Electron tomography in the (S)TEM: From nanoscale morphological analysis to 3D atomic imaging

Annual Review of Materials Research

Volumn 42, Issue , 2012, Pages 59-79

  Saghi, Zineb ^a   Midgley, Paul A ^b  

^a Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina IBIMA Plataforma Bionand   (Spain)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

3D imaging; Aberration correction; Atomic resolution; Nanotechnology; Reconstruction algorithms; Transmission electron microscopy

Indexed keywords

3D IMAGING; ABERRATION CORRECTION; ABERRATION-CORRECTED; ATOMIC IMAGING; ATOMIC LEVELS; ATOMIC RESOLUTION; ELECTRON TOMOGRAPHY; MORPHOLOGICAL ANALYSIS; NANO SCALE; PROJECTION DATA; RECONSTRUCTION ALGORITHMS; TECHNIQUE DEVELOPMENT;

ALGORITHMS; ELECTRIC IMPEDANCE TOMOGRAPHY; NANOTECHNOLOGY; THREE DIMENSIONAL; TRANSMISSION ELECTRON MICROSCOPY;

ATOMS;

EID: 84864185409     PISSN: 15317331     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev-matsci-070511-155019     Document Type: Review

References (86)

1. Belloni F, Küutahyali C, Rondinella VV, Carbol P, Wiss T, Mangione A. 2009. Can carbon nanotubes play a role in the field of nuclear waste management? Environ. Sci. Technol. 43:1250-55
2. Konstantatos G, Sargent EH. Nanostructured materials for photon detection. Nat. Nano 5:391-400
3. KooOM, Rubinstein I, Onyuksel H. 2005. Role of nanotechnology in targeted drug delivery and imaging: a concise review. Nanomed. Nanotechnol. Biol. Med. 1:193-212
4. Liang Y,Wu Y, Feng D, Tsai S-T, Son H-J, et al. 2008. Development of new semiconducting polymers for high performance solar cells. J. Am. Chem. Soc. 131:56-57
5. Steele BCH, Heinzel A. 2001. Materials for fuel-cell technologies. Nature 414:345-52
6. Thomas JM, Midgley PA. The modern electron microscope: a cornucopia of chemico-physical insights. Chem. Phys. 385:1-10
7. Wang ZL, Poncharal P, de Heer WA. 2000. Measuring physical and mechanical properties of individual carbon nanotubes by in situ TEM. J. Phys. Chem. Solids 61:1025-30
8. Helveg S, Lopez-Cartes C, Sehested J, Hansen PL, Clausen BS, et al. 2004. Atomic-scale imaging of carbon nanofibre growth. Nature 427:426-29
9. Midgley PA,Dunin-Borkowski RE. 2009. Electron tomography and holography in materials science. Nat. Mater. 8:271-80
10. DeRosier D, Klug A. 1968. Reconstruction of three dimensional structures from electron micrographs. Nature 217:130-34
11. Hart RG. 1968. Electron microscopy of unstained biological material: the polytropic montage. Science 159:1464-67
12. Hoppe W, Langer R, Knesch G, Poppe C. 1968. Protein crystal structure analysis with electron radiation. Transl. Naturwiss. 55:333-36
13. Frank J, ed. 2007. Electron Tomography:Methods for Three-Dimensional Visualization of Structures in the Cell. New York: Springer
14. Midgley PA, Weyland M. 2003. 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography. Ultramicroscopy 96:413-31
15. Ward EPW, Yates TJV, Fernandez J-J, Vaughan DEW, Midgley PA. 2007. Three-dimensional nanoparticle distribution and local curvature of heterogeneous catalysts revealed by electron tomography. J. Phys. Chem. C 111:11501-5
16. Midgley PA,Ward EPW, Hungria AB, Thomas JM. 2007. Nanotomography in the chemical, biological and materials sciences. Chem. Soc. Rev. 36:1477-94
17. Koster AJ, Grimm R, Typke D, Hegerl R, Stoschek A, et al. 1997. Perspectives of molecular and cellular electron tomography. J. Struct. Biol. 120:276-308
18. Spontak RJ, Williams MC, Agard DA. 1988. Three-dimensional study of cylindrical morphology in a styrene-butadiene-styrene block copolymer. Polymer 29:387-95
19. Koster AJ, Ziese U, Verkleij AJ, Janssen AH, Graaf Jd, et al. 2000. Development and application of 3- dimensional transmission electron microscopy (3D-TEM) for the characterization ofmetal-zeolite catalyst systems. Stud. Surf. Sci. Catal. 130:329-34
20. Friedrich H, McCartneyMR, Buseck PR. 2005. Comparison of intensity distributions in tomograms from BF TEM, ADF TEM, HAADF STEM, and calculated tilt series. Ultramicroscopy 106:18-27
21. Kübel C, Voigt A, Schoenmakers R, Otten M, Su D, et al. 2005. Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications. Microsc. Microanal. 11:378-400
22. Weyland M, Midgley PA, Thomas JM. 2001. Electron tomography of nanoparticle catalysts on porous supports: a new technique based on Rutherford scattering. J. Phys. Chem. B 105:7882-86
23. Thomas JM, Midgley PA, Yates TJV, Barnard JS, Raja R, et al. 2004. The chemical application of highresolution electron tomography: bright field or dark field? Angew. Chem. Int. Ed. 43:6745-47
24. Arslan I, Yates TJV, Browning ND, Midgley PA. 2005. Embedded nanostructures revealed in three dimensions. Science 309:2195-98
25. Weyland M. 2002. Electron tomography of catalysts. Top. Catal. 21:175-83
26. Friedrich H, Gommes CJ, Overgaag K, Meeldijk JD, Evers WH, et al. 2009. Quantitative structural analysis of binary nanocrystal superlattices by electron tomography. Nano Lett. 9:2719-24
27. Jinnai H, Nishikawa Y, Spontak RJ, Smith SD, Agard DA, Hashimoto T. 2000. Direct measurement of interfacial curvature distributions in a bicontinuous block copolymer morphology. Phys. Rev. Lett. 84:518-21
28. Yates TJV, Thomas JM, Fernandez J-J, Terasaki O, Ryoo R, Midgley PA. 2006. Three-dimensional real-space crystallography of MCM-48 mesoporous silica revealed by scanning transmission electron tomography. Chem. Phys. Lett. 418:540-43
29. Ercius P,WeylandM,Muller DA, Gignac LM. 2006. Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography. Appl. Phys. Lett. 88:243116
30. Saghi Z, Xu X, Peng Y, Inkson BJ, Moebus G. 2007. Three-dimensional chemical analysis of tungsten probes by energy dispersive X-ray nanotomography. Appl. Phys. Lett. 91:251906
31. Hohmann-MarriottMF, Sousa AA, Azari AA, Glushakova S, Zhang G, et al. 2009. Nanoscale 3D cellular imaging by axial scanning transmission electron tomography. Nat. Methods 6:729-31
32. Porter AE,GassM,MullerK, Skepper JN, Midgley PA,WellandM. 2007. Direct imaging of single-walled carbon nanotubes in cells. Nat. Nano 2:713-17
33. Bals S, Kabius B, Haider M, Radmilovic V, Kisielowski C. 2004. Annular dark field imaging in a TEM. Solid State Commun. 130:675-80
34. Rebled JM, Yedra L, Estrade S, Portillo J, Peiro F. 2011. A new approach for 3D reconstruction from bright field TEM imaging: beam precession assisted electron tomography. Ultramicroscopy 111:1504-11
35. Gass MH, Koziol KKK, Windle AH, Midgley PA. 2006. Four-dimensional spectral tomography of carbonaceous nanocomposites. Nano Lett. 6:376-79
36. Yurtsever A, WeylandM,Muller DA. 2006. Three-dimensional imaging of nonspherical silicon nanoparticles embedded in silicon oxide by plasmon tomography. Appl. Phys. Lett. 89:1519201-3
37. Möbus G, Doole RC, Inkson BJ. 2003. Spectroscopic electron tomography. Ultramicroscopy 96:433-51
38. Heidari Mezerji H, Van den Broek W, Bals S. 2011. A practical method to determine the effective resolution in incoherent experimental electron tomography. Ultramicroscopy 111:330-36
39. Aronova MA, Kim YC, Harmon R, Sousa AA, Zhang G, Leapman RD. 2007. Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST). J. Struct. Biol. 160:35-48
40. Schlossmacher P, Klenov DO, Freitag B, von Harrach HS. 2010. Enhanced detection sensitivity with a newwindowlessXEDSsystem forAEMbased on silicon drift detector technology. Microsc. Today 18:14-20
41. Jarausch K, Thomas P, Leonard DN, Twesten R, Booth CR. 2009. Four-dimensional STEM-EELS: enabling nano-scale chemical tomography. Ultramicroscopy 109:326-37
42. Barnard JS, Sharp J, Tong JR, Midgley PA. 2006. High-resolution three-dimensional imaging of dislocations. Science 313:319
43. Sharp JH, Barnard JS, Kaneko K, Higashida K, Midgley PA. 2008. Dislocation tomography made easy: a reconstruction from ADF STEM images obtained using automated image shift correction. J. Phys. Conf. Ser. 126:012013
44. Hata S, Miyazaki H, Miyazaki S, Mitsuhara M, Tanaka M, et al. 2011. High-angle triple-axis specimen holder for three-dimensional diffraction contrast imaging in transmission electron microscopy. Ultramicroscopy 111:1168-75
45. Bracewell RN. 1956. Strip integration in radio astronomy. Aust. J. Phys. 9:198-217
46. Arslan I, Tong JR,Midgley PA. 2006. Reducing the missing wedge: high-resolution dual axis tomography of inorganic materials. Ultramicroscopy 106:994-1000
47. Kawase N, Kato M, Nishioka H, Jinnai H. 2007. Transmission electron microtomography without the "missing wedge" for quantitative structural analysis. Ultramicroscopy 107:8-15
48. Dierksen K, Typke D, Hegerl R, Koster AJ, Baumeister W. 1992. Towards automatic electron tomography. Ultramicroscopy 40:71-87
49. Baumeister W, Grimm R, Walz J. 1999. Electron tomography of molecules and cells. Trends Cell Biol. 9:81-85
50. Bals S, Batenburg KJ, Verbeeck J, Sijbers J, Tandeloo GV. 2007. Quantitative three-dimensional reconstruction of catalyst particles for bamboo-like carbon nanotubes. Nano Lett. 7:3669-74
51. Batenburg KJ, Sijbers J. 2007. DART: a fast heuristic algebraic reconstruction algorithm for discrete tomography. Proc. IEEE Int. Conf. on Image Processing (ICIP), San Antonio, Texas, Sep. 16-19, TP-L5.2
52. LebbinkMN,Geerts WJ, van derKrift TP, Bouwhuis M, HertzbergerLO, et al. 2007. Templatematching as a tool for annotation of tomograms of stained biological structures. J. Struct. Biol. 158:327-35
53. Fernandez J-J, Li S. 2003. An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms. J. Struct. Biol. 144:152-61
54. Sorzano COS,Ortiz E, LopezM, Rodrigo J. 2006. Improved Bayesian image denoising based on wavelets with applications to electron microscopy. Pattern Recognit. 39:1205-13
55. Narasimha R, Aganj I, Bennett AE, Borgnia MJ, Zabransky D, et al. 2008. Evaluation of denoising algorithms for biological electron tomography. J. Struct. Biol. 164:7-17
56. Saghi Z, Xu X, Moebus G. 2008. Three-dimensional metrology and fractal analysis of dendritic nanostructures. Phys. Rev. B 78:205428
57. Saghi Z, Holland DJ, Leary R, Falqui A, Bertoni G, et al. 2011. Three-dimensional morphology of iron oxide nanoparticles with reactive concave surfaces. A compressed sensing-electron tomography (CS-ET) approach. Nano Lett. 11:4666-73
58. Perassi EM, Hernandez-Garrido JC, Moreno MS, Encina ER, Coronado EA, Midgley PA. 2010. Using highly accurate 3D nanometrology to model the optical properties of highly irregular nanoparticles: a powerful tool for rational design of plasmonic devices. Nano Lett. 10:2097-104
59. Hindson JC, Saghi Z, Hernandez-Garrido J-C, Midgley PA, Greenham NC. 2011. Morphological study of nanoparticle-polymer solar cells using high-angle annular dark-field electron tomography. Nano Lett. 11:904-9
60. Tanaka N. 2008. Present status and future prospects of spherical aberration corrected TEM/STEM for study of nanomaterials. Sci. Technol. Adv. Mater. 9:014111
61. Howie A. 2009. Aberration correction: zooming out to overview. Philos. Trans. A Math. Phys. Eng. Sci. 367:3859-70
62. Gai PL, Boyes ED. 2009. Advances in atomic resolution in situ environmental transmission electron microscopy and 1 A aberration corrected in situ electron microscopy. Microsc. Res. Tech. 72:153-64
63. Crowther RA, De Rosier DJ, Klug A. 1970. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc. R. Soc. Lond. A 317:319-40
64. Li ZY, Young NP, Vece MD, Palomba S, Palmer RE, et al. 2008. Three-dimensional atomic-scale structure of size-selected gold nanoclusters. Nature 451:46-48
65. Möbus G, Saghi Z, Sayle DC, Bhatta UM, Stringfellow A, Sayle TXT. 2011. Dynamics of polar surfaces on ceria nanoparticles observed in situ with single-atom resolution. Adv. Funct. Mater. 21:1971-76
66. Chang LY, Barnard AS, Gontard LC, Dunin-Borkowski RE. 2010. Resolving the structure of active sites on platinum catalytic nanoparticles. Nano Lett. 10:3073-76
67. van Benthem K, Lupini AR,Kim M, Baik HS, Doh S, et al. 2005. Three-dimensional imaging of individual hafnium atoms inside a semiconductor device. Appl. Phys. Lett. 87:034104
68. Borisevich AY, Lupini AR, Pennycook SJ. 2006. Depth sectioning with the aberration-corrected scanning transmission electron microscope. Proc. Natl. Acad. Sci. USA 103:3044-48
69. Allen JE, Hemesath ER, Perea DE, Lensch-Falk JL, LiZ Y, et al. 2008. High-resolution detection of Au catalyst atoms in Si nanowires. Nat. Nano 3:168-73
70. Nellist PD. 2006. Confocal operation of a transmission electron microscope with two aberration correctors. Appl. Phys. Lett. 89:124105
71. Wang P, Behan G, Takeguchi M, Hashimoto A,Mitsuishi K, et al. 2010. Nanoscale energy-filtered scanning confocal electron microscopy using a double-aberration-corrected transmission electron microscope. Phys. Rev. Lett. 104:200801
72. Van Dyck D, Van Aert S, Croitoru M. 2006. Atomic resolution electron tomography: a dream? Int. J. Mater. Res. 97:872-79
73. Bar Sadan M, Houben L,Wolf SG, Enyashin A, Seifert G, et al. 2008. Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures. Nano Lett. 8:801-6
74. Saghi Z, Xu X, Moebus G. 2009. Model based atomic resolution tomography. J. Appl. Phys. 106:024304
75. Jinschek JR,BatenburgKJ, Calderon HA,Kilaas R, RadmilovicV,Kisielowski C. 2008. 3-D reconstruction of the atomic positions in a simulated gold nanocrystal based on discrete tomography: prospects of atomic resolution electron tomography. Ultramicroscopy 108:589-604
76. Van Aert S, Batenburg KJ, Rossell MD, Erni R, Van Tendeloo G. 2011. Three-dimensional atomic imaging of crystalline nanoparticles. Nature 470:374-77
77. Bals S, Casavola M, van Huis MA, Van Aert S, Batenburg KJ, et al. 2011. Three-dimensional atomic imaging of colloidal core-shell nanocrystals. Nano Lett. 11:3420-24
78. ScottMC, Chen C-C, MecklenburgM, Zhu C, Xu R, et al. 2012. Electron tomography at 2.4-A ngstrom resolution. Nature 483:444-47
79. Candes E, Romberg J,Tao T. 2006. Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information. IEEE Trans. Inf. Theory 52:489-509
80. Donoho DL. 2006. Compressed sensing. IEEE Trans. Inf. Theory 52:1289-306
81. Houben L, Bar SadanM. 2011. Refinement procedure for the image alignment in high-resolution electron tomography. Ultramicroscopy 111:1512-20
82. Kwon O-H, Zewail AH. 2010. 4D Electron tomography. Science 328:1668-73
83. Blavette D, Cadel E, Fraczkiewicz A, Menand A. 1999. Three-dimensional atomic-scale imaging of impurity segregation to line defects. Science 286:2317-19
84. Kelly T, Miller M, Rajan K, Ringer S, Borisevich A, et al. 2011. Toward atomic-scale tomography: the ATOM project. Microsc. Microanal. 17:708-9
85. Huang WJ, Sun R, Tao J, Menard LD, Nuzzo RG, Zuo JM. 2008. Coordination-dependent surface atomic contraction in nanocrystals revealed by coherent diffraction. Nat. Mater. 7:308-13
86. Zuo JM, Vartanyants I, Gao M, Zhang R, Nagahara LA. 2003. Atomic resolution imaging of a carbon nanotube from diffraction intensities. Science 300:1419-21