Image registration of low signal-to-noise cryo-STEM data

Savitzky, Benjamin H.; El Baggari, Ismail; Clement, Colin B.; Waite, Emily; Goodge, Berit H.; Baek, David J.; Sheckelton, John P.; Pasco, Christopher; Nair, Hari; Schreiber, Nathaniel J.; Hoffman, Jason; Admasu, Alemayehu S.; Kim, Jaewook; Cheong, Sang -Wook; Bhattacharya, Anand; Schlom, Darrell G.; McQueen, Tyrel M.; Hovden, Robert; Kourkoutis, Lena F.

doi:10.1016/j.ultramic.2018.04.008

Title: Image registration of low signal-to-noise cryo-STEM data

Journal Article · Fri Apr 27 00:00:00 EDT 2018 · Ultramicroscopy

DOI:https://doi.org/10.1016/j.ultramic.2018.04.008· OSTI ID:1479486

Savitzky, Benjamin H. ^[1]; El Baggari, Ismail ^[1]; Clement, Colin B. ^[1]; Waite, Emily ^[1];

^[1]; Baek, David J. ^[1]; Sheckelton, John P. ^[2];

^[2]; Nair, Hari ^[1]; Schreiber, Nathaniel J. ^[1]; Hoffman, Jason ^[3]; Admasu, Alemayehu S. ^[4]; Kim, Jaewook ^[4]; Cheong, Sang -Wook ^[4]; Bhattacharya, Anand ^[5]; Schlom, Darrell G. ^[1]; McQueen, Tyrel M. ^[2]; Hovden, Robert ^[6]; Kourkoutis, Lena F. ^[1]

Cornell Univ., Ithaca, NY (United States)
The Johns Hopkins Univ., Baltimore, MD (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); Harvard Univ., Cambridge, MA (United States)
Rutgers Univ., Piscataway, NJ (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
Cornell Univ., Ithaca, NY (United States); Univ. of Michigan, Ann Arbor, MI (United States)

Combining multiple fast image acquisitions to mitigate scan noise and drift artifacts has proven essential for picometer precision, quantitative analysis of atomic resolution scanning transmission electron microscopy (STEM) data. For very low signal-to-noise ratio (SNR) image stacks – frequently required for undistorted imaging at liq- uid nitrogen temperatures – image registration is particularly delicate, and standard approaches may either fail, or produce subtly specious reconstructed lattice images. We present an approach which effectively registers and averages image stacks which are challenging due to their low-SNR and propensity for unit cell misalignments. Registering all possible image pairs in a multi-image stack leads to significant information surplus. In combination with a simple physical picture of stage drift, this enables identi cation of incorrect image registrations, and determination of the optimal image shifts from the complete set of relative shifts. Here, we demonstrate the effectiveness of our approach on experimental, cryogenic STEM datasets, highlighting subtle artifacts endemic to low-SNR lattice images and how they can be avoided. High-SNR average images with information transfer out to 0.72 Å are achieved at 300 kV and with the sample cooled to near liquid nitrogen temperature.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Gordon and Betty Moore Foundation; Air Force Research Laboratory (AFRL), Air Force Office of Scientific Research (AFOSR); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division; National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1479486

Alternate ID(s):: OSTI ID: 1703388

Journal Information:: Ultramicroscopy, Vol. 191, Issue C; ISSN 0304-3991

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 31 works

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References (37)

Upper limits for the residual aberrations of a high-resolution aberration-corrected STEM Haider, M.; Uhlemann, S.; Zach, J. Ultramicroscopy, Vol. 81, Issue 3-4 https://doi.org/10.1016/S0304-3991(99)00194-1	journal	April 2000
Sub-ångstrom resolution using aberration corrected electron optics Batson, P. E.; Dellby, N.; Krivanek, O. L. Nature, Vol. 418, Issue 6898 https://doi.org/10.1038/nature00972	journal	August 2002
Present status and future prospects of spherical aberration corrected TEM/STEM for study of nanomaterials ^∗ Tanaka, Nobuo Science and Technology of Advanced Materials, Vol. 9, Issue 1 https://doi.org/10.1088/1468-6996/9/1/014111	journal	January 2008
Room design for high-performance electron microscopy Muller, David A.; Kirkland, Earl J.; Thomas, Malcolm G. Ultramicroscopy, Vol. 106, Issue 11-12 https://doi.org/10.1016/j.ultramic.2006.04.017	journal	October 2006
Revolving scanning transmission electron microscopy: Correcting sample drift distortion without prior knowledge Sang, Xiahan; LeBeau, James M. Ultramicroscopy, Vol. 138 https://doi.org/10.1016/j.ultramic.2013.12.004	journal	March 2014
Optimized imaging using non-rigid registration Berkels, Benjamin; Binev, Peter; Blom, Douglas A. Ultramicroscopy, Vol. 138 https://doi.org/10.1016/j.ultramic.2013.11.007	journal	March 2014
Correcting nonlinear drift distortion of scanning probe and scanning transmission electron microscopies from image pairs with orthogonal scan directions Ophus, Colin; Ciston, Jim; Nelson, Chris T. Ultramicroscopy, Vol. 162 https://doi.org/10.1016/j.ultramic.2015.12.002	journal	March 2016
Correcting the linear and nonlinear distortions for atomically resolved STEM spectrum and diffraction imaging Wang, Yi; Suyolcu, Y. Eren; Salzberger, Ute Microscopy, Vol. 67, Issue suppl_1 https://doi.org/10.1093/jmicro/dfy002	journal	January 2018
Nature and evolution of incommensurate charge order in manganites visualized with cryogenic scanning transmission electron microscopy El Baggari, Ismail; Savitzky, Benjamin H.; Admasu, Alemayehu S. Proceedings of the National Academy of Sciences, Vol. 115, Issue 7 https://doi.org/10.1073/pnas.1714901115	journal	January 2018
Site-Specific Preparation of Intact Solid–Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out Zachman, Michael J.; Asenath-Smith, Emily; Estroff, Lara A. Microscopy and Microanalysis, Vol. 22, Issue 6 https://doi.org/10.1017/S1431927616011892	journal	November 2016
Cryo-scanning transmission electron tomography of vitrified cells Wolf, Sharon Grayer; Houben, Lothar; Elbaum, Michael Nature Methods, Vol. 11, Issue 4 https://doi.org/10.1038/nmeth.2842	journal	February 2014
Dose-Efficient Cryo-STEM Imaging of Whole Cells Using the Electron Microscope Pixel Array Detector Spoth, Katherine A.; Nguyen, Kayla X.; Muller, David A. Microscopy and Microanalysis, Vol. 23, Issue S1 https://doi.org/10.1017/S1431927617004688	journal	July 2017
Local crystal structure analysis with several picometer precision using scanning transmission electron microscopy Kimoto, Koji; Asaka, Toru; Yu, Xiuzhen Ultramicroscopy, Vol. 110, Issue 7 https://doi.org/10.1016/j.ultramic.2009.11.014	journal	June 2010
Multiferroic and magnetoelectric materials Eerenstein, W.; Mathur, N. D.; Scott, J. F. Nature, Vol. 442, Issue 7104 https://doi.org/10.1038/nature05023	journal	August 2006
The dynamics of charge-density waves Grüner, G. Reviews of Modern Physics, Vol. 60, Issue 4 https://doi.org/10.1103/RevModPhys.60.1129	journal	October 1988
Correlation functions revisited van Heel, Marin; Schatz, Michael; Orlova, Elena Ultramicroscopy, Vol. 46, Issue 1-4 https://doi.org/10.1016/0304-3991(92)90021-B	journal	October 1992
Extension of phase correlation to subpixel registration Foroosh, H.; Zerubia, J. B.; Berthod, M. IEEE Transactions on Image Processing, Vol. 11, Issue 3 https://doi.org/10.1109/83.988953	journal	March 2002
Deconvolution processing of HAADF STEM images Watanabe, K.; Kotaka, Y.; Nakanishi, N. Ultramicroscopy, Vol. 92, Issue 3-4 https://doi.org/10.1016/S0304-3991(02)00132-8	journal	August 2002
IMAGE-WARP: A real-space restoration method for high-resolution STEM images using quantitative HRTEM analysis Rečnik, Aleksander; Möbus, Günter; Šturm, Sašo Ultramicroscopy, Vol. 103, Issue 4 https://doi.org/10.1016/j.ultramic.2005.01.003	journal	July 2005
An approach to the systematic distortion correction in aberration-corrected HAADF images Sanchez, A. M.; Galindo, P. L.; Kret, S. Journal of Microscopy, Vol. 221, Issue 1 https://doi.org/10.1111/j.1365-2818.2006.01533.x	journal	January 2006
Quantitative measurement of displacement and strain fields from HREM micrographs Hÿtch, M. J.; Snoeck, E.; Kilaas, R. Ultramicroscopy, Vol. 74, Issue 3, p. 131-146 https://doi.org/10.1016/S0304-3991(98)00035-7	journal	August 1998
Correcting scanning instabilities from images of periodic structures Braidy, Nadi; Le Bouar, Yann; Lazar, Sorin Ultramicroscopy, Vol. 118 https://doi.org/10.1016/j.ultramic.2012.04.001	journal	July 2012
Identifying and Correcting Scan Noise and Drift in the Scanning Transmission Electron Microscope Jones, Lewys; Nellist, Peter D. Microscopy and Microanalysis, Vol. 19, Issue 4 https://doi.org/10.1017/S1431927613001402	journal	May 2013
Image registration methods: a survey Zitová, Barbara; Flusser, Jan Image and Vision Computing, Vol. 21, Issue 11 https://doi.org/10.1016/S0262-8856(03)00137-9	journal	October 2003
Determining optical flow Horn, Berthold K. P.; Schunck, Brian G. Artificial Intelligence, Vol. 17, Issue 1-3 https://doi.org/10.1016/0004-3702(81)90024-2	journal	August 1981
Fundamental Performance Limits in Image Registration Robinson, D.; Milanfar, P. IEEE Transactions on Image Processing, Vol. 13, Issue 9 https://doi.org/10.1109/TIP.2004.832923	journal	September 2004
Fundamental Limits in Multi-Image Alignment Aguerrebere, Cecilia; Delbracio, Mauricio; Bartesaghi, Alberto IEEE Transactions on Signal Processing, Vol. 64, Issue 21 https://doi.org/10.1109/TSP.2016.2600517	journal	November 2016
Analysis of Descent-Based Image Registration Vural, Elif; Frossard, Pascal SIAM Journal on Imaging Sciences, Vol. 6, Issue 4 https://doi.org/10.1137/130909858	journal	January 2013
Efficiency of 2D alignment methods Joyeux, Laurent; Penczek, Pawel A. Ultramicroscopy, Vol. 92, Issue 2 https://doi.org/10.1016/S0304-3991(01)00154-1	journal	July 2002
A method for the alignment of heterogeneous macromolecules from electron microscopy Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E. Journal of Structural Biology, Vol. 166, Issue 1 https://doi.org/10.1016/j.jsb.2008.12.008	journal	April 2009
Alignment of cryo-EM movies of individual particles by optimization of image translations Rubinstein, John L.; Brubaker, Marcus A. Journal of Structural Biology, Vol. 192, Issue 2 https://doi.org/10.1016/j.jsb.2015.08.007	journal	November 2015
Computer averaging of electron micrographs of 40S ribosomal subunits Frank, J.; Verschoor, A.; Boublik, M. Science, Vol. 214, Issue 4527 https://doi.org/10.1126/science.7313694	journal	December 1981
Characterizing the response of a scintillator-based detector to single electrons Sang, Xiahan; LeBeau, James M. Ultramicroscopy, Vol. 161 https://doi.org/10.1016/j.ultramic.2015.11.008	journal	February 2016
Bending and breaking of stripes in a charge ordered manganite Savitzky, Benjamin H.; El Baggari, Ismail; Admasu, Alemayehu S. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02156-1	journal	December 2017
Atomic lattice disorder in charge-density-wave phases of exfoliated dichalcogenides (1T-TaS ₂ ) Hovden, Robert; Tsen, Adam W.; Liu, Pengzi Proceedings of the National Academy of Sciences, Vol. 113, Issue 41 https://doi.org/10.1073/pnas.1606044113	journal	September 2016
Rearrangement of van der Waals stacking and formation of a singlet state at T = 90 K in a cluster magnet Sheckelton, John P.; Plumb, Kemp W.; Trump, Benjamin A. Inorganic Chemistry Frontiers, Vol. 4, Issue 3 https://doi.org/10.1039/C6QI00470A	journal	January 2017
Atomically engineered ferroic layers yield a room-temperature magnetoelectric multiferroic Mundy, Julia A.; Brooks, Charles M.; Holtz, Megan E. Nature, Vol. 537, Issue 7621 https://doi.org/10.1038/nature19343	journal	September 2016

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Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study Ziatdinov, Maxim; Dyck, Ondrej; Li, Xin Science Advances, Vol. 5, Issue 9 https://doi.org/10.1126/sciadv.aaw8989	journal	September 2019
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Cryogenic STEM (cryo-STEM)
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