Gi; Kohno, Yuji
- Science Advances, Vol. 2, Issue 2
Convergent beam electron diffraction of multilayer Van der Waals structures
journal, May 2020
- Latychevskaia, Tatiana; Woods, Colin Robert; Wang, Yi Bo
- Ultramicroscopy, Vol. 212
Nonlocal Transform-Domain Filter for Volumetric Data Denoising and Reconstruction
journal, January 2013
- Maggioni, M.; Katkovnik, V.; Egiazarian, K.
- IEEE Transactions on Image Processing, Vol. 22, Issue 1
Automatic denoising of functional MRI data: Combining independent component analysis and hierarchical fusion of classifiers
journal, April 2014
- Salimi-Khorshidi, Gholamreza; Douaud, Gwenaëlle; Beckmann, Christian F.
- NeuroImage, Vol. 90
On the Tensor SVD and the Optimal Low Rank Orthogonal Approximation of Tensors
journal, January 2009
- Chen, Jie; Saad, Yousef
- SIAM Journal on Matrix Analysis and Applications, Vol. 30, Issue 4
Video Denoising, Deblocking, and Enhancement Through Separable 4-D Nonlocal Spatiotemporal Transforms
journal, September 2012
- Maggioni, Matteo; Boracchi, Giacomo; Foi, Alessandro
- IEEE Transactions on Image Processing, Vol. 21, Issue 9
Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage
journal, July 2020
- Nord, Magnus; Webster, Robert W. H.; Paton, Kirsty A.
- Microscopy and Microanalysis, Vol. 26, Issue 4
Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy
journal, December 2014
- McMullan, G.; Faruqi, A. R.; Clare, D.
- Ultramicroscopy, Vol. 147
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
MULTIVARIATE STATISTICAL ANALYSIS OF FEG-STEM EDX SPECTRA
journal, December 1996
- Titchmarsh, J. M.; Dumbill, S.
- Journal of Microscopy, Vol. 184, Issue 3
Mapping chemical and bonding information using multivariate analysis of electron energy-loss spectrum images
journal, October 2006
- Bosman, M.; Watanabe, M.; Alexander, D. T. L.
- Ultramicroscopy, Vol. 106, Issue 11-12, p. 1024-1032
Observation of three-dimensional elemental distributions of a Si device using a 360°-tilt FIB and the cold field-emission STEM system
journal, November 2008
- Yaguchi, Toshie; Konno, Mitsuru; Kamino, Takeo
- Ultramicroscopy, Vol. 108, Issue 12, p. 1603-1615
Non-rigid registration and non-local principle component analysis to improve electron microscopy spectrum images
journal, August 2016
- Yankovich, Andrew B.; Zhang, Chenyu; Oh, Albert
- Nanotechnology, Vol. 27, Issue 36
On the Origin of Nanochessboard Superlattices in A-Site-Deficient Ca-Stabilized Nd 2/3 TiO 3
journal, January 2015
- Azough, Feridoon; Kepaptsoglou, Demie; Ramasse, Quentin M.
- Chemistry of Materials, Vol. 27, Issue 2
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
Measurement of effective source distribution and its importance for quantitative interpretation of STEM images
journal, July 2010
- Dwyer, C.; Erni, R.; Etheridge, J.
- Ultramicroscopy, Vol. 110, Issue 8
Independent component analysis: algorithms and applications
journal, June 2000
- Hyvärinen, A.; Oja, E.
- Neural Networks, Vol. 13, Issue 4-5
Fluctuation microscopy in the STEM
journal, November 2002
- Voyles, P. M.; Muller, D. A.
- Ultramicroscopy, Vol. 93, Issue 2
Informatics and data science in materials microscopy
journal, June 2017
- Voyles, Paul M.
- Current Opinion in Solid State and Materials Science, Vol. 21, Issue 3
Algorithms and applications for approximate nonnegative matrix factorization
journal, September 2007
- Berry, Michael W.; Browne, Murray; Langville, Amy N.
- Computational Statistics & Data Analysis, Vol. 52, Issue 1
Sub-100 nanosecond temporally resolved imaging with the Medipix3 direct electron detector
journal, March 2020
- Paterson, Gary W.; Lamb, Raymond J.; Ballabriga, Rafael
- Ultramicroscopy, Vol. 210
Direct determination of structural heterogeneity in metallic glasses using four-dimensional scanning transmission electron microscopy
journal, December 2018
- Im, Soohyun; Chen, Zhen; Johnson, Jared M.
- Ultramicroscopy, Vol. 195