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2016.03.018
51. D. Nemecek, J.B. Heymann, J. Qiao, L. Mindich, A.C. Steven, Cryo-electron tomography of
bacteriophage u6 procapsids shows random occupancy of the binding sites for RNA
polymerase and packaging NTPase. J. Struct. Biol. 171(3), 389–396 (2010). doi:10.1016/j.jsb.
2010.06.005
52. P. van der Heide, X.P. Xu, B.J. Marsh, D. Hanein, N. Volkmann, Efficient automatic noise
reduction of electron tomographic reconstructions based on iterative median filtering.
J. Struct. Biol. 158(2), 196–204 (2007). doi:10.1016/j.jsb.2006.10.030
53. W. Jiang, M.L. Baker, Q. Wu, C. Bajaj, W. Chiu, Applications of a bilateral denoising filter in
biological electron microscopy. J. Struct. Biol. 144(1–2), 114–122 (2003)
54. R.A. Ali, M.J. Landsberg, E. Knauth, G.P. Morgan, B.J. Marsh, B. Hankamer, A 3D image
filter for parameter-free segmentation of macromolecular structures from electron tomograms.
PLoS ONE 7(3), e33697 (2012). doi:10.1371/journal.pone.0033697
55. J.R. Bilbao-Castro, C.O. Sorzano, I. Garcia, J.J. Fernandez, XMSF: structure-preserving noise
reduction and pre-segmentation in microscope tomography. Bioinformatics 26(21), 2786–
2787 (2010). doi:10.1093/bioinformatics/btq496
56. D.Y. Wei, C.C. Yin, An optimized locally adaptive non-local means denoising filter for
cryo-electron microscopy data. J. Struct. Biol. 172(3), 211–218 (2010). doi:10.1016/j.jsb.
2010.06.021
57. J.J. Fernandez, TOMOBFLOW: feature-preserving noise filtering for electron tomography.
BMC Bioinform. 10, 178 (2009). doi:10.1186/1471-2105-10-178
58. A.S. Frangakis, R. Hegerl, Noise reduction in electron tomographic reconstructions using
nonlinear anisotropic diffusion. J. Struct. Biol. 135(3), 239–250 (2001)
59. J.J. Fernandez, S. Li, An improved algorithm for anisotropic nonlinear diffusion for denoising
cryo-tomograms. J. Struct. Biol. 144(1–2), 152–161 (2003)
60. D.N. Mastronarde, Fiducial marker and hybrid alignment methods for single- and double-axis
tomography, in Electron Tomography: Methods for Three-Dimensional Visualization of
Structures in the Cell ed. by J. Frank. (Springer New York, 2006), pp. 163–185. doi:10.1007/
978-0-387-69008-7_6
61. C.V. Iancu, E.R. Wright, J. Benjamin, W.F. Tivol, D.P. Dias, G.E. Murphy, R.C. Morrison,
J.B. Heymann, G.J. Jensen, A “flip-flop” rotation stage for routine dual-axis electron
cryotomography. J. Struct. Biol. 151(3), 288–297 (2005)
62. J. Tong, I. Arslan, P. Midgley, A novel dual-axis iterative algorithm for electron tomography.
J. Struct. Biol. 153(1), 55–63 (2006). doi:10.1016/j.jsb.2005.10.005
63. G.A. Zampighi, L. Zampighi, N. Fain, E.M. Wright, F. Cantele, S. Lanzavecchia, Conical
tomography II: A method for the study of cellular organelles in thin sections. J. Struct. Biol.
151(3), 263–274 (2005). doi:10.1016/j.jsb.2005.05.008
64. L. Kovacik, S. Kereiche, P. Matula, I. Raska, Sub-volume averaging of repetitive structural
features in angularly filtered electron tomographic reconstructions. Folia Biol. (Praha) 60
(Suppl 1), 66–70 (2014)
65. L. Kovacik, S. Kereiche, J.L. Hoog, P. Juda, P. Matula, I. Raska, A simple Fourier filter for
suppression of the missing wedge ray artefacts in single-axis electron tomographic
reconstructions. J. Struct. Biol. 186(1), 141–152 (2014). doi:10.1016/j.jsb.2014.02.004
66. J.M. Carazo, J.L. Carrascosa, Restoration of direct Fourier three-dimensional reconstructions
of crystalline specimens by the method of convex projections. J. Microsc. 145(Pt 2), 159–177
(1987)
67. Y. Deng, Y. Chen, Y. Zhang, S. Wang, F. Zhang, F. Sun, ICON: 3D reconstruction with
‘missing-information’ restoration in biological electron tomography. J. Struct. Biol. 195(1),
100–112 (2016). doi:10.1016/j.jsb.2016.04.004
68. D.N. Mastronarde, Dual-axis tomography: an approach with alignment methods that preserve
resolution. J. Struct. Biol. 120(3), 343–352 (1997). doi:10.1006/jsbi.1997.3919
69. G. Cardone, K. Grunewald, A.C. Steven, A resolution criterion for electron tomography based
on cross-validation. J. Struct. Biol. 151(2), 117–129 (2005)
234
J. Bernard Heymann
2016.03.018
51. D. Nemecek, J.B. Heymann, J. Qiao, L. Mindich, A.C. Steven, Cryo-electron tomography of
bacteriophage u6 procapsids shows random occupancy of the binding sites for RNA
polymerase and packaging NTPase. J. Struct. Biol. 171(3), 389–396 (2010). doi:10.1016/j.jsb.
2010.06.005
52. P. van der Heide, X.P. Xu, B.J. Marsh, D. Hanein, N. Volkmann, Efficient automatic noise
reduction of electron tomographic reconstructions based on iterative median filtering.
J. Struct. Biol. 158(2), 196–204 (2007). doi:10.1016/j.jsb.2006.10.030
53. W. Jiang, M.L. Baker, Q. Wu, C. Bajaj, W. Chiu, Applications of a bilateral denoising filter in
biological electron microscopy. J. Struct. Biol. 144(1–2), 114–122 (2003)
54. R.A. Ali, M.J. Landsberg, E. Knauth, G.P. Morgan, B.J. Marsh, B. Hankamer, A 3D image
filter for parameter-free segmentation of macromolecular structures from electron tomograms.
PLoS ONE 7(3), e33697 (2012). doi:10.1371/journal.pone.0033697
55. J.R. Bilbao-Castro, C.O. Sorzano, I. Garcia, J.J. Fernandez, XMSF: structure-preserving noise
reduction and pre-segmentation in microscope tomography. Bioinformatics 26(21), 2786–
2787 (2010). doi:10.1093/bioinformatics/btq496
56. D.Y. Wei, C.C. Yin, An optimized locally adaptive non-local means denoising filter for
cryo-electron microscopy data. J. Struct. Biol. 172(3), 211–218 (2010). doi:10.1016/j.jsb.
2010.06.021
57. J.J. Fernandez, TOMOBFLOW: feature-preserving noise filtering for electron tomography.
BMC Bioinform. 10, 178 (2009). doi:10.1186/1471-2105-10-178
58. A.S. Frangakis, R. Hegerl, Noise reduction in electron tomographic reconstructions using
nonlinear anisotropic diffusion. J. Struct. Biol. 135(3), 239–250 (2001)
59. J.J. Fernandez, S. Li, An improved algorithm for anisotropic nonlinear diffusion for denoising
cryo-tomograms. J. Struct. Biol. 144(1–2), 152–161 (2003)
60. D.N. Mastronarde, Fiducial marker and hybrid alignment methods for single- and double-axis
tomography, in Electron Tomography: Methods for Three-Dimensional Visualization of
Structures in the Cell ed. by J. Frank. (Springer New York, 2006), pp. 163–185. doi:10.1007/
978-0-387-69008-7_6
61. C.V. Iancu, E.R. Wright, J. Benjamin, W.F. Tivol, D.P. Dias, G.E. Murphy, R.C. Morrison,
J.B. Heymann, G.J. Jensen, A “flip-flop” rotation stage for routine dual-axis electron
cryotomography. J. Struct. Biol. 151(3), 288–297 (2005)
62. J. Tong, I. Arslan, P. Midgley, A novel dual-axis iterative algorithm for electron tomography.
J. Struct. Biol. 153(1), 55–63 (2006). doi:10.1016/j.jsb.2005.10.005
63. G.A. Zampighi, L. Zampighi, N. Fain, E.M. Wright, F. Cantele, S. Lanzavecchia, Conical
tomography II: A method for the study of cellular organelles in thin sections. J. Struct. Biol.
151(3), 263–274 (2005). doi:10.1016/j.jsb.2005.05.008
64. L. Kovacik, S. Kereiche, P. Matula, I. Raska, Sub-volume averaging of repetitive structural
features in angularly filtered electron tomographic reconstructions. Folia Biol. (Praha) 60
(Suppl 1), 66–70 (2014)
65. L. Kovacik, S. Kereiche, J.L. Hoog, P. Juda, P. Matula, I. Raska, A simple Fourier filter for
suppression of the missing wedge ray artefacts in single-axis electron tomographic
reconstructions. J. Struct. Biol. 186(1), 141–152 (2014). doi:10.1016/j.jsb.2014.02.004
66. J.M. Carazo, J.L. Carrascosa, Restoration of direct Fourier three-dimensional reconstructions
of crystalline specimens by the method of convex projections. J. Microsc. 145(Pt 2), 159–177
(1987)
67. Y. Deng, Y. Chen, Y. Zhang, S. Wang, F. Zhang, F. Sun, ICON: 3D reconstruction with
‘missing-information’ restoration in biological electron tomography. J. Struct. Biol. 195(1),
100–112 (2016). doi:10.1016/j.jsb.2016.04.004
68. D.N. Mastronarde, Dual-axis tomography: an approach with alignment methods that preserve
resolution. J. Struct. Biol. 120(3), 343–352 (1997). doi:10.1006/jsbi.1997.3919
69. G. Cardone, K. Grunewald, A.C. Steven, A resolution criterion for electron tomography based
on cross-validation. J. Struct. Biol. 151(2), 117–129 (2005)
234
J. Bernard Heymann