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Electron Tomography in Materials Science

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Part of the book series: Springer Handbooks ((SHB))

Abstract

This chapter illustrates how electron tomography has become a technique of primary importance in the three-dimensional () microscopic analysis of materials. The foundations of tomography are set out with descriptions of the Radon transform and its inverse and its relationship to the Fourier transform and the Fourier slice theorem. The acquisition of a tilt series of images is described and how the angular sampling in the series affects the overall 3-D resolution in the tomogram. The imaging modes available in the (scanning) transmission electron microscope are explored with reference to their application in electron tomography and how each mode can provide complementary information on the structural, chemical, electronic, and magnetic properties of the material studied. The chapter also sets out in detail methods for tomographic reconstruction from backprojection and iterative methods, such as simultaneous iterative reconstruction technique ( ) and algebraic reconstruction technique ( ), through to more recent compressed sensing approaches that aim to build in prior knowledge about the specimen into the reconstruction process. The chapter concludes with a look to the future.

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References

  • A.J. Koster, R. Grimm, D. Typke, R. Hegerl, A. Stoschek, J. Walz, W. Baumeister: Perspectives of molecular and cellular electron tomography, J. Struct. Biol. 120(3), 276–308 (1997)

    CAS  Google Scholar 

  • P.A. Midgley, M. Weyland: 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography, Ultramicroscopy 96(3/4), 413–431 (2003)

    CAS  Google Scholar 

  • J. Radon: Über die Bestimmung von Funktionen durch ihre Integralwerte längs gewisser Mannigfaltigkeiten, Ber. Verh. K. Sächs. Ges. Wiss. Leipz. Math.-Phys. Kl. 69, 262–277 (1917)

    Google Scholar 

  • R.N. Bracewell: Two-dimensional aerial smoothing in radio astronomy, Aust. J. Phys. 9, 297–314 (1956)

    Google Scholar 

  • J. Frank: Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State (Oxford Univ. Press, New York 2006)

    Google Scholar 

  • S.R. Deans: The Radon Transform and Some of its Applications (Wiley, New York, Chichester 1983)

    Google Scholar 

  • A.C. Kak, M. Slaney: Principles of Computerized Tomographic Imaging (IEEE, New York 1988)

    Google Scholar 

  • G.T. Herman, A. Kuba: Advances in Discrete Tomography and Its Applications (Birkhauser, Boston 2007)

    Google Scholar 

  • P.A. Penczek, J.J. Grant: Fundamentals of three-dimensional reconstruction from projections, Methods Enzymol. 482, 1–33 (2010)

    Google Scholar 

  • J. Banhart: Advanced Tomographic Methods in Materials Research and Engineering (Oxford Univ. Press, Oxford 2008)

    Google Scholar 

  • D.J. De Rosier, A. Klug: Reconstruction of three dimensional structures from electron micrographs, Nature 217(5124), 130–134 (1968)

    Google Scholar 

  • W. Hoppe, R. Langer, G. Knesch, C. Poppe: Proteinkristallstrukturanalyse mit Elektronenstrahlen, Naturwissenschaften 55(7), 333–336 (1968)

    CAS  Google Scholar 

  • R.G. Hart: Electron microscopy of unstained biological material: The polytropic montage, Science 159(3822), 1464–1467 (1968)

    CAS  Google Scholar 

  • T. Dahmen, P. Trampert, N. De Jonge, P. Slusallek: Advanced recording schemes for electron tomography, MRS Bulletin 41(7), 537–541 (2016)

    Google Scholar 

  • R. Leary, R. Brydson: Chromatic aberration correction: The next step in electron microscopy, Adv. Imaging Electron Phys. 165, 73–130 (2011)

    Google Scholar 

  • R.A. Crowther, D.J. DeRosier, A. Klug: The reconstruction of a three-dimensional structure from projections and its application to electron microscopy, Proc. Royal Soc. A 317(1530), 319–340 (1970)

    Google Scholar 

  • D.N. Mastronarde: Dual-axis tomography: An approach with alignment methods that preserve resolution, J. Struct. Biol. 120(3), 343–352 (1997)

    CAS  Google Scholar 

  • P. Penczek, M. Marko, K. Buttle, J. Frank: Double-tilt electron tomography, Ultramicroscopy 60(3), 393–410 (1995)

    CAS  Google Scholar 

  • J. Tong, I. Arslan, P. Midgley: A novel dual-axis iterative algorithm for electron tomography, J. Struct. Biol. 153(1), 55–63 (2006)

    Google Scholar 

  • I. Arslan, J.R. Tong, P.A. Midgley: Reducing the missing wedge: High-resolution dual axis tomography of inorganic materials, Ultramicroscopy 106(11/12), 994–1000 (2006)

    CAS  Google Scholar 

  • N. Kawase, M. Kato, H. Nishioka, H. Jinnai: Transmission electron microtomography without the ‘‘missing wedge'' for quantitative structural analysis, Ultramicroscopy 107(1), 8–15 (2007)

    CAS  Google Scholar 

  • K. Jarausch, P. Thomas, D.N. Leonard, R. Twesten, C.R. Booth: Four-dimensional STEM-EELS: Enabling nano-scale chemical tomography, Ultramicroscopy 109(4), 326–337 (2009)

    CAS  Google Scholar 

  • M. Koguchi, H. Kakibayashi, R. Tsuneta, M. Yamaoka, T. Niino, N. Tanaka, K. Kase, M. Iwaki: Three-dimensional STEM for observing nanostructures, J. Electron Microsc. 50(3), 235–241 (2001)

    CAS  Google Scholar 

  • M. Kato, N. Kawase, T. Kaneko, S. Toh, S. Matsumura, H. Jinnai: Maximum diameter of the rod-shaped specimen for transmission electron microtomography without the ‘‘missing wedge'', Ultramicroscopy 108(3), 221–229 (2008)

    CAS  Google Scholar 

  • E. Biermans, L. Molina, K.J. Batenburg, S. Bals, G. Van Tendeloo: Measuring porosity at the nanoscale by quantitative electron tomography, Nano Lett. 10(12), 5014–5019 (2010)

    CAS  Google Scholar 

  • J. Leschner, J. Biskupek, A. Chuvilin, U. Kaiser: Accessing the local three-dimensional structure of carbon materials sensitive to an electron beam, Carbon 48(14), 4042–4048 (2010)

    CAS  Google Scholar 

  • H. Friedrich, P.E. de Jongh, A.J. Verkleij, K.P. de Jong: Electron tomography for heterogeneous catalysts and related nanostructured materials, Chem. Rev. 109(5), 1613–1629 (2009)

    CAS  Google Scholar 

  • S.S. van Bavel, J. Loos: Volume organization of polymer and hybrid solar cells as revealed by electron tomography, Adv. Funct. Mater. 20, 3217–3234 (2010)

    Google Scholar 

  • X.Y. Wang, R. Lockwood, M. Malac, H. Furukawa, P. Li, A. Meldrum: Reconstruction and visualization of nanoparticle composites by transmission electron tomography, Ultramicroscopy 113, 96–105 (2012)

    CAS  Google Scholar 

  • H. Sugimori, T. Nishi, H. Jinnai: Dual-axis electron tomography for three-dimensional observations of polymeric nanostructures, Macromolecules 38(24), 10226–10233 (2005)

    CAS  Google Scholar 

  • M. Radermacher, W. Hoppe: Properties of 3-D reconstruction from projections by conical tilting compared to single-axis tilting. In: 7th Eur. Congr. Electron Microsc., Den Haag, Leiden, The Netherlands, ed. by P. Brederoo, G. Boom (1980) pp. 132–133

    Google Scholar 

  • D. Chen, H. Friedrich, G. de With: On resolution in electron tomography of beam sensitive materials, J. Phys. Chem. C 118(2), 1248–1257 (2013)

    Google Scholar 

  • R.N. Bracewell, A.C. Riddle: Inversion of fan-beam scans in radio astronomy, Astrophys. J. 150, 427–434 (1967)

    Google Scholar 

  • H. Heidari Mezerji, W. Van den Broek, S. Bals: A practical method to determine the effective resolution in incoherent experimental electron tomography, Ultramicroscopy 111(5), 330–336 (2011)

    Google Scholar 

  • P.A. Midgley, M. Weyland, J.M. Thomas, B.F.G. Johnson: Z-contrast tomography: A technique in three-dimensional nanostructural analysis based on Rutherford scattering, Chem. Commun. 18(10), 907–908 (2001)

    Google Scholar 

  • A.J. Koster, U. Ziese, A.J. Verkleij, A.H. Janssen, K.P. de Jong: Three-dimensional transmission electron microscopy: A novel imaging and characterization technique with nanometer scale resolution for materials science, J. Phys. Chem. B 104(40), 9368–9370 (2000)

    CAS  Google Scholar 

  • M. Bar Sadan, L. Houben, S.G. Wolf, A. Enyashin, G. Seifert, R. Tenne, K. Urban: Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures, Nano Lett. 8(3), 891–896 (2008)

    CAS  Google Scholar 

  • S. Van Aert, K.J. Batenburg, M.D. Rossell, R. Erni, G. Van Tendeloo: Three-dimensional atomic imaging of crystalline nanoparticles, Nature 470(7334), 374–377 (2011)

    Google Scholar 

  • B. Goris, S. Bals, W. Van den Broek, E. Carbó-Argibay, S. Gómez-Graña, L.M. Liz-Marzán, G. Van Tendeloo: Atomic-scale determination of surface facets in gold nanorods, Nat. Mater. 11, 930–935 (2012)

    CAS  Google Scholar 

  • J.-P. Baudoin, J.R. Jinschek, C.B. Boothroyd, R.E. Dunin-Borkowski, N. de Jonge: Chromatic aberration-corrected tilt series transmission electron microscopy of nanoparticles in a whole mount macrophage cell, Microsc. Microanal. 19(04), 814–820 (2013)

    CAS  Google Scholar 

  • J.S. Barnard, J. Sharp, J.R. Tong, P.A. Midgley: High-resolution three-dimensional imaging of dislocations, Science 313(5785), 319 (2006)

    CAS  Google Scholar 

  • S. Bals, G. Van Tendeloo, C. Kisielowski: A new approach for electron tomography: Annular dark-field transmission electron microscopy, Adv. Mater. 18(7), 892–895 (2006)

    CAS  Google Scholar 

  • J.M. Rebled, L. Yedra, S. Estradé, J. Portillo, F. Peiró: A new approach for 3D reconstruction from bright field TEM imaging: Beam precession assisted electron tomography, Ultramicroscopy 111(9/10), 1504–1511 (2011)

    CAS  Google Scholar 

  • A.A. Sousa, A.A. Azari, G. Zhang, R.D. Leapman: Dual-axis electron tomography of biological specimens: extending the limits of specimen thickness with bright-field STEM imaging, J. Struct. Biol. 174(1), 107–114 (2011)

    Google Scholar 

  • P. Ercius, M. Weyland, D.A. Muller, L.M. Gignac: Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography, Appl. Phys. Lett. 88(24), 243116 (2006)

    Google Scholar 

  • J.H. Sharp, J.S. Barnard, K. Kaneko, K. Higashida, P.A. Midgley: Dislocation tomography made easy: a reconstruction from ADF STEM images obtained using automated image shift correction, J. Phys. Conf. Ser. 126(1), 012013 (2008)

    Google Scholar 

  • P. Jornsanoh, G. Thollet, J. Ferreira, K. Masenelli-Varlot, C. Gauthier, A. Bogner: Electron tomography combining ESEM and STEM: a new 3D imaging technique, Ultramicroscopy 111(8), 1247–1254 (2011)

    CAS  Google Scholar 

  • M. Weyland, P.A. Midgley: 3D-EFTEM: Tomographic reconstruction from tilt series of energy loss images. In: Proc. Inst. Phys. EMAG Conf. Ser. 2001, Vol. 161 (2001) p. 239

    Google Scholar 

  • G. Möbus, B.J. Inkson: Three-dimensional reconstruction of buried nanoparticles by element-sensitive tomography based on inelastically scattered electrons, Appl. Phys. Lett. 79, 1369 (2001)

    Google Scholar 

  • G. Möbus, R.C. Doole, B.J. Inkson: Spectroscopic electron tomography, Ultramicroscopy 96, 433 (2003)

    Google Scholar 

  • K. Lepinay, F. Lorut, R. Pantel, T. Epicier: Chemical 3D tomography of 28 nm high K metal gate transistor: STEM XEDS experimental method and results, Micron 47, 43–49 (2013)

    CAS  Google Scholar 

  • U. Kolb, T. Gorelik, C. Kübel, M.T. Otten, D. Hubert: Towards automated diffraction tomography: Part I—Data acquisition, Ultramicroscopy 107(6/7), 507–513 (2007)

    CAS  Google Scholar 

  • A.C. Twitchett-Harrison, T.J.V. Yates, S.B. Newcomb, R.E. Dunin-Borkowski, P.A. Midgley: High-resolution three-dimensional mapping of semiconductor dopant potentials, Nano Lett. 7(7), 2020–2023 (2007)

    CAS  Google Scholar 

  • O.-H. Kwon, A.H. Zewail: 4D electron tomography, Science 328(5986), 1668–1673 (2010)

    CAS  Google Scholar 

  • D.B. Williams, C.B. Carter: Transmission Electron Microscopy: A Textbook for Materials Science (Springer, New York 2009)

    Google Scholar 

  • J.C.H. Spence: High-Resolution Electron Microscopy, 4th edn. (Oxford Univ. Press, Oxford 2013)

    Google Scholar 

  • D. Cockayne, A.I. Kirkland, P.D. Nellist, A. Bleloch: New possibilities with aberration-corrected electron microscopy, Philos. Trans. Royal Soc. A 367(1903), 3633–3870 (2009)

    Google Scholar 

  • M. Weyland, P.A. Midgley, J.M. Thomas: Electron tomography of nanoparticle catalysts on porous supports: A new technique based on Rutherford scattering, J. Phys. Chem. B 105(33), 7882–7886 (2001)

    CAS  Google Scholar 

  • P.A. Midgley, R.E. Dunin-Borkowski: Electron tomography and holography in materials science, Nat. Mater. 8(4), 271–280 (2009)

    CAS  Google Scholar 

  • P.A. Midgley, M. Weyland, T.J.V. Yates, I. Arslan, R.E. Dunin-Borkowski, J.M. Thomas: Nanoscale scanning transmission electron tomography, J. Microsc. 223(3), 185–190 (2006)

    CAS  Google Scholar 

  • P.A. Midgley, E.P.W. Ward, A.B. Hungria, J.M. Thomas: Nanotomography in the chemical, biological and materials sciences, Chem. Soc. Rev. 36, 1477–1494 (2007)

    CAS  Google Scholar 

  • M. Weyland, P.A. Midgley: Electron tomography. In: Nanocharacterisation, 2nd edn., ed. by A.I. Kirkland, S.J. Haigh (Royal Society of Chemistry, Cambridge 2007)

    Google Scholar 

  • H. Jinnai, R.J. Spontak: Transmission electron microtomography in polymer research, Polymer 50(5), 1067–1087 (2009)

    CAS  Google Scholar 

  • H. Jinnai, R.J. Spontak, T. Nishi: Transmission electron microtomography and polymer nanostructures, Macromolecules 43(4), 1675–1688 (2010)

    CAS  Google Scholar 

  • C. Kübel, A. Voigt, R. Schoenmakers, M. Otten, D. Su, T.-C. Lee, A. Carlsson, J. Bradley: Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications, Microsc. Microanal. 11, 378–400 (2005)

    Google Scholar 

  • G. Möbus, B.J. Inkson: Nanoscale tomography in materials science, Mater. Today 10(12), 18–25 (2007)

    Google Scholar 

  • Z. Saghi, X. Xu, G. Möbus: Electron tomography of regularly shaped nanostructures under non-linear image acquisition, J. Microsc. 232(1), 186–195 (2008)

    CAS  Google Scholar 

  • H. Friedrich, M.R. McCartney, P.R. Buseck: Comparison of intensity distributions in tomograms from BF TEM, ADF STEM, HAADF STEM, and calculated tilt series, Ultramicroscopy 106(1), 18–27 (2005)

    CAS  Google Scholar 

  • F. Leroux, E. Bladt, J.-P. Timmermans, G. Van Tendeloo, S. Bals: Annular dark-field transmission electron microscopy for low contrast materials, Microsc. Microanal. 19(03), 629–634 (2013)

    CAS  Google Scholar 

  • G. Prieto, J. Zečević, H. Friedrich, K.P. de Jong, P.E. de Jongh: Towards stable catalysts by controlling collective properties of supported metal nanoparticles, Nat. Mater. 12(1), 34–39 (2013)

    CAS  Google Scholar 

  • R.J. Spontak, M.C. Williams, D.A. Agard: Three-dimensional study of cylindrical morphology in a styrene-butadiene-styrene block copolymer, Polymer 29(3), 387–395 (1988)

    CAS  Google Scholar 

  • H. Jinnai, X. Jiang: Electron tomography in soft materials, Curr. Opin. Solid State Mater. Sci. 17(3), 135–142 (2013)

    CAS  Google Scholar 

  • P. Yuan, L. Tan, D. Pan, Y. Guo, L. Zhou, J. Yang, J. Zou, C. Yu: A systematic study of long-range ordered 3D-SBA-15 materials by electron tomography, New J. Chem. 35, 2456–2461 (2011)

    CAS  Google Scholar 

  • K.P. de Jong, J. Zečević, H. Friedrich, P.E. de Jongh, M. Bulut, S. van Donk, R. Kenmogne, A. Finiels, V. Hulea, F. Fajula: Zeolite Y crystals with trimodal porosity as ideal hydrocracking catalysts, Angew. Chem. Int. Ed. 49, 10074–10078 (2010)

    Google Scholar 

  • J. Zečević, K.P. de Jong, P.E. de Jongh: Progress in electron tomography to assess the 3D nanostructure of catalysts, Curr. Opin. Solid State Mater. Sci. 17(3), 115–125 (2013)

    Google Scholar 

  • R. Leary, P.A. Midgley, J.M. Thomas: Recent advances in the application of electron tomography to materials chemistry, Acc. Chem. Res. 45(10), 1782–1791 (2012)

    CAS  Google Scholar 

  • M. Weyland: Electron tomography of catalysts, Top. Catal. 21(4), 175–183 (2002)

    CAS  Google Scholar 

  • S.J. Pennycook, P.D. Nellist: Scanning Transmission Electron Microscopy (Springer, New York 2011)

    Google Scholar 

  • O.L. Krivanek, M.F. Chisholm, V. Nicolosi, T.J. Pennycook, G.J. Corbin, N. Dellby, M.F. Murfitt, C.S. Own, Z.S. Szilagyi, M.P. Oxley, S.T. Pantelides, S.J. Pennycook: Atom-by-atom structural and chemical analysis by annular dark-field electron microscopy, Nature 464(7288), 571–574 (2010)

    CAS  Google Scholar 

  • M.M.J. Treacy: Z dependence of electron scattering by single atoms into annular dark-field detectors, Microsc. Microanal. 17(06), 847–858 (2011)

    CAS  Google Scholar 

  • P. Ercius, O. Alaidi, M.J. Rames, G. Ren: Electron tomography: A three-dimensional analytic tool for hard and soft materials research, Adv. Mater. 27, 5638–5663 (2015)

    CAS  Google Scholar 

  • M. Weyland, P.A. Midgley: Electron tomography, Mater. Today 7(12), 32–40 (2004)

    CAS  Google Scholar 

  • E.P.W. Ward, T.J.V. Yates, J.-J. Fernandez, D.E.W. Vaughan, P.A. Midgley: Three-dimensional nanoparticle distribution and local curvature of heterogeneous catalysts revealed by electron tomography, J. Phys. Chem. C 111(31), 11501–11505 (2007)

    CAS  Google Scholar 

  • J.C. Hernández-Garrido, K. Yoshida, P.L. Gai, E.D. Boyes, C.H. Christensen, P.A. Midgley, N.C. Greenham: The location of gold nanoparticles on titania: A study by high resolution aberration-corrected electron microscopy and 3D electron tomography, Catal. Today 160, 165–169 (2011)

    Google Scholar 

  • J.M. Thomas, P.A. Midgley, T.J.V. Yates, J.S. Barnard, R. Raja, I. Arslan, M. Weyland: The chemical application of high-resolution electron tomography: Bright field or dark field?, Angew. Chem. Int. Ed. 43(48), 6745–6747 (2004)

    CAS  Google Scholar 

  • K. Lu, E. Sourty, R. Guerra, G. Bar, J. Loos: Critical comparisonof volume data obtained by different electron tomography techniques, Macromolecules 43(3), 1444–1448 (2010)

    CAS  Google Scholar 

  • P.B. Hirsch, A. Howie, P.B. Nicholson, D.W. Pashley, W.J. Whelan: Electron Microscopy of Thin Crystals (Krieger, New York 1977)

    Google Scholar 

  • I. Arslan, T.J.V. Yates, N.D. Browning, P.A. Midgley: Embedded nanostructures revealed in three dimensions, Science 309(5744), 2195–2198 (2005)

    CAS  Google Scholar 

  • Z.Y. Li, N.P. Young, M.D. Vece, S. Palomba, R.E. Palmer, A.L. Bleloch, B.C. Curley, R.L. Johnston, J. Jiang, J. Yuan: Three-dimensional atomic-scale structure of size-selected gold nanoclusters, Nature 451, 46 (2008)

    CAS  Google Scholar 

  • M. Azubel, J. Koivisto, S. Malola, D. Bushnell, G.L. Hura, A. Koh, H. Tsunoyama, T. Tsukuda, M. Pettersson, H. Häkkinen, R.D. Kornberg: Electron microscopy of gold nanoparticles at atomic resolution, Science 345(6199), 909–912 (2014)

    CAS  Google Scholar 

  • C.-C. Chen, C. Zhu, E.R. White, C.-Y. Chiu, M.C. Scott, B.C. Regan, L.D. Marks, Y. Huang, J. Miao: Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution, Nature 496(7443), 74–77 (2013)

    CAS  Google Scholar 

  • B. Goris, J. De Beenhouwer, A. De Backer, D. Zanaga, K.J. Batenburg, A. Sánchez-Iglesias, L.M. Liz-Marzán, S. Van Aert, S. Bals, J. Sijbers, G. Van Tendeloo: Measuring lattice strain in three dimensions through electron microscopy, Nano Lett. 15, 6996–7001 (2015)

    Google Scholar 

  • G. Haberfehlner, P. Thaler, D. Knez, A. Volk, F. Hofer, W.E. Ernst, G. Kothleitner: Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography, Nat. Commun. 6, 8779 (2015)

    CAS  Google Scholar 

  • M.C. Scott, C.-C. Chen, M. Mecklenburg, C. Zhu, R. Xu, P. Ercius, U. Dahmen, B.C. Regan, J. Miao: Electron tomography at 2.4-ångström resolution, Nature 483(7390), 444–447 (2012)

    CAS  Google Scholar 

  • J. Park, H. Elmlund, P. Ercius, J.M. Yuk, D.T. Limmer, Q. Chen, K. Kim, S.H. Han, D.A. Weitz, A. Zettl, A.P. Alivisatos: 3D structure of individual nanocrystals in solution by electron microscopy, Science 349, 290–295 (2015)

    CAS  Google Scholar 

  • T. Willhammar, K. Sentosun, S. Mourdikoudis, B. Goris, M. Kurttepeli, M. Bercx, D. Lamoen, B. Partoens, I. Pastoriza-Santos, J. Perez-Juste, L.M. Liz-Marzan, S. Bals, G. Van Tendeloo: Structure and vacancy distribution in copper telluride nanoparticles influence plasmonic activity in the near-infrared, Nat. Commun. 8, 14925–14932 (2017)

    CAS  Google Scholar 

  • B. Goris, T. Roelandts, K.J. Batenburg, H. Heidari Mezerji, S. Bals: Advanced reconstruction algorithms for electron tomography: From comparison to combination, Ultramicroscopy 127, 40–47 (2013)

    CAS  Google Scholar 

  • Y. Yang, C.-C. Chen, M.C. Scott, C. Ophus, R. Xu, A. Pryor, L. Wu, F. Sun, W. Theis, J. Zhou, M. Eisenbach, P.R.C. Kent, R.F. Sabirianov, H. Zeng, P. Ercius, J. Miao: Deciphering chemical order/disorder and material properties at the single-atom level, Nature 542(7639), 75–79 (2017)

    CAS  Google Scholar 

  • L.D. Marks: Experimental studies of small particle structures, Rep. Prog. Phys. 57(6), 603–649 (1994)

    CAS  Google Scholar 

  • T.J.A. Slater, A. Macedo, S.L.M. Schroeder, M.G. Burke, P. O'Brien, P.H.C. Camargo, S.J. Haigh: Correlating catalytic activity of Ag-Au nanoparticles with 3D compositional variations, Nano Lett. 14, 1921 (2014)

    CAS  Google Scholar 

  • P. Burdet, Z. Saghi, A.N. Filippin, A. Borrás, P.A. Midgley: A novel 3D absorption correction method for quantitative EDX-STEM tomography, Ultramicroscopy 160, 118 (2016)

    CAS  Google Scholar 

  • G. Haberfehlner, A. Orthacker, M. Albu, J. Li, G. Kothleitner: Nanoscale voxel spectroscopy by simultaneous EELS and EDS tomography, Nanoscale 6, 14563 (2014)

    CAS  Google Scholar 

  • B. Goris, S. Turner, S. Bals, G. Van Tendeloo: Three-dimensional valency mapping in ceria nanocrystals, ACS Nano 8, 10878 (2014)

    CAS  Google Scholar 

  • O. Nicoletti, F. de la Pena, R.K. Leary, D.J. Holland, C. Ducati, P.A. Midgley: Three-dimensional imaging of localized surface plasmon resonances of metal nanoparticles, Nature 502, 80 (2013)

    CAS  Google Scholar 

  • N.Y. Jin-Phillipp, C.T. Koch, P.A. van Aken: Toward quantitative core-loss EFTEM tomography, Ultramicroscopy 111, 1255 (2011)

    CAS  Google Scholar 

  • M.H. Gass, K.K.K. Koziol, A.H. Windle, P.A. Midgley: Four-dimensional spectral tomography of carbonaceous nanocomposites, Nano Lett. 6(3), 376–379 (2006)

    CAS  Google Scholar 

  • P. Torruella, R. Arenal, F. de la Peña, Z. Saghi, L. Yedra, A. Eljarrat, L. López-Conesa, M. Estrader, A. López-Ortega, G. Salazar-Alvarez, J. Nogués, C. Ducati, P.A. Midgley, F. Peiró, S. Estradé: 3D visualization of the iron oxidation state in FeO/Fe3O4 core–shell nanocubes from electron energy loss tomography, Nano Lett. 16, 5068–5073 (2016)

    CAS  Google Scholar 

  • F. de la Peña, T. Ostaševičius, R.K. Leary, C. Ducati, P.A. Midgley, R. Arenal: Quantitative elemental and bonding EELS tomography of a complex nanoparticle. In: Proc. Eur. Microsc. Congr. (2016), https://doi.org/10.1002/9783527808465.EMC2016.6431

    Chapter  Google Scholar 

  • A. Yurtsever, M. Weyland, D.A. Muller: Three-dimensional imaging of nonspherical silicon nanoparticles embedded in silicon oxide by plasmon tomography, Appl. Phys. Lett. 89, 151920 (2006)

    Google Scholar 

  • A.C. Atre, B.J.M. Brenny, T. Coenen, A. García-Etxarri, A. Polman, J.A. Dionne: Nanoscale optical tomography with cathodoluminescence spectroscopy, Nat. Nanotechnol. 10, 429 (2015)

    CAS  Google Scholar 

  • R.F. Egerton: Electron Energy-Loss Spectroscopy in the Electron Microscope (Springer, New York 2011)

    Google Scholar 

  • J. Scott, P.J. Thomas, M. Mackenzie, S. McFadzean, J. Wilbrink, A.J. Craven, W.A. Nicholson: Near-simultaneous dual energy range EELS spectrum imaging, Ultramicroscopy 108(12), 1586–1594 (2008)

    CAS  Google Scholar 

  • A. Al-Afeef, W.P. Cockshott, I. MacLaren, S. McVitie: Electron tomography image reconstruction using data-driven adaptive compressed sensing, Scanning 38, 251–276 (2016)

    CAS  Google Scholar 

  • Z. Saghi, X. Xu, Y. Peng, B. Inkson, G. Mobus: Three-dimensional chemical analysis of tungsten probes by energy dispersive x-ray nanotomography, Appl. Phys. Lett. 91, 251906 (2007)

    Google Scholar 

  • T.J.A. Slater, A. Janssen, P.H.C. Camargo, M.G. Burke, N.J. Zaluzec, S.J. Haigh: STEM-EDX tomography of bimetallic nanoparticles: A methodological investigation, Ultramicroscopy 162, 61–73 (2016)

    CAS  Google Scholar 

  • C.S. Yeoh, D. Rossouw, Z. Saghi, P. Burdet, R.K. Leary, P.A. Midgley: The dark side of EDX tomography: Modeling detector shadowing to aid 3D elemental signal analysis, Microsc. Microanal. 21(3), 759–764 (2015)

    CAS  Google Scholar 

  • D. Zanaga, T. Altantzis, J. Sanctorum, B. Freitag, S. Bals: An alternative approach for ζ-factor measurement using pure element nanoparticles, Ultramicroscopy 164, 11–16 (2016)

    CAS  Google Scholar 

  • Z. Saghi, G. Divitini, B. Winter, R. Leary, E. Spiecker, C. Ducati, P.A. Midgley: Compressed sensing electron tomography of needle-shaped biological specimens – Potential for improved reconstruction fidelity with reduced dose, Ultramicroscopy 160, 230–238 (2016)

    CAS  Google Scholar 

  • D. Wolf, A. Lubk, F. Röder, H. Lichte: Electron holographic tomography, Curr. Opin. Solid State Mater. Sci. 17(3), 126–134 (2013)

    CAS  Google Scholar 

  • U. Kolb, E. Mugnaioli, T.E. Gorelik: Automated electron diffraction tomography—A new tool for nano crystal structure analysis, Cryst. Res. Technol. 46(6), 542–554 (2011)

    CAS  Google Scholar 

  • K. Kimura, S. Hata, S. Matsumura, T. Horiuchi: Dark-field transmission electron microscopy for a tilt series of ordering alloys: Toward electron tomography, J. Electron Microsc. 54(4), 373–377 (2005)

    CAS  Google Scholar 

  • R. Beanland, A. Sánchez, J. Hernandez-Garrido, D. Wolf, P. Midgley: Electron tomography of III-V quantum dots using dark field 002 imaging conditions, J. Microsc. 237(2), 148–154 (2010)

    CAS  Google Scholar 

  • H.H. Liu, S. Schmidt, H.F. Poulsen, A. Godfrey, Z.Q. Liu, J.A. Sharon, X. Huang: Three-dimensional orientation mapping in the transmission electron microscope, Science 332, 833–834 (2011)

    CAS  Google Scholar 

  • A.S. Eggeman, R. Krakow, P.A. Midgley: Scanning precession electron tomography for three-dimensional nanoscale orientation imaging and crystallographic analysis, Nat. Commun. 6, 7267 (2015)

    CAS  Google Scholar 

  • Y. Meng, J.-M. Zuo: Three-dimensional nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction, IUCr Journal 3, 300–308 (2016)

    CAS  Google Scholar 

  • D. Johnstone, A. Van Helvoort, P. Midgley: Nanoscale strain tomography by scanning precession electron diffraction, Microsc. Microanal. 23(S1), 1710–1711 (2017)

    Google Scholar 

  • S.J. Lade, D. Paganin, M.J. Morgan: Electron tomography of electromagnetic fields, potentials and sources, Opt. Commun. 253(4–6), 392–400 (2005)

    CAS  Google Scholar 

  • G. Lai, T. Hirayama, K. Ishizuka, T. Tanji, A. Tonomura: Three-dimensional reconstruction of electric-potential distribution in electron-holographic interferometry, Appl. Opt. 33(5), 829–833 (1994)

    CAS  Google Scholar 

  • C. Phatak, M. Beleggia, M. De Graef: Vector field electron tomography of magnetic materials: Theoretical development, Ultramicroscopy 108, 503–513 (2008)

    CAS  Google Scholar 

  • V. Stolojan, R.E. Dunin-Borkowski, M. Weyland, P.A. Midgley: Three-dimensional magnetic fields of nanoscale elements determined by electron-holographic tomography, Electron Microsc. Anal. 2001, 243–246 (2001)

    Google Scholar 

  • C. Phatak, A.K. Petford-Long, M. De Graef: Three-dimensional study of the vector potential of magnetic structures, Phys. Rev. Lett. 104, 253901 (2010)

    Google Scholar 

  • D. Wolf, L.A. Rodriguez, A. Béché, E. Javon, L. Serrano, C. Magen, C. Gatel, A. Lubk, H. Lichte, S. Bals, G. Van Tendeloo, A. Fernández-Pacheco, J.M. De Teresa, E. Snoeck: 3D magnetic induction maps of nanoscale materials revealed by electron holographic tomography, Chem. Mater. 27(19), 6771–6778 (2015)

    CAS  Google Scholar 

  • P. Simon, D. Wolf, C. Wang, A.A. Levin, A. Lubk, S. Sturm, H. Lichte, G.H. Fecher, C. Felser: Synthesis and three-dimensional magnetic field mapping of Co2FeGa Heusler nanowires at 5 nm resolution, Nano Lett. 16, 114 (2016)

    CAS  Google Scholar 

  • V. Migunov, H. Ryll, X. Zhuge, M. Simson, L. Strüder, K.J. Batenburg, L. Houben, R.E. Dunin-Borkowski: Rapid low dose electron tomography using a direct electron detection camera, Sci. Rep. 5, 14516 (2015)

    CAS  Google Scholar 

  • R. Guckenberger: Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy, Ultramicroscopy 9, 167–173 (1982)

    Google Scholar 

  • L. Houben, M. Bar Sadan: Refinement procedure for the image alignment in high-resolution electron tomography, Ultramicroscopy 111(9/10), 1512–1520 (2011)

    CAS  Google Scholar 

  • T. Sanders, M. Prange, C. Akatay, P. Binev: Physically motivated global alignment method for electron tomography, Adv. Struct. Chem. Imaging 1, 1–11 (2015)

    CAS  Google Scholar 

  • D. Gürsoy, Y.P. Hong, K. He, K. Hujsak, S. Yoo, S. Chen, Y. Li, M. Ge, L.M. Miller, Y.S. Chu, V. De Andrade, K. He, O. Cossairt, A.K. Katsaggelos, C. Jacobsen: Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection, Sci. Rep. 7, 11818 (2017)

    Google Scholar 

  • C.O. Sanchez Sorzano, C. Messaoudi, M. Eibauer, J.R. Bilbao-Castro, R. Hegerl, S. Nickell, S. Marco, J.M. Carazo: Marker-free image registration of electron tomography tilt-series, BMC Bioinformatics 10, 124 (2009)

    Google Scholar 

  • J. Kwon, J.E. Barrera, T.Y. Jung, S.P. Most: Measurements of orbital volume change using computed tomography in isolated orbital blowout fractures, Arch. Facial Plast. Surg. 11(6), 395–398 (2009)

    Google Scholar 

  • T. Furnival, R.K. Leary, P.A. Midgley: Denoising time-resolved microscopy image sequences with singular value thresholding, Ultramicroscopy 178, 112–124 (2017)

    CAS  Google Scholar 

  • P.C. Hansen, M. Saxild-Hansen: AIR Tools—a MATLAB package of algebraic iterative reconstruction methods, J. Comput. Appl. Math. 236(8), 2167–2178 (2012)

    Google Scholar 

  • P.F.C. Gilbert: The reconstruction of a three-dimensional structure from projections and its application to electron microscopy, II. Direct methods, Proc. Royal Soc. B 182(1066), 89–102 (1972)

    CAS  Google Scholar 

  • E. Lee, B.P. Fahimian, C.V. Iancu, C. Suloway, G.E. Murphy, E.R. Wright, D. Castaño Díez, G.J. Jensen, J. Miao: Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography, J. Struct. Biol. 164(2), 221–227 (2008)

    CAS  Google Scholar 

  • Y. Chen, F. Förster: Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms, J. Struct. Biol. 185(3), 309–316 (2014)

    Google Scholar 

  • Z. Saghi, D.J. Holland, R. Leary, A. Falqui, G. Bertoni, A.J. Sederman, L.F. Gladden, P.A. Midgley: Three-dimensional morphology of iron oxide nanoparticles with reactive concave surfaces, a compressed sensing-electron tomography (CS-ET) approach, Nano Lett. 11(11), 4666–4673 (2011)

    CAS  Google Scholar 

  • R. Leary, Z. Saghi, P.A. Midgley, D.J. Holland: Compressed sensing electron tomography, Ultramicroscopy 131, 70–91 (2013)

    CAS  Google Scholar 

  • J. Miao, F. Förster, O. Levi: Equally sloped tomography with oversampling reconstruction, Phys. Rev. B 72(5), 052103 (2005)

    Google Scholar 

  • C. Zhu, C.-C. Chen, J. Du, M.R. Sawaya, M.C. Scott, P. Ercius, J. Ciston, J. Miao: Towards three-dimensional structural determination of amorphous materials at atomic resolution, Phys. Rev. B 88, 100201 (2013)

    Google Scholar 

  • M.I. Sezan: An overview of convex projections theory and its application to image recovery problems, Ultramicroscopy 40(1), 55–67 (1992)

    Google Scholar 

  • R. Gordon, R. Bender, G.T. Herman: Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and X-ray photography, J. Theor. Biol. 29(3), 471–481 (1970)

    CAS  Google Scholar 

  • P. Gilbert: Iterative methods for the three-dimensional reconstruction of an object from projections, J. Theor. Biol. 36(1), 105–117 (1972)

    CAS  Google Scholar 

  • J.I. Agulleiro, J.J. Fernandez: Fast tomographic reconstruction on multicore computers, Bioinformatics 27(4), 582–583 (2011)

    CAS  Google Scholar 

  • S. Kaczmarz: Angenäherte Auflösung von Systemen linearer Gleichungen, Bull. Int. Acad. Pol. Sci. Lett. A 35, 355–357 (1937)

    Google Scholar 

  • P.P.B. Eggermont, G.T. Herman, A. Lent: Iterative algorithms for large partitioned linear systems, with applications to image reconstruction, Linear Algebra Appl. 40, 37–67 (1981)

    Google Scholar 

  • Y. Censor, S.A. Zenios: Parallel Optimization: Theory and Algorithms (Oxford Univ. Press, New York 1997)

    Google Scholar 

  • A.H. Andersen, A.C. Kak: Simultaneous algebraic reconstruction technique (SART): A superior implementation of the ART algorithm, Ultrason. Imaging 6(1), 81–94 (1984)

    CAS  Google Scholar 

  • L. Landweber: An iteration formula for Fredholm integral equations of the first kind, Am. J. Math. 73(3), 615–624 (1951)

    Google Scholar 

  • J. Gregor, T. Benson: Computational analysis and improvement of SIRT, IEEE Trans. Med. Imaging 27(7), 918–924 (2008)

    Google Scholar 

  • E. Elfving, T. Nikazad, P.C. Hansen: Semi-convergence and relaxation parameters for a class of SIRT algorithms, Electron. Trans. Numer. Anal. 37, 321–336 (2010)

    Google Scholar 

  • J. Tong, I. Arslan, P. Midgley: A novel dual-axis iterative algorithm for electron tomography, J. Struct. Biol. 153(1), 55–63 (2006)

    Google Scholar 

  • D. Wolf, A. Lubk, H. Lichte: Weighted simultaneous iterative reconstruction technique for single-axis tomography, Ultramicroscopy 136, 15–25 (2014)

    CAS  Google Scholar 

  • A. Lange, A. Kupsch, M.P. Hentschel, I. Manke, N. Kardjilov, T. Arlt, R. Grothausmann: Reconstruction of limited computed tomography data of fuel cell components using direct iterative reconstruction of computed tomography trajectories, J. Power Sources 196(12), 5293–5298 (2011)

    CAS  Google Scholar 

  • S. Lück, A. Kupsch, A. Lange, M.P. Hentschel, V. Schmidt: Statistical analysis of tomographic reconstruction algorithms by morphological image characteristics, Image Anal. Stereol. 29(2), 61–77 (2010)

    Google Scholar 

  • E.J. Candès, J. Romberg, T. Tao: Robust uncertainty principles: Exact signal reconstruction from highly incomplete frequency information, IEEE Trans. Inf. Theory 52(2), 489–509 (2006)

    Google Scholar 

  • D.L. Donoho: Compressed sensing, IEEE Trans. Inf. Theory 52(4), 1289–1306 (2006)

    Google Scholar 

  • E.Y. Sidky, X.C. Pan: Image reconstruction in circular cone-beam computed tomography by constrained, total-variation minimization, Phys. Med. Biol. 53(17), 4777–4807 (2008)

    Google Scholar 

  • D.J. Holland, D.M. Malioutov, A. Blake, A.J. Sederman, L.F. Gladden: Reducing data acquisition times in phase-encoded velocity imaging using compressed sensing, J. Magn. Reson. 203(2), 236–246 (2010)

    CAS  Google Scholar 

  • M. Lustig, D. Donoho, J.M. Pauly: Sparse MRI: The application of compressed sensing for rapid MR imaging, Magn. Reson. Med. 58(6), 1182–1195 (2007)

    Google Scholar 

  • M.W. Kim, J. Choi, L. Yu, K.E. Lee, S.S. Han, J.C. Ye: Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory, Proceedings SPIE 6498, 64981G (2007)

    Google Scholar 

  • C. Vonesch, W. Lanhui, Y. Shkolnisky, A. Singer: Fast wavelet-based single-particle reconstruction in cryo-EM. In: IEEE Symp. Biomed. Imaging (2011), https://doi.org/10.1109/ISBI.2011.5872791

    Chapter  Google Scholar 

  • D.S. Taubman, M.W. Marcellin: JPEG2000: Standard for interactive imaging, Proceedings IEEE 90(8), 1336–1357 (2002)

    Google Scholar 

  • J.L. Starck, F. Murtagh, J.M. Fadili: Sparse Image and Signal Processing: Wavelets, Curvelets, Morphological Diversity (Cambridge Univ. Press, Cambridge 2010)

    Google Scholar 

  • L. Rudin, S. Osher, E. Fatemi: Non-linear total variation noise removal algorithm, Physica D 60, 259–268 (1992)

    Google Scholar 

  • S. Mallat: A Wavelet Tour of Signal Processing (Academic Press, Burlington 2008)

    Google Scholar 

  • A. Stoschek, R. Hegerl: Denoising of electron tomographic reconstructions using multiscale transformations, J. Struct. Biol. 120(3), 257–265 (1997)

    CAS  Google Scholar 

  • C.O.S. Sorzano, E. Ortiz, M. López, J. Rodrigo: Improved Bayesian image denoising based on wavelets with applications to electron microscopy, Pattern Recognit. 39(6), 1205–1213 (2006)

    Google Scholar 

  • C.O.S. Sorzano, S. Jonić, C. El-Bez, J.M. Carazo, S. De Carlo, P. Thévenaz, M. Unser: A multiresolution approach to orientation assignment in 3D electron microscopy of single particles, J. Struct. Biol. 146(3), 381–392 (2004)

    CAS  Google Scholar 

  • K. Song, L.R. Comolli, M. Horowitz: Removing high contrast artifacts via digital inpainting in cryo-electron tomography: An application of compressed sensing, J. Struct. Biol. 178(2), 108–120 (2012)

    Google Scholar 

  • J.L. Starck, M. Elad, D.L. Donoho: Image decomposition via the combination of sparse representations and a variational approach, IEEE Trans. Image Process. 14(10), 1570–1582 (2005)

    Google Scholar 

  • G.T. Herman, A. Kuba: Discrete Tomography: Foundations, Algorithms and Applications (Birkhauser, Boston 1999)

    Google Scholar 

  • K.J. Batenburg, S. Bals, J. Sijbers, C. Kübel, P.A. Midgley, J.C. Hernandez, U. Kaiser, E.R. Encina, E.A. Coronado, G. Van Tendeloo: 3D imaging of nanomaterials by discrete tomography, Ultramicroscopy 109(6), 730–740 (2009)

    CAS  Google Scholar 

  • J.R. Jinschek, K.J. Batenburg, H.A. Calderon, R. Kilaas, V. Radmilovic, C. Kisielowski: 3-D reconstruction of the atomic positions in a simulated gold nanocrystal based on discrete tomography: Prospects of atomic resolution electron tomography, Ultramicroscopy 108(6), 589–604 (2008)

    CAS  Google Scholar 

  • K. Batenburg, J. Sijbers: DART: A practical reconstruction algorithm for discrete tomography, IEEE Trans. Image Process. 20(9), 2542–2553 (2011)

    Google Scholar 

  • S. Bals, M. Casavola, M.A. van Huis, S. Van Aert, K.J. Batenburg, G. Van Tendeloo, D.L. Vanmaekelbergh: Three-dimensional atomic imaging of colloidal core-shell nanocrystals, Nano Lett. 11(8), 3420–3424 (2011)

    CAS  Google Scholar 

  • F.J. Maestre-Deusto, G. Scavello, J. Pizarro, P.L. Galindo: ADART: an adaptive algebraic reconstruction algorithm for discrete tomography, IEEE Trans. Image Process. 20(8), 2146–2152 (2011)

    Google Scholar 

  • K.J. Batenburg, W. van Aarle, J. Sijbers: A semi-automatic algorithm for grey level estimation in tomography, Pattern Recognit. Lett. 32(9), 1395–1405 (2011)

    Google Scholar 

  • A. Zürner, M. Döblinger, V. Cauda, R. Wei, T. Bein: Discrete tomography of demanding samples based on a modified SIRT algorithm, Ultramicroscopy 115, 41–49 (2012)

    Google Scholar 

  • T. Roelandts, K.J. Batenburg, E. Biermans, C. Kübel, S. Bals, J. Sijbers: Accurate segmentation of dense nanoparticles by partially discrete electron tomography, Ultramicroscopy 114, 96–105 (2012)

    CAS  Google Scholar 

  • X. Zhuge, W.J. Palenstijn, K.J. Batenburg: TVR-DART: A more robust algorithm for discrete tomography from limited projection data with automated gray value estimation, IEEE Trans. Image Process. 25(1), 455–468 (2016)

    Google Scholar 

  • A. Alpers, R.J. Gardner, S. König, R.S. Pennington, C.B. Boothroyd, L. Houben, R.E. Dunin-Borkowski, K.J. Batenburg: Geometric reconstruction methods for electron tomography, Ultramicroscopy 128, 42–54 (2013)

    Google Scholar 

  • M. Wollgarten, M. Habeck: Autonomous reconstruction and segmentation of tomographic data, Micron 63, 20–27 (2014)

    Google Scholar 

  • R.J. Gardner: Geometric Tomography (Cambridge Univ. Press, Cambridge 2006)

    Google Scholar 

  • T.C. Petersen, S.P. Ringer: Electron tomography using a geometric surface-tangent algorithm: Application to atom probe specimen morphology, J. Appl. Phys. 105(10), 103518 (2009)

    Google Scholar 

  • W.O. Saxton, W. Baumeister, M. Hahn: Three-dimensional reconstruction of imperfect two-dimensional crystals, Ultramicroscopy 13(1/2), 57–70 (1984)

    CAS  Google Scholar 

  • Y. Cheng: Single-particle cryo-EM at crystallographic resolution, Cell 161(3), 450–457 (2015)

    CAS  Google Scholar 

  • M. Shalev-Benami, Y. Zhang, D. Matzov, Y. Halfon, A. Zackay, H. Rozenberg, E. Zimmerman, A. Bashan, C.L. Jaffe, A. Yonath, G. Skiniotis: 2.8-Å cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania, Cell Rep. 16(2), 288–294 (2016)

    CAS  Google Scholar 

  • E. Callaway: The revolution will not be crystallized: A new method sweeps through structural biology, Nature 525, 172–174 (2015)

    CAS  Google Scholar 

  • N. Grigorieff: Direct detection pays off for electron cryo-microscopy, eLife 2, e00573 (2013)

    Google Scholar 

  • D. Rossouw, R. Krakow, Z. Saghi, C.S.M. Yeoh, P. Burdet, R.K. Leary, F. de la Peña, C. Ducati, C.M.F. Rae, P.A. Midgley: Blind source separation aided characterization of the γ' strengthening phase in an advanced nickel-based superalloy by spectroscopic 4D electron microscopy, Acta Mater. 107, 229–238 (2016)

    CAS  Google Scholar 

  • S.M. Collins, E. Ringe, M. Duchamp, Z. Saghi, R.E. Dunin-Borkowski, P.A. Midgley: Eigenmode tomography of surface charge oscillations of plasmonic nanoparticles by electron energy loss spectroscopy, ACS Photonics 2(11), 1628–1635 (2015)

    CAS  Google Scholar 

  • S.M. Collins, S. Fernandez-Garcia, J.J. Calvino, P.A. Midgley: Sub-nanometer surface chemistry and orbital hybridization in lanthanum-doped ceria nano-catalysts revealed by 3D electron microscopy, Sci. Rep. 7, 5406 (2017)

    Google Scholar 

  • J.-J. Fernandez: Computational methods for materials characterization by electron tomography, Curr. Opin. Solid State Mater. Sci. 17(3), 93–106 (2013)

    CAS  Google Scholar 

  • N. Volkmann, J.J. Grant: Methods for segmentation and interpretation of electron tomographic reconstructions, Methods Enzymol. 483, 31–46 (2010)

    Google Scholar 

  • R. Narasimha, I. Aganj, A.E. Bennett, M.J. Borgnia, D. Zabransky, G. Sapiro, S.W. McLaughlin, J.L.S. Milne, S. Subramaniam: Evaluation of denoising algorithms for biological electron tomography, J. Struct. Biol. 164(1), 7–17 (2008)

    Google Scholar 

  • J.-J. Fernández, S. Li: An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms, J. Struct. Biol. 144(1/2), 152–161 (2003)

    Google Scholar 

  • C. Bajaj, Z. Yu, M. Auer: Volumetric feature extraction and visualization of tomographic molecular imaging, J. Struct. Biol. 144(1/2), 132–143 (2003)

    Google Scholar 

  • J.-J. Fernandez: TOMOBFLOW: feature-preserving noise filtering for electron tomography, BMC Bioinformatics 10, 178 (2009)

    Google Scholar 

  • E. Garduño, M. Wong-Barnum, N. Volkmann, M.H. Ellisman: Segmentation of electron tomographic data sets using fuzzy set theory principles, J. Struct. Biol. 162(3), 368–379 (2008)

    Google Scholar 

  • K. Sandberg, M. Brega: Segmentation of thin structures in electron micrographs using orientation fields, J. Struct. Biol. 157(2), 403–415 (2007)

    CAS  Google Scholar 

  • R. Leary, Z. Saghi, M. Armbrüster, G. Wowsnick, R. Schlögl, J.M. Thomas, P.A. Midgley: Quantitative high-angle annular dark-field scanning transmission electron microscope (HAADF-STEM) tomography and high-resolution electron microscopy of unsupported intermetallic GaPd2 catalysts, J. Phys. Chem. C 116(24), 13343–13352 (2012)

    CAS  Google Scholar 

  • R. Thiedmann, A. Spettl, O. Stenzel, T. Zeibig, J.C. Hindson, Z. Saghi, N.C. Greenham, P.A. Midgley, V. Schmidt: Networks of nanoparticles in organic-inorganic composites: Algorithmic extraction and statistical analysis, Image Anal. Stereol. 31(1), 27–42 (2011)

    Google Scholar 

  • C.J. Gommes, K. de Jong, J.-P. Pirard, S. Blacher: Assessment of the 3D localization of metallic nanoparticles in Pd/SiO2 cogelled catalysts by electron tomography, Langmuir 21(26), 12378–12385 (2005)

    Google Scholar 

  • R. Grothausmann, G. Zehl, I. Manke, S. Fiechter, P. Bogdanoff, I. Dorbandt, A. Kupsch, A. Lange, M.P. Hentschel, G. Schumacher, J. Banhart: Quantitative structural assessment of heterogeneous catalysts by electron tomography, J. Am. Chem. Soc. 133(45), 18161–18171 (2011)

    CAS  Google Scholar 

  • J.C. Russ, F.B. Neal: The Image Processing Handbook, 7th edn. (CRC, Boca Raton 2015)

    Google Scholar 

  • H. Li, H.L. Xin, D.A. Muller, L.A. Estroff: Visualizing the 3D internal structure of calcite single crystals grown in agarose hydrogels, Science 326(5957), 1244–1247 (2009)

    CAS  Google Scholar 

  • M. Sezgin, B. Sankur: Survey over image thresholding techniques and quantitative performance evaluation, J. Electron. Imaging 13(1), 146–168 (2004)

    Google Scholar 

  • W. van Aarle, K.J. Batenburg, J. Sijbers: Optimal threshold selection for segmentation of dense homogeneous objects in tomographic reconstructions, IEEE Trans. Med. Imaging 30(4), 980–989 (2011)

    Google Scholar 

  • N. Otsu: A threshold selection method from gray-level histograms, IEEE Trans. Syst. Man Cybern. 9(1), 62–66 (1979)

    Google Scholar 

  • J.C. Hindson, Z. Saghi, J.-C. Hernandez-Garrido, P.A. Midgley, N.C. Greenham: Morphological study of nanoparticle-polymer solar cells using high-angle annular dark-field electron tomography, Nano Lett. 11(2), 904–909 (2011)

    CAS  Google Scholar 

  • H. Friedrich, S. Guo, P.E. de Jongh, X. Pan, X. Bao, K.P. de Jong: A quantitative electron tomography study of ruthenium particles on the interior and exterior surfaces of carbon nanotubes, ChemSusChem 4(7), 957–963 (2011)

    CAS  Google Scholar 

  • K.J. Batenburg, J. Sijbers: Optimal threshold selection for tomogram segmentation by projection distance minimization, IEEE Trans. Med. Imaging 28(5), 676–686 (2009)

    CAS  Google Scholar 

  • M.N. Lebbink, W.J.C. Geerts, T.P. van der Krift, M. Bouwhuis, L.O. Hertzberger, A.J. Verkleij, A.J. Koster: Template matching as a tool for annotation of tomograms of stained biological structures, J. Struct. Biol. 158(3), 327–335 (2007)

    Google Scholar 

  • N. Volkmann: A novel three-dimensional variant of the watershed transform for segmentation of electron density maps, J. Struct. Biol. 138(1/2), 123–129 (2002)

    CAS  Google Scholar 

  • H. Katz-Boon, C.J. Rossouw, M. Weyland, A.M. Funston, P. Mulvaney, J. Etheridge: Three-dimensional morphology and crystallography of gold nanorods, Nano Lett. 11(1), 273–278 (2011)

    CAS  Google Scholar 

  • C.M.A. Parlett, M.A. Isaacs, S.K. Beaumont, L.M. Bingham, N.S. Hondow, K. Wilson, A.F. Lee: Spatially orthogonal chemical functionalization of a hierarchical pore network for catalytic cascade reactions, Nat. Mater. 15, 178–182 (2016)

    CAS  Google Scholar 

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Acknowledgements

The research leading to these results was possible through funding from the European Union Seventh Framework Program under Grant Agreement 312483-ESTEEM2 (Integrated Infrastructure Initiative–I3), from the European Research Council under the European Union's Seventh Framework Program (FP/2007–2013)/ERC Grant Agreement 291522–3-DIMAGE, and funding from the EPSRC, grant number EP/R008779/1. R.K.L. acknowledges a Junior Research Fellowship at Clare College. The authors acknowledge the many people with whom they have worked, including most recently Sir John Meurig Thomas, Francisco de la Pena, Sean Collins, Adam Lee, Emilie Ringe, Alex Eggeman, Jon Barnard, Duncan Johnstone, and David Rossouw.

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Leary, R.K., Midgley, P.A. (2019). Electron Tomography in Materials Science. In: Hawkes, P.W., Spence, J.C.H. (eds) Springer Handbook of Microscopy. Springer Handbooks. Springer, Cham. https://doi.org/10.1007/978-3-030-00069-1_26

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