Computational methods for materials characterization by electron tomography

Current Opinion in Solid State and Materials Science

Volumn 17, Issue 3, 2013, Pages 93-106

  Fernandez, Jose Jesus ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

Computational methods; Electron tomography; Image processing; Materials science; Segmentation; Tomographic reconstruction

Indexed keywords

COMPUTATIONAL METHODS; ELECTRIC IMPEDANCE TOMOGRAPHY; IMAGE PROCESSING; IMAGE SEGMENTATION; MATERIALS SCIENCE; THREE DIMENSIONAL COMPUTER GRAPHICS;

3D VISUALIZATION; ELECTRON TOMOGRAPHY; MATERIALS CHARACTERIZATION; MORPHOLOGICAL STUDY; STRUCTURAL INFORMATION; TECHNICAL ADVANCES; THREE-DIMENSIONAL (3D) ANALYSIS; TOMOGRAPHIC RECONSTRUCTION;

CHARACTERIZATION;

EID: 84882250012     PISSN: 13590286     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cossms.2013.03.002     Document Type: Review

References (72)

1. P.A. Midgley, and R.E. Dunin-Borkowski Electron tomography and holography in materials science Nat Mater 8 2009 272 280
2. R. Leary, P.A. Midgley, and J.M. Thomas Recent advances in the application of electron tomography to materials chemistry Accounts Chem Res 45 2012 1782 1791
3. G. van Tendeloo, S. Bals, S. van Aert, J. Verbeeck, and D. van Dyck Advanced electron microscopy for advanced materials Adv Mater 24 2012 5655 5675
4. Z. Saghi, and P.A. Midgley Electron tomography in the (S)TEM: from nanoscale morphological analysis to 3D atomic imaging Annu Rev Mater Res 42 2012 59 79
5. J. Frank Electron tomography: methods for three-dimensional visualization of structures in the cell 2nd ed. 2006 Springer New York
6. K. Fridman, A. Mader, M. Zwerger, N. Elia, and O. Medalia Advances in tomography: probing the molecular architecture of cells Nat Rev Mol Cell Biol 13 2012 736 742
7. A.J. Koster, U. Ziese, A.J. Verkleij, A.H. Janssen, and 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 2000 9368 9370
8. P.A. Midgley, M. Weyland, J.M. Thomas, and B.F.G. Johnson Z-contrast tomography: a technique in three-dimensional nanostructural analysis based on Rutherford scattering Chem Commun 2001 907 908
9. G. Mobus, and B.J. Inkson Three-dimensional reconstruction of buried nanoparticles by element-sensitive tomography based on inelastically scattered electrons Appl Phys Lett 79 2001 1369 1371
10. K.P. de Jong, and A.J. Koster Three-dimensional electron microscopy of mesoporous materials - recent strides towards spatial imaging at the nanometer scale ChemPhysChem 3 2002 776 780
11. P.A. Midgley, and M. Weyland 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography Ultramicroscopy 96 2003 413 431
12. I. Arslan, T.J.V. Yates, N.D. Browning, and P.A. Midgley Embedded nanostructures revealed in three dimensions Science 309 2005 2195 2198
13. J.S. Barnard, J. Sharp, J.R. Tong, and P.A. Midgley High-resolution three-dimensional imaging of dislocations Science 313 2006 319
14. H. Li, H.L. Xin, D.A. Muller, and L.A. Estroff Visualizing the 3D internal structure of calcite single crystals grown in agarose hydrogels Science 326 2009 1244 1247
15. S. van Aert, K.J. Batenburg, M.D. Rossell, R. Erni, and G. van Tendeloo Three-dimensional atomic imaging of crystalline nanoparticles Nature 470 2011 374 377
16. M.C. Scott, C.C. Chen, M. Mecklenburg, C. Zhu, R. Xu, and P. Ercius Electron tomography at 2.4 Å resolution Nature 483 2012 444 447
17. J.J. Fernandez Computational methods for electron tomography Micron 43 2012 1010 1030
18. J. Verbeeck, D. van Dyck, and G. van Tendeloo Energy-filtered transmission electron microscopy: an overview Spectrochim Acta Part B - Atom Spectrosc 59 2004 1529 1534
19. K. Dierksen, D. Typke, R. Hegerl, A.J. Koster, and W. Baumeister Towards automatic electron tomography Ultramicroscopy 40 1992 71 87
20. U. Ziese, A.H. Janssen, J.L. Murk, W.J.C. Geerts, T. van der Krift, and A.J. Verkleij Automated high-throughput electron tomography by pre-calibration of image shifts J Microsc 205 2002 187 200
21. A.J. Koster, R. Grimm, D. Typke, R. Hegerl, A. Stoschek, and J. Walz Perspectives of molecular and cellular electron tomography J Struct Biol 120 1997 276 308
22. I. Arslan, J.R. Tong, and P.A. Midgley Reducing the missing wedge: high-resolution dual axis tomography of inorganic materials Ultramicroscopy 106 2006 994 1000
23. J. Tong, I. Arslan, and P.A. Midgley A novel dual-axis iterative algorithm for electron tomography J Struct Biol 153 2006 55 63
24. M. Cao, H.B. Zhang, Y. Lu, R. Nishi, and A. Takaoka Formation and reduction of streak artefacts in electron tomography J Microsc 239 2010 66 71
25. F. Amat, D. Castano-Diez, A. Lawrence, F. Moussavi, H. Winkler, and M. Horowitz Alignment of cryo-electron tomography datasets Methods Enzymol 482 2010 343 367
26. L. Roiban, L. Hartmann, A. Fiore, D. Djurado, F. Chandezon, and P. Reiss Mapping the 3D distribution of CdSe nanocrystals in highly oriented and nanostructured hybrid P3HT-CdSe films grown by directional epitaxial crystallization Nanoscale 4 2012 7212 7220
27. O.H. Kwon, and A.H. Zewail 4D electron tomography Science 328 2010 1668 1673
28. L. Houben, and M. bar Sadan Refinement procedure for the image alignment in high-resolution electron tomography Ultramicroscopy 111 2011 1512 1520
29. J. Leschner, J. Biskupek, A. Chuvilin, and U. Kaiser Accessing the local three-dimensional structure of carbon materials sensitive to an electron beam Carbon 48 2010 4042 4048
30. B. Goris, S. Bals, W. van den Broek, E. Carbo-Argibay, S. Gomez-Grana, and L.M. Liz-Marzan Atomic-scale determination of surface facets in gold nanorods Nat Mater 11 2012 930 935
31. G.T. Herman Image reconstruction from projections: the fundamentals of computerized tomography 2nd ed. 2009 Springer London
32. P. Gilbert Iterative methods for the 3D reconstruction of an object from projections J Theor Biol 36 1972 105 117
33. T.J.V. Yates, J.M. Thomas, J.J. Fernandez, O. Terasaki, R. Ryoo, and P.A. Midgley Three-dimensional real-space crystallography of MCM-48 mesoporous silica revealed by scanning transmission electron tomography Chem Phys Lett 418 2006 540 543
34. G. Prieto, J. Zecevic, H. Friedrich, K.P. de Jong, and P.E. de Jongh Towards stable catalysts by controlling collective properties of supported metal nanoparticles Nat Mater 12 2013 34 39
35. H.H. Mezerji, W. van den Broek, and S. Bals A practical method to determine the effective resolution in incoherent experimental electron tomography Ultramicroscopy 111 2011 330 336
36. J.J. Fernandez High performance computing in structural determination by electron cryomicroscopy J Struct Biol 164 2008 1 6
37. J.I. Agulleiro, and J.J. Fernandez Fast tomographic reconstruction on multicore computers Bioinformatics 27 2011 582 583
38. F. Vazquez, E.M. Garzon, and J.J. Fernandez A matrix approach to tomographic reconstruction and its implementation on GPUs J Struct Biol 170 2010 146 151
39. J.I. Agulleiro, F. Vazquez, E.M. Garzon, and J.J. Fernandez Hybrid computing: CPU + GPU co-processing and its application to tomographic reconstruction Ultramicroscopy 115 2012 109 114
40. R.A. Crowther, D.J. de Rosier, and A. Klug The reconstruction of a three-dimensional structure from projections and its applications to electron microscopy Proc R Soc London A 317 1970 319 340
41. 2 cogelled catalysts by electron tomography Langmuir 21 2005 12378 12385
42. B.V. Andersson, A. Herland, S. Masich, and O. Inganas Imaging of the 3D nanostructure of a polymer solar cell by electron tomography Nano Lett 9 2009 853 855
43. R. Thiedmann, A. Spettl, O. Stenzel, T. Zeibig, J.C. Hindson, and Z. Saghi Networks of nanoparticles in organic-inorganic composites: algorithmic extraction and statistical analysis Image Anal Stereol 31 2012 27 42
44. J.J. Fernandez, and S. Li An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms J Struct Biol 144 2003 152 161
45. E.P.W. Ward, T.J.V. Yates, J.J. Fernandez, D.E.W. Vaughan, and P.A. Midgley Three-dimensional nanoparticle distribution and local curvature of heterogeneous catalysts revealed by electron tomography J Phys Chem C 111 2007 11501 11505
46. C.J. Gommes, H. Friedrich, M. Wolters, P.E. de Jongh, and K.P. de Jong Quantitative characterization of pore corrugation in ordered mesoporous materials using image analysis of electron tomograms Chem Mater 21 2009 1311 1317
47. V. Ortalan, M. Herrera, D.G. Morgan, and N.D. Browning Application of image processing to STEM tomography of low-contrast materials Ultramicroscopy 110 2009 67 81
48. Z. Saghi, D.J. Holland, R. Leary, A. Falqui, G. Bertoni, and A.J. Sederman Three-dimensional morphology of iron oxide nanoparticles with reactive concave surfaces. A compressed sensing-electron tomography (CS-ET) approach Nano Lett 11 2011 4666 4673
49. R. Leary, Z. Saghi, M. Armbruster, G. Wowsnick, R. Schlogl, and J.M. Thomas 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 2012 13343 13352
50. S.D. Oosterhout, M.M. Wienk, S.S. van Bavel, R. Thiedmann, L.J. Koster, and J. Gilot The effect of three-dimensional morphology on the efficiency of hybrid polymer solar cells Nat Mater 8 2009 818 824
51. N. Otsu A threshold selection method from gray-level histograms IEEE Trans Syst Man Cybern 9 1979 62 66
52. R. Grothausmann, G. Zehl, I. Manke, S. Fiechter, P. Bogdanoff, and I. Dorbandt Quantitative structural assessment of heterogeneous catalysts by electron tomography J Am Chem Soc 133 2011 18161 18171
53. J.C. Hindson, Z. Saghi, J.C. Hernandez-Garrido, P.A. Midgley, and N.C. Greenham Morphological study of nanoparticle-polymer solar cells using high-angle annular dark-field electron tomography Nano Lett 11 2011 904 909
54. K.J. Batenburg, and J. Sijbers Adaptive thresholding of tomograms by projection distance minimization Pattern Recognit 42 2009 2297 2305
55. H. Friedrich, J.R.A. Sietsma, P.E. de Jongh, A.J. Verkleij, and K.P. de Jong Measuring location, size, distribution, and loading of NiO crystallites in individual SBA-15 pores by electron tomography J Am Chem Soc 129 2007 10249 10254
56. 2 nanotubes by electron tomography Catal Today 143 2009 225 229
57. A. Martinez-Sanchez, I. Garcia, and J.J. Fernandez A differential structure approach to membrane segmentation in electron tomography J Struct Biol 175 2011 372 383
58. H. Jinnai, T. Kaneko, H. Nishioka, H. Hasegawa, and T. Nishi Spatial arrangement of metal nanoparticles supported by porous polymer substrates studied by transmission electron microtomography Chem Rec 6 2006 267 274
59. E. Biermans, L. Molina, K.J. Batenburg, S. Bals, and G. van Tendeloo Measuring porosity at the nanoscale by quantitative electron tomography Nano Lett 10 2010 5014 5019
60. E.M. Perassi, J.C. Hernandez-Garrido, M.S. Moreno, E.R. Encina, E.A. Coronado, and P.A. Midgley 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 2010 2097 2104
61. B. Goris, T. Roelandts, K.J. Batenburg, H.H. Mezerji, and S. Bals Advanced reconstruction algorithms for electron tomography: from comparison to combination, Ultramicroscopy 127 2013 40 47
62. A. Lange, A. Kupsch, M.P. Hentschel, I. Manke, N. Kardjilov, and T. Arlt Reconstruction of limited computed tomography data of fuel cell components using direct iterative reconstruction of computed tomography trajectories J Power Sources 196 2011 5293 5298
63. S. Luck, A. Kupsch, A. Lange, M.P. Hentschel, and V. Schmidt Statistical analysis of tomographic reconstruction algorithms by morphological image characteristics Image Anal Stereol 29 2010 61 77
64. K.J. Batenburg, S. Bals, J. Sijbers, C. Kubel, P.A. Midgley, and J.C. Hernandez 3D imaging of nanomaterials by discrete tomography Ultramicroscopy 109 2009 730 740
65. A. Zurner, M. Doblinger, V. Cauda, R. Wei, and T. Bein Discrete tomography of demanding samples based on a modified SIRT algorithm Ultramicroscopy 115 2012 41 49
66. W. van Aarle, K.J. Batenburg, and J. Sijbers Automatic parameter estimation for the discrete algebraic reconstruction technique (DART) IEEE Trans Image Process 21 2012 4608 4621
67. T. Roelandts, K.J. Batenburg, E. Biermans, C. Kubel, S. Bals, and J. Sijbers Accurate segmentation of dense nanoparticles by partially discrete electron tomography Ultramicroscopy 114 2012 96 105
68. B. Goris, W. van den Broek, K.J. Batenburg, H.H. Mezerji, and S. Bals Electron tomography based on a total variation minimization reconstruction technique Ultramicroscopy 113 2012 120 130
69. T. Altantzis, B. Goris, A. Sanchez-Iglesias, M. Grzelczak, L.M. Liz-Marzan, and S. Bals Quantitative structure determination of large three-dimensional nanoparticle assemblies Part Part Syst Charact 84-88 2013 30
70. J.M. Thomas, R. Leary, P.A. Midgley, and D.J. Holland A new approach to the investigation of nanoparticles: electron tomography with compressed sensing J Colloid Interface Sci 392 2013 7 14
71. Y.C. Eldar, and G. Kutyniok Compressed sensing: theory and applications 2012 Cambridge University Press
72. E.J. Candes, J. Romberg, and T. Tao Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information IEEE Trans Inf Theory 52 2006 489 509