Hostname: page-component-cd9895bd7-mkpzs Total loading time: 0 Render date: 2024-12-24T01:53:52.211Z Has data issue: false hasContentIssue false

Scattering Matrix Determination in Crystalline Materials from 4D Scanning Transmission Electron Microscopy at a Single Defocus Value

Published online by Cambridge University Press:  27 July 2021

Scott D. Findlay*
Affiliation:
School of Physics and Astronomy, Monash University, Clayton, VIC3800, Australia
Hamish G. Brown
Affiliation:
National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC3052, Australia
Philipp M. Pelz
Affiliation:
National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA Department of Materials Science and Engineering, University of California, Berkeley, CA94720, USA
Colin Ophus
Affiliation:
National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
Jim Ciston
Affiliation:
National Center for Electron Microscopy Facility, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA94720, USA
Leslie J. Allen
Affiliation:
School of Physics, University of Melbourne, Parkville, VIC3010, Australia
*
*Author for correspondence: Scott D. Findlay, E-mail: [email protected]
Get access

Abstract

Recent work has revived interest in the scattering matrix formulation of electron scattering in transmission electron microscopy as a stepping stone toward atomic-resolution structure determination in the presence of multiple scattering. We discuss ways of visualizing the scattering matrix that make its properties clear. Through a simulation-based case study incorporating shot noise, we shown how regularizing on this continuity enables the scattering matrix to be reconstructed from 4D scanning transmission electron microscopy (STEM) measurements from a single defocus value. Intriguingly, for crystalline samples, this process also yields the sample thickness to nanometer accuracy with no a priori knowledge about the sample structure. The reconstruction quality is gauged by using the reconstructed scattering matrix to simulate STEM images at defocus values different from that of the data from which it was reconstructed.

Type
Software and Instrumentation
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of the Microscopy Society of America

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.)

References

Allars, F, Lu, PH, Kruth, M, Dunin-Borkowski, RE, Rodenburg, JM & Maiden, AM (2021). Efficient large field of view electron phase imaging using near-field electron ptychography with a diffuser. Ultramicroscopy, 113257.CrossRefGoogle ScholarPubMed
Allen, LJ, Faulkner, HML & Leeb, H (2000). Inversion of dynamical electron diffraction data including absorption. Acta Crystallogr A 56, 119126.CrossRefGoogle ScholarPubMed
Bendory, T, Beinert, R & Eldar, YC (2017. Fourier Phase Retrieval: Uniqueness and Algorithms. In Compressed Sensing and its Applications. Applied and Numerical Harmonic Analysis, Boche, H., Caire, G., Calderbank, R., März, M., Kutyniok, G. & Mathar, R. (Eds.), pp. 5591. Cham: Birkhäuser. https://doi.org/10.1007/978-3-319-69802-1_2.Google Scholar
Bosch, EGT & Lazić, I (2019). Analysis of depth-sectioning STEM for thick samples and 3D imaging. Ultramicroscopy 207, 112831.CrossRefGoogle ScholarPubMed
Bredies, K, Kunisch, K & Pock, T (2010). Total generalized variation. SIAM J Imaging Sci 3, 492526.CrossRefGoogle Scholar
Brown, HG, Chen, Z, Weyland, M, Ophus, C, Ciston, J, Allen, LJ & Findlay, SD (2018). Structure retrieval at atomic resolution in the presence of multiple scattering of the electron probe. Phys Rev Lett 121, 266102.CrossRefGoogle ScholarPubMed
Brown, HG, Pelz, PM, Hsu, SL, Zhang, Z, Ramesh, R, Inzani, K, Sheridan, E, Griffin, SM, Findlay, SD, Allen, LJ, Scott, MC, Ophus, C & Ciston, J (2020). A three-dimensional reconstruction algorithm for scanning transmission electron microscopy data. arXiv preprint arXiv:201107652.Google Scholar
Chapman, HN (1997). Phase-retrieval X-ray microscopy by Wigner-distribution deconvolution: Signal processing. Scan Microsc 11, 6780.Google Scholar
Chen, Z, Jiang, Y, Shao, YT, Holtz, ME, Odstrčil, M, Guizar-Sicairos, M, Hanke, I, Ganschow, S, Schlom, DG & Muller, DA (2020). Electron ptychography achieves atomic-resolution limits set by lattice vibrations. arXiv preprint arXiv:210100465.Google Scholar
Chen, Z, Weyland, M, Ercius, P, Ciston, J, Zheng, C, Fuhrer, MS, D'Alfonso, AJ, Allen, LJ & Findlay, SD (2016). Practical aspects of diffractive imaging using an atomic-scale coherent electron probe. Ultramicroscopy 169, 107121.CrossRefGoogle ScholarPubMed
Close, R, Chen, Z, Shibata, N & Findlay, SD (2015). Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons. Ultramicroscopy 159, 124137.CrossRefGoogle ScholarPubMed
Donatelli, JJ & Spence, JCH (2020). Inversion of many-beam Bragg intensities for phasing by iterated projections: Removal of multiple scattering artifacts from diffraction data. Phys Rev Lett 125, 065502.CrossRefGoogle ScholarPubMed
Dronyak, R, Liang, KS, Stetsko, YP, Lee, TK, Feng, CK, Tsai, JS & Chen, FR (2009). Electron diffractive imaging of nano-objects using a guided method with a dynamic support. Appl Phys Lett 95, 111908.CrossRefGoogle Scholar
Dwyer, C (2010). Simulation of scanning transmission electron microscope images on desktop computers. Ultramicroscopy 110, 195198.CrossRefGoogle ScholarPubMed
Elser, V (2003). Phase retrieval by iterated projections. J Opt Soc Am A 20, 4055.CrossRefGoogle ScholarPubMed
Faulkner, HML & Rodenburg, JM (2004). Movable aperture lensless transmission microscopy: A novel phase retrieval algorithm. Phys Rev Lett 93, 023903.CrossRefGoogle ScholarPubMed
Fienup, JR (1987). Reconstruction of a complex-valued object from the modulus of its Fourier transform using a support constraint. J Opt Soc Am A 4, 118123.CrossRefGoogle Scholar
Findlay, SD (2005). Quantitative structure retrieval using scanning transmission electron microscopy. Acta Crystallogr A 61, 397404.CrossRefGoogle ScholarPubMed
Findlay, SD, Allen, LJ, Oxley, MP & Rossouw, CJ (2003). Lattice-resolution contrast from a focused coherent electron probe. Part II. Ultramicroscopy 96, 6581.CrossRefGoogle ScholarPubMed
Gao, S, Wang, P, Zhang, F, Martinez, GT, Nellist, PD, Pan, X & Kirkland, AI (2017). Electron ptychographic microscopy for three-dimensional imaging. Nat Commun 8, 163.CrossRefGoogle ScholarPubMed
Gureyev, TE, Quiney, HM, Kozlov, A & Allen, LJ (2020 a). Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons. Ultramicroscopy 218, 113094.CrossRefGoogle ScholarPubMed
Gureyev, TE, Quiney, HM, Kozlov, A, Paganin, DM, Schmalz, G & Allen, LJ (2020 b). Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons, Part II: Differential holographic tomography. arXiv preprint arXiv:201207012.CrossRefGoogle Scholar
Hachtel, JA, Idrobo, JC & Chi, M (2018). Sub-Ångstrom electric field measurements on a universal detector in a scanning transmission electron microscope. Adv Struct Chem Imaging 4, 10.CrossRefGoogle Scholar
Jiang, Y, Chen, Z, Han, Y, Deb, P, Gao, H, Xie, S, Purohit, P, Tate, MW, Park, J, Gruner, SM, Elser, V & Muller, DA (2018). Electron ptychography of 2D materials to deep sub-ångström resolution. Nature 559, 343349.CrossRefGoogle Scholar
Kazantsev, D, Pasca, E, Turner, MJ & Withers, PJ (2019). CCPi-regularisation toolkit for computed tomographic image reconstruction with proximal splitting algorithms. SoftwareX 9, 317323.CrossRefGoogle Scholar
Koch, CT (2011). Aberration-compensated large-angle rocking-beam electron diffraction. Ultramicroscopy 111, 828840.CrossRefGoogle ScholarPubMed
Köhl, M, Minkevich, AA & Baumbach, T (2012). Improved success rate and stability for phase retrieval by including randomized overrelaxation in the hybrid input output algorithm. Opt Express 20, 1709317106.CrossRefGoogle Scholar
Kovesi, P (2015 a). Good colour maps: How to design them. arXiv preprint arXiv:1509.03700.Google Scholar
Kovesi, P (2015 b). ColorCET perceptually uniform colour maps. Available at https://colorcet.com/ (retrieved March 28, 2021).CrossRefGoogle Scholar
Krumm, J (2001). Savitzky–Golay filters for 2D images. Available at http://homepages.inf.ed.ac.uk/rbf/CVonline/LOCAL_COPIES/KRUMM1/SavGol.htm (retrieved October 28, 2020).Google Scholar
Lazić, I, Bosch, EGT & Lazar, S (2016). Phase contrast STEM for thin samples: Integrated differential phase contrast. Ultramicroscopy 160, 265280.CrossRefGoogle ScholarPubMed
LeBeau, JM, Findlay, SD, Allen, LJ & Stemmer, S (2010). Position averaged convergent beam electron diffraction: Theory and applications. Ultramicroscopy 110, 118125.CrossRefGoogle ScholarPubMed
Maiden, A, Sarahan, M, Stagg, M, Schramm, S & Humphry, M (2015). Quantitative electron phase imaging with high sensitivity and an unlimited field of view. Sci Rep 5, 18.CrossRefGoogle Scholar
Maiden, AM, Humphry, MJ & Rodenburg, JM (2012). Ptychographic transmission microscopy in three dimensions using a multi-slice approach. J Opt Soc Am A 29, 16061614.CrossRefGoogle ScholarPubMed
Maiden, AM & Rodenburg, JM (2009). An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy 109, 12561262.CrossRefGoogle ScholarPubMed
Marchesini, S (2007). Invited article: A unified evaluation of iterative projection algorithms for phase retrieval. Rev Sci Instrum 78, 011301.CrossRefGoogle ScholarPubMed
Martin, AV, Wang, F, Loh, ND, Ekeberg, T, Maia, FR, Hantke, M, van der Schot, G, Hampton, CY, Sierra, RG, Aquila, A, Bajt, S, Barthelmess, M, Bostedt, C, Bozek, JD, Coppola, N, Epp, SW, Erk, B, Fleckenstein, H, Foucar, L, Frank, M, Graafsma, H, Gumprecht, L, Hartmann, A, Hartmann, R, Hauser, G, Hirsemann, H, Holl, P, Kassemeyer, S, Kimmel, N, Liang, M, Lomb, L, Marchesini, S, Nass, K, Pedersoli, E, Reich, C, Rolles, D, Rudek, B, Rudenko, A, Schulz, J, Shoeman, RL, Soltau, H, Starodub, D, Steinbrener, J, Stellato, F, Strüder, L, Ullrich, J, Weidenspointner, G, White, TA, Wunderer, CB, Barty, A, Schlichting, I, Bogan, MJ & Chapman, HN (2012). Noise-robust coherent diffractive imaging with a single diffraction pattern. Opt Express 20, 1665016661.CrossRefGoogle Scholar
McBride, W, O'Leary, N & Allen, L (2004). Retrieval of a complex-valued object from its diffraction pattern. Phys Rev Lett 93, 233902.CrossRefGoogle ScholarPubMed
Moler, C & Van Loan, C (2003). Nineteen dubious ways to compute the exponential of a matrix, twenty-five years later. SIAM Rev 45, 349.CrossRefGoogle Scholar
Morishita, S, Yamasaki, J, Nakamura, K, Kato, T & Tanaka, N (2008). Diffractive imaging of the dumbbell structure in silicon by spherical-aberration-corrected electron diffraction. Appl Phys Lett 93, 183103.CrossRefGoogle Scholar
Müller, K, Krause, FF, Béché, A, Schowalter, M, Galioit, V, Löffler, S, Verbeeck, J, Zweck, J, Schattschneider, P & Rosenauer, A (2014). Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction. Nat Commun 5, 5653.CrossRefGoogle ScholarPubMed
Müller-Caspary, K, Krause, FF, Grieb, T, Löffler, S, Schowalter, M, Béché, A, Galioit, V, Marquardt, D, Zweck, J, Schattschneider, P, Verbeeck, J & Rosenauer, A (2017). Measurement of atomic electric fields and charge densities from average momentum transfers using scanning transmission electron microscopy. Ultramicroscopy 178, 6280.CrossRefGoogle ScholarPubMed
Ophus, C (2017). A fast image simulation algorithm for scanning transmission electron microscopy. Adv Struct Chem Imaging 3, 13.CrossRefGoogle ScholarPubMed
Ophus, C, Harvey, TR, Yasin, FS, Brown, HG, Pelz, PM, Savitzky, BH, Ciston, J & McMorran, BJ (2019). Advanced phase reconstruction methods enabled by four-dimensional scanning transmission electron microscopy. Microsc Microanal 25(Suppl 2), 1011.CrossRefGoogle Scholar
Pelz, PM, Brown, HG, Ciston, J, Findlay, SD, Zhang, Y, Scott, M & Ophus, C (2020). Reconstructing the scattering matrix from scanning electron diffraction measurements alone. arXiv preprint arXiv:200812768.Google Scholar
Plamann, T & Rodenburg, JM (1998). Electron ptychography. II. Theory of three-dimensional propagation effects. Acta Crystallogr A 54, 6173.CrossRefGoogle Scholar
Ren, D, Ophus, C, Chen, M & Waller, L (2020). A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography. Ultramicroscopy 208, 112860.CrossRefGoogle ScholarPubMed
Rodenburg, J & Maiden, A (2019). Springer Handbooks. In Springer Handbook of Microscopy, Hawkes, PW & Spence, JCH (Eds.), pp. 819904. Cham: Springer. https://doi.org/10.1007/978-3-030-00069-1.CrossRefGoogle Scholar
Schloz, M, Pekin, TC, Chen, Z, Broek, WVd., Muller, DA & Koch, CT (2020). Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization. Opt Express 28, 2830628323.CrossRefGoogle ScholarPubMed
Spence, JCH (1998). Direct inversion of dynamical electron diffraction patterns to structure factors. Acta Crystallogr A 54, 718.CrossRefGoogle Scholar
Sturkey, L (1962). The calculation of electron diffraction intensities. Proc Phys Soc 80, 321354.CrossRefGoogle Scholar
Tate, MW, Purohit, P, Chamberlain, D, Nguyen, KX, Hovden, R, Chang, CS, Deb, P, Turgut, E, Heron, JT, Schlom, DG, Ralph, DC, Fuchs, GD, Shanks, KS, Philipp, HT, Muller, DA & Gruner, SM (2016). High dynamic range pixel array detector for scanning transmission electron microscopy. Microsc Microanal 22, 237249.CrossRefGoogle ScholarPubMed
Van den Broek, W & Koch, CT (2012). Method for retrieval of the three-dimensional object potential by inversion of dynamical electron scattering. Phys Rev Lett 109, 245502.CrossRefGoogle ScholarPubMed
Van den Broek, W & Koch, CT (2013). General framework for quantitative three-dimensional reconstruction from arbitrary detection geometries in TEM. Phys Rev B 87, 184108.CrossRefGoogle Scholar
Van Dyck, D (1985). Image calculations in high-resolution electron microscopy: Problems, progress, and prospects. Adv Electron Electron Phys 65, 295355.CrossRefGoogle Scholar
Wang, F, Pennington, RS & Koch, CT (2016). Inversion of dynamical scattering from large-angle rocking-beam electron diffraction patterns. Phys Rev Lett 117, 015501.CrossRefGoogle ScholarPubMed
Waters, MJ, Walker, JM, Nelson, CT, Joester, D & Rondinelli, JM (2020). Exploiting colorimetry for fidelity in data visualization. Chem Mater 32, 54555460.CrossRefGoogle Scholar
Winkler, F, Barthel, J, Dunin-Borkowski, RE & Mueller-Caspary, K (2020). Direct measurement of electrostatic potentials at the atomic scale: A conceptual comparison between electron holography and scanning transmission electron microscopy. Ultramicroscopy 210, 112926.CrossRefGoogle Scholar
Yamasaki, J, Morishita, S, Shimaoka, Y, Ohta, K & Sasaki, H (2019). Phase imaging and atomic-resolution imaging by electron diffractive imaging. Jpn J Appl Phys 58, 120502.CrossRefGoogle Scholar
Yang, H, Pennycook, TJ & Nellist, PD (2015). Efficient phase contrast imaging in STEM using a pixelated detector. Part II: Optimisation of imaging conditions. Ultramicroscopy 151, 232239.CrossRefGoogle ScholarPubMed
Yang, H, Rutte, RN, Jones, L, Simson, M, Sagawa, R, Ryll, H, Huth, M, Pennycook, TJ, Green, MLH, Soltau, H, Kondo, Y, Davis, BG & Nellist, PD (2016). Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures. Nat Commun 7, 12532.CrossRefGoogle ScholarPubMed
Zuo, J, Vartanyants, I, Gao, M, Zhang, R & Nagahara, L (2003). Atomic resolution imaging of a carbon nanotube from diffraction intensities. Science 300, 14191421.CrossRefGoogle ScholarPubMed