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Compressed Sensing of Scanning Transmission Electron Microscopy (STEM) With Nonrectangular Scans

  • Xin Li (a1) (a2) (a3) (a4), Ondrej Dyck (a1) (a2), Sergei V. Kalinin (a1) (a2) and Stephen Jesse (a1) (a2)

Abstract

Scanning transmission electron microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In recent years, attention has focused on the potential of STEM to explore beam induced chemical processes and especially manipulating atomic motion, enabling atom-by-atom fabrication. These applications, as well as traditional imaging of beam sensitive materials, necessitate increasing the dynamic range of STEM in imaging and manipulation modes, and increasing the absolute scanning speed which can be achieved by combining sparse sensing methods with nonrectangular scanning trajectories. Here we have developed a general method for real-time reconstruction of sparsely sampled images from high-speed, noninvasive and diverse scanning pathways, including spiral scan and Lissajous scan. This approach is demonstrated on both the synthetic data and experimental STEM data on the beam sensitive material graphene. This work opens the door for comprehensive investigation and optimal design of dose efficient scanning strategies and real-time adaptive inference and control of e-beam induced atomic fabrication.

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*Authors for correspondence: Sergei V. Kalinin, E-mail: sergei2@ornl.gov; Stephen Jesse, E-mail: sjesse@ornl.gov

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Cite this article: Li X, Dyck O, Kalinin SV and Jesse S (2018) Compressed sensing of scanning transmission electron microscopy (STEM) with nonrectangular scans. Microsc Microanal 24(6), 623–633. doi: 10.1017/S143192761801543X

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Batson, PE (1993) Simultaneous STEM imaging and electron energy-loss spectroscopy with atomic-column sensitivity. Nature 366(6457), 727728.
Bazaei, A, Yong, YK Reza Moheimani, SO (2012) High-speed Lissajous-scan atomic force microscopy: Scan pattern planning and control design issues. Rev Sci Instrum 83(6), 063701.
Benthem, KV, Lupini, AR, Oxley, MP, Findlay, SD, Allen, LJ Pennycook, SJ (2006) Three-dimensional ADF imaging of individual atoms by through-focal series scanning transmission electron microscopy. Ultramicroscopy 106(11–12), 10621068.
Borisevich, AY, Lupini, AR, Travaglini, S Pennycook, S (2006 a) Depth sectioning of aligned crystals with the aberration-corrected scanning transmission electron microscope. Journal of Electron Microscopy 55(1), 712.
Borisevich, AY, Lupini, AR Pennycook, SJ (2006 b) Depth sectioning with the aberration-corrected scanning transmission electron microscope. Proc Natl Acad Sci USA 103(9), 30443048.
Browning, ND, Chisholm, MF Pennycook, SJ (1993) Atomic-resolution chemical analysis using a scanning transmission electron microscope. Nature 366(6451), 143146.
Crewe, AV, Wall, J Langmore, J (1970) Visibility of single atoms. Science (New York, N.Y.) 168(3937), 13381340.
Daubechies, I (1992) Ten lectures on wavelets, vol. 61. Siam.
Daubechies, I, Defrise, M De Mol, C (2004) An iterative thresholding algorithm for linear inverse problems with a sparsity constraint. Commun Pure Appl Math. https://doi.org/10.1002/cpa.20042.
Dyck, O, Kim, S, Kalinin, SV Jesse, S (2017a) Placing single atoms in graphene with a scanning transmission electron microscope. Appl Phys Lett https://doi.org/10.1063/1.4998599.
Dyck, O, Kim, S, Kalinin, SV Jesse, S (2017b) Mitigating e-beam-induced hydrocarbon deposition on graphene for atomic-scale scanning transmission electron microscopy studies. J Vac Sci Technol, B: Nanotechnol Microelectron: Mater, Process, Meas, Phenom 36, 011801.
Egerton, RF (2011) Electron Energy-Loss Spectroscopy in the Electron Microscope. Springer, US, https://doi.org/10.1007/978-1-4419-9583-4_2.
Findlay, SD, Shibata, N, Sawada, H, Okunishi, E, Kondo, Y, Yamamoto, T Ikuhara, Y (2009) Robust atomic resolution imaging of light elements using scanning transmission electron microscopy. Appl Phys Lett 95(19), 191913.
Findlay, SD, Shibata, N, Sawada, H, Okunishi, E, Kondo, Y Ikuhara, Y (2010) Dynamics of annular bright field imaging in scanning transmission electron microscopy. Ultramicroscopy 110(7), 903923.
Jesse, S, He, Q, Lupini, AR, Leonard, DN, Oxley, MP, Ovchinnikov, O, Unocic, RR, Tselev, A, Fuentes‐Cabrera, M, Sumpter, BG Pennycook, SJ (2015) Atomic-level sculpting of crystalline oxides: toward bulk nanofabrication with single atomic plane precision. Small 11(44), 58955900.
Jesse, S, Hudak, BM, Zarkadoula, E, Song, J, Maksov, A, Fuentes-Cabrera, M, Ganesh, P, Kravchenko, I, Snijders, PC, Lupini, AR Borisevich, AY (2018) Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback. Nanotechnology 29(25), 255303.
Jiang, N (2016) Electron beam damage in oxides: A review. Rep Prog Phys 79(1), 016501.
Jiang, N, Zarkadoula, E, Narang, P, Maksov, A, Kravchenko, I, Borisevich, A, Jesse, S Kalinin, SV (2017) Atom-by-atom fabrication by electron beam via induced phase transformations. MRS Bulletin 42(09), 653659.
Jones, L Nellist, PD (2013) Identifying and correcting scan noise and drift in the scanning transmission electron microscope. Microsc Microanal 19(4), 1050–1060.
Kalinin, SV, Borisevich, A Jesse, S (2016) Fire up the atom forge. Nature 539(7630), 485487.
Kalinin, SV Pennycook, SJ, (2017) Single-atom fabrication with electron and ion beams: From surfaces and two-dimensional materials toward three-dimensional atom-by-atom assembly. MRS Bulletin 42(09), 637643.
Kovarik, L, Stevens, A, Liyu, A Browning, ND (2016) Implementing an accurate and rapid sparse sampling approach for low-dose atomic resolution STEM imaging. Appl Phys Lett 109(16), 164102.
Krivanek, OL, Chisholm, MF, Nicolosi, V, Pennycook, TJ, Corbin, GJ, Dellby, N, Murfitt, MF, Own, CS, Szilagyi, ZS, Oxley, MP Pantelides, ST (2010) Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy. Nature 464(7288), 571574.
Krivanek, OL, Lovejoy, TC, Dellby, N, Aoki, T, Carpenter, RW, Rez, P, Soignard, E, Zhu, J, Batson, PE, Lagos, MJ Egerton, RF (2014) Vibrational spectroscopy in the electron microscope. Nature 514(7521), 209212.
Mallat, S (2009) A Wavelet Tour of Signal Processing. A Wavelet Tour of Signal Processing . Elsevier/Academic Press, https://doi.org/10.1016/B978-0-12-374370-1.50001-9.
McMullan, G, Clark, AT, Turchetta, R Faruqi, AR (2009) Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 109(12), 14111416.
McMullan, G, Faruqi, AR, Clare, D Henderson, R (2014) Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy. Ultramicroscopy 147(December), 156163.
Muller, A Grazul, J (2001) Optimizing the environment for sub-0.2 Nm scanning transmission electron microscopy. J Electron Microsc 50(3), 219226.
Okunishi, E, Ishikawa, I, Sawada, H, Hosokawa, F, Hori, M Kondo, Y (2009) Visualization of light elements at ultrahigh resolution by STEM annular bright field microscopy. Microsc Microanal 15(S2), 164165.
Paleo, P (2016) PDWT: A GPU implementation of the wavelet transform. https://github.com/pierrepaleo/PDWT.
Pennycook, SJ (2017) The impact of STEM aberration correction on materials science. Ultramicroscopy 180, 2233.
Pennycook, TJ, Lupini, AR, Yang, H, Murfitt, MF, Jones, L Nellist, PD (2015) Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution. Ultramicroscopy 151(April), 160167.
Peyré, G (2011) The mumerical tours of signal processing. Comput Sci Eng 13(4), 9497.
Reed, BW, Park, ST Masiel, DJ (2016) Quantifying the advantages of compressive sensing and sparse reconstruction for scanning transmission electron microscopy. Microsc Microanal 22(S3), 286287.
Rose, H (1974) Phase contrast in scanning transmission electron microscopy. OPTIK 39, 416436.
Sang, X, Lupini, AR, Unocic, RR, Chi, M, Borisevich, AY, Kalinin, SV, Endeve, E, Archibald, RK Jesse, S (2017) Dynamic scan control in STEM: Spiral scans. Adv Struct Chem Imaging 2 (1), 6.
Stevens, A, Luzi, L, Yang, H, Kovarik, L, Mehdi, BL, Liyu, A, Gehm, ME Browning, ND (2018) A sub-sampled approach to extremely low-sose STEM. Appl Phys Lett 112(4), 043104.
Stevens, A, Yang, H, Carin, L, Arslan, I Browning, ND (2014) The potential for Bayesian compressive sensing to significantly reduce electron dose in high-resolution STEM images. Microscopy 63(1), 4151.
Susi, T, Kepaptsoglou, D, Lin, Y-C, Ramasse, QM, Meyer, JC, Suenaga, K Kotakoski, J (2017) Towards atomically precise manipulation of 2D nanostructures in the electron microscope. 2D Mater 4(4), 042004.
Susi, T, Kotakoski, J, Kepaptsoglou, D, Mangler, C, Lovejoy, TC, Krivanek, OL, Zan, R, Bangert, U, Ayala, P, Meyer, JC Ramasse, Q (2014) Silicon–carbon bond inversions driven by 60-KeV electrons in graphene. Phys Rev Lett 113(11), 115501.
Susi, T, Meyer, JC Kotakoski, J (2017) Manipulating low-dimensional materials down to the level of single atoms with electron irradiation. Ultramicroscopy 180(September), 163172.
Tuma, T, Lygeros, J, Kartik, V, Sebastian, A Pantazi, A (2012) High-speed multiresolution scanning probe microscopy based on Lissajous scan trajectories. Nanotechnology 23(18), 185501.
Tuma, T, Lygeros, J, Sebastian, A Pantazi, A (2013) Analysis and design of multiresolution scan trajectories for high-speed scanning probe microscopy. IFAC Proc Vol (IFAC-PapersOnline) 46, 138–144.
van Benthem, K, Lupini, AR, Kim, M, Baik, HS, Doh, S, Lee, JH, Oxley, MP, Findlay, SD, Allen, LJ, Luck, JT Pennycook, SJ (2005) Three-dimensional imaging of individual hafnium atoms inside a semiconductor device. Appl Phys Lett 87(3), 034104.
Wang, Z, Bovik, AC, Sheikh, HR Simoncelli, EP (2004) Image quality assessment: From error visibility to structural similarity. IEEE Trans Image Process 13(4), 600612.
Yong, YK, Bazaei, A, Moheimani, SOR Allg, F (2012) Design and control of a novel non-Raster scan pattern for fast scanning probe microscopy. Advanced Intelligent Mechatronics (AIM), 2012 IEEE/ASME International Conference on Ieeexplore.Ieee.Org, pp. 456461. Available at https://ieeexplore.ieee.org/document/6266062
Zhao, X, Kotakoski, J, Meyer, JC, Sutter, E, Sutter, P, Krasheninnikov, AV, Kaiser, U Zhou, W (2017) Engineering and modifying two-dimensional materials by electron beams. MRS Bulletin 42(09), 667676.
Zhou, W, Oxley, MP, Lupini, AR, Krivanek, OL, Pennycook, SJ Idrobo, J-C (2012) Single atom microscopy. Microsc Microanal 18(06), 13421354.

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