31. R. Marabini, G.T. Herman, J.M. Carazo, 3D reconstruction in electron microscopy using ART
with smooth spherically symmetric volume elements (blobs). Ultramicr 72(1–2), 53–65 (1998)
32. D. Wolf, A. Lubk, H. Lichte, Weighted simultaneous iterative reconstruction technique for
single-axis tomography. Ultramicr 136, 15–25 (2014). doi:10.1016/j.ultramic.2013.07.016
33. K.J. Batenburg, J. Sijbers, DART: a practical reconstruction algorithm for discrete
tomography. IEEE Trans. Image Process. 20(9), 2542–2553 (2011). doi:10.1109/TIP.2011.
2131661
34. J. Skilling, R.K. Bryan, Maximum entropy image reconstruction: general algorithm. Mon.
Not. R. Astron. Soc. 211(1), 111–124 (1984). doi:10.1093/mnras/211.1.111
35. J. Cope, J. Heumann, A. Hoenger, Cryo-electron tomography for structural characterization of
macromolecular complexes. Curr. Protoc. Protein Sci. Chapter 17(Unit17), 13 (2011). doi:10.
1002/0471140864.ps1713s65
36. 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). doi:10.1016/j.jsb.2012.01.003
37. M. Maiorca, C. Millet, E. Hanssen, B. Abbey, E. Kazmierczak, L. Tilley, Local regularization
of tilt projections reduces artifacts in electron tomography. J. Struct. Biol. 186(1), 28–37
(2014). doi:10.1016/j.jsb.2014.03.009
38. M. Defrise, F. Noo, H. Kudo, A solution to the long-object problem in helical cone-beam
tomography. Phys. Med. Biol. 45(3), 623–643 (2000)
39. W. Xu, F. Xu, M. Jones, B. Keszthelyi, J. Sedat, D. Agard, K. Mueller, High-performance
iterative electron tomography reconstruction with long-object compensation using graphics
processing units (GPUs). J. Struct. Biol. 171(2), 142–153 (2010). doi:10.1016/j.jsb.2010.03.
018
40. B. Turonova, L. Marsalek, P. Slusallek, On geometric artifacts in cryo electron tomography.
Ultramicr 163, 48–61 (2016). doi:10.1016/j.ultramic.2016.01.002
41. M. Maiorca, E. Hanssen, E. Kazmierczak, B. Maco, M. Kudryashev, R. Hall, H. Quiney,
L. Tilley, Improving the quality of electron tomography image volumes using pre-reconstruction
filtering. J. Struct. Biol. 180(1), 132–142 (2012). doi:10.1016/j.jsb.2012.05.019
42. V. Abrishami, J.R. Bilbao-Castro, J. Vargas, R. Marabini, J.M. Carazo, C.O. Sorzano, A fast
iterative convolution weighting approach for gridding-based direct Fourier three-dimensional
reconstruction with correction for the contrast transfer function. Ultramicr 157, 79–87 (2015).
doi:10.1016/j.ultramic.2015.05.018
43. J.J. Fernandez, S. Li, R.A. Crowther, CTF determination and correction in electron
cryotomography. Ultramicr 106(7), 587–596 (2006). doi:10.1016/j.ultramic.2006.02.004
44. J.A. Mindell, N. Grigorieff, Accurate determination of local defocus and specimen tilt in
electron microscopy. J. Struct. Biol. 142(3), 334–347 (2003)
45. H. Winkler, K.A. Taylor, Focus gradient correction applied to tilt series image data used in
electron tomography. J. Struct. Biol. 143(1), 24–32 (2003)
46. Q. Xiong, M.K. Morphew, C.L. Schwartz, A.H. Hoenger, D.N. Mastronarde, CTF
determination and correction for low dose tomographic tilt series. J. Struct. Biol. 168(3),
378–387 (2009). doi:10.1016/j.jsb.2009.08.016
47. M. Eibauer, C. Hoffmann, J.M. Plitzko, W. Baumeister, S. Nickell, H. Engelhardt, Unraveling
the structure of membrane proteins in situ by transfer function corrected cryo-electron
tomography. J. Struct. Biol. 180(3), 488–496 (2012). doi:10.1016/j.jsb.2012.09.008
48. F.K. Schur, W.J. Hagen, A. de Marco, J.A. Briggs, Determination of protein structure at 8.5A
resolution using cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 184
(3), 394–400 (2013). doi:10.1016/j.jsb.2013.10.015
49. A. Bartesaghi, F. Lecumberry, G. Sapiro, S. Subramaniam, Protein secondary structure
determination by constrained single-particle cryo-electron tomography. Structure 20(12),
2003–2013 (2012). doi:10.1016/j.str.2012.10.016
50. J.G. Galaz-Montoya, C.W. Hecksel, P.R. Baldwin, E. Wang, S.C. Weaver, M.F. Schmid,
S.J. Ludtke, W. Chiu, Alignment algorithms and per-particle CTF correction for single
8 Tomographic Reconstruction from Electron Micrographs
233
with smooth spherically symmetric volume elements (blobs). Ultramicr 72(1–2), 53–65 (1998)
32. D. Wolf, A. Lubk, H. Lichte, Weighted simultaneous iterative reconstruction technique for
single-axis tomography. Ultramicr 136, 15–25 (2014). doi:10.1016/j.ultramic.2013.07.016
33. K.J. Batenburg, J. Sijbers, DART: a practical reconstruction algorithm for discrete
tomography. IEEE Trans. Image Process. 20(9), 2542–2553 (2011). doi:10.1109/TIP.2011.
2131661
34. J. Skilling, R.K. Bryan, Maximum entropy image reconstruction: general algorithm. Mon.
Not. R. Astron. Soc. 211(1), 111–124 (1984). doi:10.1093/mnras/211.1.111
35. J. Cope, J. Heumann, A. Hoenger, Cryo-electron tomography for structural characterization of
macromolecular complexes. Curr. Protoc. Protein Sci. Chapter 17(Unit17), 13 (2011). doi:10.
1002/0471140864.ps1713s65
36. 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). doi:10.1016/j.jsb.2012.01.003
37. M. Maiorca, C. Millet, E. Hanssen, B. Abbey, E. Kazmierczak, L. Tilley, Local regularization
of tilt projections reduces artifacts in electron tomography. J. Struct. Biol. 186(1), 28–37
(2014). doi:10.1016/j.jsb.2014.03.009
38. M. Defrise, F. Noo, H. Kudo, A solution to the long-object problem in helical cone-beam
tomography. Phys. Med. Biol. 45(3), 623–643 (2000)
39. W. Xu, F. Xu, M. Jones, B. Keszthelyi, J. Sedat, D. Agard, K. Mueller, High-performance
iterative electron tomography reconstruction with long-object compensation using graphics
processing units (GPUs). J. Struct. Biol. 171(2), 142–153 (2010). doi:10.1016/j.jsb.2010.03.
018
40. B. Turonova, L. Marsalek, P. Slusallek, On geometric artifacts in cryo electron tomography.
Ultramicr 163, 48–61 (2016). doi:10.1016/j.ultramic.2016.01.002
41. M. Maiorca, E. Hanssen, E. Kazmierczak, B. Maco, M. Kudryashev, R. Hall, H. Quiney,
L. Tilley, Improving the quality of electron tomography image volumes using pre-reconstruction
filtering. J. Struct. Biol. 180(1), 132–142 (2012). doi:10.1016/j.jsb.2012.05.019
42. V. Abrishami, J.R. Bilbao-Castro, J. Vargas, R. Marabini, J.M. Carazo, C.O. Sorzano, A fast
iterative convolution weighting approach for gridding-based direct Fourier three-dimensional
reconstruction with correction for the contrast transfer function. Ultramicr 157, 79–87 (2015).
doi:10.1016/j.ultramic.2015.05.018
43. J.J. Fernandez, S. Li, R.A. Crowther, CTF determination and correction in electron
cryotomography. Ultramicr 106(7), 587–596 (2006). doi:10.1016/j.ultramic.2006.02.004
44. J.A. Mindell, N. Grigorieff, Accurate determination of local defocus and specimen tilt in
electron microscopy. J. Struct. Biol. 142(3), 334–347 (2003)
45. H. Winkler, K.A. Taylor, Focus gradient correction applied to tilt series image data used in
electron tomography. J. Struct. Biol. 143(1), 24–32 (2003)
46. Q. Xiong, M.K. Morphew, C.L. Schwartz, A.H. Hoenger, D.N. Mastronarde, CTF
determination and correction for low dose tomographic tilt series. J. Struct. Biol. 168(3),
378–387 (2009). doi:10.1016/j.jsb.2009.08.016
47. M. Eibauer, C. Hoffmann, J.M. Plitzko, W. Baumeister, S. Nickell, H. Engelhardt, Unraveling
the structure of membrane proteins in situ by transfer function corrected cryo-electron
tomography. J. Struct. Biol. 180(3), 488–496 (2012). doi:10.1016/j.jsb.2012.09.008
48. F.K. Schur, W.J. Hagen, A. de Marco, J.A. Briggs, Determination of protein structure at 8.5A
resolution using cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 184
(3), 394–400 (2013). doi:10.1016/j.jsb.2013.10.015
49. A. Bartesaghi, F. Lecumberry, G. Sapiro, S. Subramaniam, Protein secondary structure
determination by constrained single-particle cryo-electron tomography. Structure 20(12),
2003–2013 (2012). doi:10.1016/j.str.2012.10.016
50. J.G. Galaz-Montoya, C.W. Hecksel, P.R. Baldwin, E. Wang, S.C. Weaver, M.F. Schmid,
S.J. Ludtke, W. Chiu, Alignment algorithms and per-particle CTF correction for single
8 Tomographic Reconstruction from Electron Micrographs
233