Hostname: page-component-78c5997874-4rdpn Total loading time: 0 Render date: 2024-11-15T19:23:39.376Z Has data issue: false hasContentIssue false
  • English
  • Français

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

Published online by Cambridge University Press:  27 December 2018

Xin Li ,
Ondrej Dyck ,
Sergei V. Kalinin  and
Stephen Jesse
Xin Li
Affiliation:
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Department of Industrial Engineering, Florida State University, Tallahassee, FL 32306, USA Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
Ondrej Dyck
Affiliation:
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Sergei V. Kalinin*
Affiliation:
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Stephen Jesse*
Affiliation:
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
*
*Authors for correspondence: Sergei V. Kalinin, E-mail: [email protected]; Stephen Jesse, E-mail: [email protected]
*Authors for correspondence: Sergei V. Kalinin, E-mail: [email protected]; Stephen Jesse, E-mail: [email protected]
Get access

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.

Keywords

STEMcompressed sensingimage inpaintingreal-timesprial scanLissajous scannonrectangular scanGPU
Type
Materials Science Applications
Information
Microscopy and Microanalysis , Volume 24 , Issue 6 , December 2018 , pp. 623 - 633
Copyright
© Microscopy Society of America 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

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

References

Batson, PE (1993) Simultaneous STEM imaging and electron energy-loss spectroscopy with atomic-column sensitivity. Nature 366(6457), 727–728.Google Scholar
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.Google Scholar
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), 1062–1068.Google Scholar
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), 7–12.Google Scholar
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), 3044–3048.Google Scholar
Browning, ND, Chisholm, MF Pennycook, SJ (1993) Atomic-resolution chemical analysis using a scanning transmission electron microscope. Nature 366(6451), 143–146.Google Scholar
Crewe, AV, Wall, J Langmore, J (1970) Visibility of single atoms. Science (New York, N.Y.) 168(3937), 1338–1340.Google Scholar
Daubechies, I (1992) Ten lectures on wavelets, vol. 61. Siam.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
Egerton, RF (2011) Electron Energy-Loss Spectroscopy in the Electron Microscope. Springer, US, https://doi.org/10.1007/978-1-4419-9583-4_2.Google Scholar
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.Google Scholar
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), 903–923.Google Scholar
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), 5895–5900.Google Scholar
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.Google Scholar
Jiang, N (2016) Electron beam damage in oxides: A review. Rep Prog Phys 79(1), 016501.Google Scholar
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), 653–659.Google Scholar
Jones, L Nellist, PD (2013) Identifying and correcting scan noise and drift in the scanning transmission electron microscope. Microsc Microanal 19(4), 1050–1060.Google Scholar
Kalinin, SV, Borisevich, A Jesse, S (2016) Fire up the atom forge. Nature 539(7630), 485–487.Google Scholar
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), 637–643.Google Scholar
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.Google Scholar
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), 571–574.Google Scholar
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), 209–212.Google Scholar
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.Google Scholar
McMullan, G, Clark, AT, Turchetta, R Faruqi, AR (2009) Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 109(12), 1411–1416.Google Scholar
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), 156–163.Google Scholar
Muller, A Grazul, J (2001) Optimizing the environment for sub-0.2 Nm scanning transmission electron microscopy. J Electron Microsc 50(3), 219–226.Google Scholar
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), 164–165.Google Scholar
Paleo, P (2016) PDWT: A GPU implementation of the wavelet transform. https://github.com/pierrepaleo/PDWT.Google Scholar
Pennycook, SJ (2017) The impact of STEM aberration correction on materials science. Ultramicroscopy 180, 22–33.Google Scholar
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), 160–167.Google Scholar
Peyré, G (2011) The mumerical tours of signal processing. Comput Sci Eng 13(4), 94–97.Google Scholar
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), 286–287.Google Scholar
Rose, H (1974) Phase contrast in scanning transmission electron microscopy. OPTIK 39, 416–436.Google Scholar
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.Google Scholar
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.Google Scholar
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), 41–51.Google Scholar
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.Google Scholar
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.Google Scholar
Susi, T, Meyer, JC Kotakoski, J (2017) Manipulating low-dimensional materials down to the level of single atoms with electron irradiation. Ultramicroscopy 180(September), 163–172.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
Wang, Z, Bovik, AC, Sheikh, HR Simoncelli, EP (2004) Image quality assessment: From error visibility to structural similarity. IEEE Trans Image Process 13(4), 600–612.Google Scholar
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. 456–461. Available at https://ieeexplore.ieee.org/document/6266062 Google Scholar
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), 667–676.Google Scholar
Zhou, W, Oxley, MP, Lupini, AR, Krivanek, OL, Pennycook, SJ Idrobo, J-C (2012) Single atom microscopy. Microsc Microanal 18(06), 1342–1354.Google Scholar