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56. R. Erni, Abberation-corrected Imaging in Transmission Electron Microscopy: An
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57. G.E. Murphy, G.J. Jensen, Electron cryotomography. BioTechniques, 43(4), 413, 415, 417
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58. C.V. Iancu et al., A ‘flip-flop’ rotation stage for routine dual-axis electron cryotomography.
J. Struct. Biol. 151(3), 288–297 (2005)
59. V. Lucić, F. Förster, W. Baumeister, Structural studies by electron tomography: from cells to
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60. R.A. Crowther, D.J. DeRosier, A. Klug, The reconstruction of a three-dimensional structure
from projections and its application to electron microscopy. Proc. R. Soc. Lond. Math. Phys.
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61. W.O. Saxton, W. Baumeister, M. Hahn, Three-dimensional reconstruction of imperfect
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62. W.J.H. Hagen, W. Wan, J.A.G. Briggs, Implementation of a cryo-electron tomography
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117–124 (2013)
68. T.R. Shaikh et al., SPIDER image processing for single-particle reconstruction of biological
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69. S. Nickell et al., TOM software toolbox: acquisition and analysis for electron tomography.
J. Struct. Biol. 149(3), 227–234 (2005)
70. C. MessaoudiI, T. Boudier, C.O.S. Sorzano, S. Marco, TomoJ: tomography software for
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71. F. Amat, F. Moussavi, L.R. Comolli, G. Elidan, K.H. Downing, M. Horowitz, Markov
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Bioinforma. Oxf. Engl. 27(4), 582–583 (2011)
73. J.J. Fernández, S. Li, R.A. Crowther, CTF determination and correction in electron
cryotomography. Ultramicroscopy 106(7), 587–596 (2006)
74. 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)
75. C.O.S. Sorzano et al., Marker-free image registration of electron tomography tilt-series.
BMC Bioinformatics 10, 124 (2009)
76. D. Castaño-Díez, M. Scheffer, A. Al-Amoudi, A.S. Frangakis, Alignator: a GPU powered
software package for robust fiducial-less alignment of cryo tilt-series. J. Struct. Biol. 170(1),
117–126 (2010)
77. J.-J. Fernandez et al., Removing contamination-induced reconstruction artifacts from
cryo-electron tomograms. Biophys. J. 110(4), 850–859 (2016)
3 Electron Cryo-Tomography
91
Proc. Natl. Acad. Sci. 201411610 (2015)
55. D. Stokes, G. Owen, An introduction to low dose electron tomography—from specimen
preparation to data collection. Mod. Res. Educ. Top. Microsc 939–950 (2007)
56. R. Erni, Abberation-corrected Imaging in Transmission Electron Microscopy: An
introduction. World Scientific (2010)
57. G.E. Murphy, G.J. Jensen, Electron cryotomography. BioTechniques, 43(4), 413, 415, 417
passim, (2007)
58. C.V. Iancu et al., A ‘flip-flop’ rotation stage for routine dual-axis electron cryotomography.
J. Struct. Biol. 151(3), 288–297 (2005)
59. V. Lucić, F. Förster, W. Baumeister, Structural studies by electron tomography: from cells to
molecules. Annu. Rev. Biochem. 74, 833–865 (2005)
60. R.A. Crowther, D.J. DeRosier, A. Klug, The reconstruction of a three-dimensional structure
from projections and its application to electron microscopy. Proc. R. Soc. Lond. Math. Phys.
Eng. Sci. 317(1530), 319–340 (1970)
61. W.O. Saxton, W. Baumeister, M. Hahn, Three-dimensional reconstruction of imperfect
two-dimensional crystals. Ultramicroscopy 13(1–2), 57–70 (1984)
62. W.J.H. Hagen, W. Wan, J.A.G. Briggs, Implementation of a cryo-electron tomography
tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197(2),
191–198 (2017)
63. W. Wan, J.A.G. Briggs, Chapter thirteen—cryo-electron tomography and subtomogram
averaging, in Methods in Enzymology, vol. 579, ed. by R.A. Crowther (Academic Press,
2016), pp. 329–367
64. M. Kudryashev, H. Stahlberg, D. Castaño-Díez, Assessing the benefits of focal pair
cryo-electron tomography. J. Struct. Biol. (2011)
65. R.D. Leapman, Novel techniques in electron microscopy. Curr. Opin. Neurobiol. 14(5),
591–598 (2004)
66. J. Kremer, D. Mastronarde, J. McIntosh, Computer visualization of three-dimensional image
data using IMOD. J. Struct. Biol. 116(1), 71–76 (1996)
67. H. Winkler, K.A. Taylor, Marker-free dual-axis tilt series alignment. J. Struct. Biol. 182(2),
117–124 (2013)
68. T.R. Shaikh et al., SPIDER image processing for single-particle reconstruction of biological
macromolecules from electron micrographs. Nat. Protoc. 3(12), 1941–1974 (2008)
69. S. Nickell et al., TOM software toolbox: acquisition and analysis for electron tomography.
J. Struct. Biol. 149(3), 227–234 (2005)
70. C. MessaoudiI, T. Boudier, C.O.S. Sorzano, S. Marco, TomoJ: tomography software for
three-dimensional reconstruction in transmission electron microscopy. BMC Bioinformatics
8, 288 (2007)
71. F. Amat, F. Moussavi, L.R. Comolli, G. Elidan, K.H. Downing, M. Horowitz, Markov
random field based automatic image alignment for electron tomography. J. Struct. Biol. 161
(3), 260–275 (2008)
72. J.I. Agulleiro, J.J. Fernandez, Fast tomographic reconstruction on multicore computers.
Bioinforma. Oxf. Engl. 27(4), 582–583 (2011)
73. J.J. Fernández, S. Li, R.A. Crowther, CTF determination and correction in electron
cryotomography. Ultramicroscopy 106(7), 587–596 (2006)
74. 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)
75. C.O.S. Sorzano et al., Marker-free image registration of electron tomography tilt-series.
BMC Bioinformatics 10, 124 (2009)
76. D. Castaño-Díez, M. Scheffer, A. Al-Amoudi, A.S. Frangakis, Alignator: a GPU powered
software package for robust fiducial-less alignment of cryo tilt-series. J. Struct. Biol. 170(1),
117–126 (2010)
77. J.-J. Fernandez et al., Removing contamination-induced reconstruction artifacts from
cryo-electron tomograms. Biophys. J. 110(4), 850–859 (2016)
3 Electron Cryo-Tomography
91