Image processing approaches to biological three-dimensional electron microscopy

International Journal of Imaging Systems and Technology

Volumn 11, Issue 1, 2000, Pages 12-29

  Herman, Gabor T ^a,c   Marabini, Roberto ^a   Carazo, José María ^b   Garduño, Edgar ^a   Lewitt, Robert M ^a   Matej, Samuel ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^c Temple University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMAGE RECONSTRUCTION; MACROMOLECULES;

BIOLOGICAL THREE-DIMENSIONAL ELECTRON MICROSCOPY;

ELECTRON MICROSCOPY;

EID: 0033747828     PISSN: 08999457     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1098-1098(2000)11:1<12::AID-IMA3>3.0.CO;2-N     Document Type: Article

References (85)

1. C.W. Akey and M. Radermacher, Architecture of the Xenopus nuclear-pore complex revealed by 3-dimensional cryoelectron microscopy, J Cell Biol 122 (1993), 1-19.
2. L.A. Amos, R. Henderson, and P.N.T. Unwin, Three-dimensional structure determination by electron microscopy of two-dimensional crystals, Prog Biophys Mol Biol 39 (1982), 183-231.
3. E. Artzy, G. Frieder, and G.T. Herman, The theory, design, implementation and evaluation of a three-dimensional surface detection algorithm, Computer Graphics Image Process 15 (1981), 1-24.
4. V. Barcilon, On Chahine's relaxation method for the radiative transfer equation, J Atmos Sci 32 (1975), 1626-1630.
5. F.C. Bernstein, T.F. Koetzle, G.J. Williams, E.F. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, The protein data bank. A computer-based archival file for macromolecular structures, J Mol Biol 112 (1997), 535-542.
6. Å. Björck, "Newton and Rayleigh quotient methods for total least squares problems," Recent advances in total least squares techniques and errors-invariables modeling, S. Van Huffel (Editor). SIAM, Philadelphia, 1997, pp. 149-160.
7. N. Boisset, P. Penczek, J.C. Taveau, V. You, F. de Haas, and J. Lamy, Overabundant single-particle electron microscope views induce a three-dimensional reconstruction artifact, Ultramicroscopy 74 (1998), 201-207.
8. J.M. Carazo, "The fidelity of 3D reconstructions from incomplete data and the use of restoration methods," Electron tomography. Three-dimensional imaging with the transmission electron microscope, J. Frank (Editor), Plenum Press, New York, 1992, pp. 117-166.
9. J.M. Carazo and J.L. Carrascosa, Information recovery in missing angular data cases: An approach by the convex projections method in three dimensions, J Microsc 145 (1987a), 23-43.
10. J.M. Carazo and J.L. Carrascosa, Restoration of direct Fourier three-dimensional reconstructions of crystalline specimens by the method of convex projections, J Microsc 145 (1987b), 159-177.
11. J.M. Carazo, C.O. Sorzano, E. Rietzel, R. Schröeder, and R. Marabini, "Discrete tomography in electron microscopy," Discrete tomography: Foundations, algorithms and applications, G.T. Herman and A. Kuba (Editors), Birkhauser, Boston, 1999, pp. 405-416.
12. B.M. Carvalho, C.J. Gau, G.T. Herman, and T.Y. Kong, Algorithms for fuzzy segmentation, Pattern Analysis Appl 2 (1999), 73-81.
13. Y. Censor, T. Elfving, and G.T. Herman, A method of iterative data refinement and its applications, Math Methods Appl Sci 7 (1985), 108-123.
14. M.T. Chahine, Inverse problems in radiative transfer: Determination of atmospheric parameters, J Atmos Sci 27 (1970), 960-967.
15. M.T. Chan, G.T. Herman, and E. Levitan, A Bayesian approach to PET reconstruction using image-modeling Gibbs priors: Implementation and comparison, IEEE Trans Nucl Sci 44 (1997), 1347-1354.
16. M.T. Chan, G.T. Herman, and E. Levitan, Bayesian image reconstruction using image-modeling Gibbs priors, Int J Imaging Syst Technol 9 (1998), 85-98.
17. R. Chellappa and A. Jain, Markov random fields: Theory and application, Academic Press, San Diego, 1993.
18. L.S. Chen, G.T. Herman, R.A. Reynolds, and J.K. Udupa, Surface shading in the cuberille environment, IEEE Computer Graphics Appl 5 (1985), 33-43.
19. R.H. Cheng, V.S. Reddy, N.H Olson, A.J. Fisher, T.S. Baker, and J.E. Johnson, Functional implications of quasi-equivalence in a T = 3 icosahedral animal virus established by cryoelectron microscopy and X-ray crystallography, Structure 2 (1994), 271-282.
20. G.W. Cheong, R. Guckenberger, K.H. Fuchs, H. Gross, and W. Baumeister, The structure of the surface layer of Methanoplanus limicola obtained by a combined EM and STM approach. J Struct Biol 111 (1993), 125-134.
21. R.A. Crowther, R. Henderson, and J.M. Smith, MRC image processing programs, J Struct Biol 116 (1996), 9-16.
22. M.E. Daube-Witherspoon and G. Muehllehner, An iterative image space reconstruction algorithm suitable for volume ECT, IEEE Trans Med Imaging 5 (1986), 61-66.
23. F. de Haas, A. Kuchumov, J.C. Taveau, N. Boisset, S.N. Vinogradov, and J.N. Lamy, Three-dimensional reconstruction of native and reassembled Lumbricus terrestris extracellular hemoglobin. Localization of the monomeric globin chains, Biochemistry 36 (1997), 7330-7338.
24. A.R. De Pierro, On the convergence of the iterative image space reconstruction algorithm for volume ECT, IEEE Trans Med Imaging 6 (1987), 174-175.
25. C. Dinges and H. Rose, Simulation of filtered and unfiltered TEM images and diffraction patterns, Phys Stat Sol (A) 150 (1995), 23-30.
26. D. Fotiadis, D.J. Müller, G. Tsiotis, L. Hasler, P. Tittmann, T. Mini, P. Jeno, H. Gross, and A. Engel, Surface analysis of the photosystem I complex by electron and atomic force microscopy, J Mol Biol 283 (1998), 83-94.
27. J. Frank, Three dimensional electron microscopy of macromolecular assemblies, Academic Press, San Diego, 1996.
28. S.S. Furuie, G.T. Herman, T.K. Narayan, P.E. Kinahan, J.S. Karp, R.M. Lewitt, and S. Matej, A methodology for testing for statistically significant differences between fully 3D PET reconstruction algorithms, Phys Med Biol 39 (1994), 341-354.
29. S. Geman and D. Geman, Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images, IEEE Trans Pattern Analysis Machine Intell 6 (1984), 721-741.
30. A.D. Gross and R. Lusinyants, Fast nonparametric detection of regular structure using digital geometric primitives, Proc SPIE 3168 (1997), 338-347.
31. A. Guasch, A. Parraga, J. Pous, J.M. Valpuesta, J.L. Carrascosa, and M. Coll, Purification, crystallization and preliminary X-ray diffraction studies of the bacteriophage φ - 29 connector particle, FEBS Lett 430 (1998), 283-287.
32. P.C. Hansen and D.P. O'Leary, "Regularization algorithms based on total least squares," Recent advances in total least squares techniques and errors-in-variables modeling, S. Van Huffel (Editor), SIAM, Philadelphia, 1997, pp. 127-137.
33. P.W. Hawkes and E. Kasper, Principles of electron optics, Vol. 3: Wave optics, Academic Press, London, 1996.
34. R. Henderson, J.M. Baldwin, K.H. Downing, J. Lepault, and F. Zemlin, Structure of purple membrane from halobacterium halobium: Recording, measurement and evaluation of electron micrographs at 3.5 Å resolution, Ultramicroscopy 19 (1986), 147-178.
35. G.T. Herman, Image reconstruction from projections: The fundamentals of computerized tomography, Academic Press, New York, 1980.
36. G.T. Herman, "Algebraic reconstruction techniques in medical imaging," Medical imaging, systems techniques and applications. Vol. 6: Computational techniques, C.T. Leondes (Editor), Gordon and Breach Science Publishers, Amsterdam, 1998a, pp. 1-42.
37. G.T. Herman, Geometry of digital spaces, Birkhauser, Boston, 1998b.
38. G.T. Herman and A. Kuba (Editors), Discrete tomography: Foundations, algorithms and applications, Birkhauser, Boston, 1999.
39. G.T. Herman and H.K. Liu, Three-dimensional display of human organs from computed tomograms, Computer Graphics Image Process 9 (1979), 1-21.
40. G.T. Herman and D.W. Ro, Image recovery using iterative data refinement with relaxation, Opt Eng 29 (1990), 513-523.
41. J.B. Heymann, T. Walz, T. Hirai, K. Murata, B.L. Smith, K. Mitsuoka, and Y. Fujiyoshi, The water channel in aquaporin-1, Biophys J 74 (1998), A123.
42. G. Hommel, A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika 75 (1988), 383-386.
43. M.I. Kohn, N.K. Tanna, G.T. Herman, S.M. Resnick, P.D. Mozley, R.E. Gur, A. Alavi, R.A. Zimmerman, and R.C. Gur, Analysis of brain and cerebrospinal fluid volumes with MR imaging. Part 1: Methods, reliability, and validation, Radiology 178 (1991), 115-122.
44. R.M. Lewitt, Multidimensional digital image representations using generalized Kaiser-Bessel window functions. J Opt Soc Am [A] 7 (1990), 1834-1846.
45. R.M. Lewitt, Alternatives to voxels for image representation in iterative reconstruction algorithms, Phys Med Biol 37 (1992), 705-716.
46. R. Marabini, G.T. Herman, and J.M. Carazo, 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy 72 (1998), 53-65.
47. R. Marabini, G.T. Herman, and J.M. Carazo, "Fully three-dimensional reconstruction in electron tomography," Computational radiology and imaging: Therapy and diagnostics, C. Borgers and F. Natterer (Editors), Springer-Verlag, New York, 1999, pp. 251-281.
48. R. Marabini, E. Rietsel, R. Schröder, G.T. Herman, and J.M. Carazo, Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: Application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection, J Struct Biol 120 (1997), 363-371.
49. L.D. Marks, Wiener-filter enhancement of noisy HREM images, Ultramicroscopy 62 (1996), 43-52.
50. S. Matej, S.S. Furuie, and G.T. Herman, Relevance of statistically significant differences between reconstruction algorithms, IEEE Trans Image Process 5 (1996), 554-556.
51. S. Matej, G.T. Herman, T.K. Narayan, S.S. Furuie, R.M. Lewitt, and P.E. Kinahan, Evaluation of task-oriented performance of several fully 3D PET reconstruction algorithms, Phys Med Biol 39 (1994), 355-367.
52. S. Matej and R.M. Lewitt, Efficient 3D grids for image reconstruction using spherically-symmetric volume elements. IEEE Trans Nucl Sci 42 (1995), 1361-1370.
53. S. Matej and R.M. Lewitt, Practical considerations for 3-D image reconstruction using spherically symmetric volume elements, IEEE Trans Med Imaging 15 (1996), 68-78.
54. V.Z. Mesarović, N.P. Galatsanos, and A.K. Katsaggelos, Regularized constrained total least squares image restoration, IEEE Trans Image Process 4 (1995), 1096-1108.
55. S. Miguet and J.M. Nicod, Complexity analysis of a parallel implementation of the marching cubes algorithm, Int J Pattern Recogn 11 (1997), 1141-1156.
56. D.J. Müller, A. Engel, J.L. Carrascosa, and M. Vélez, The bacteriophage φ-29 head-tail connector imaged at high resolution with the atomic force microscope in buffer solution. EMBO J 16 (1997), 2547-2553.
57. T.K. Narayan and G.T. Herman, The use of contrast for automated pulmonary nodule detection in low-dose computed tomography, Med Phys 26 (1999), 427-437.
58. S.K. Pal and D.K. Majumder, Fuzzy mathematical approach to pattern recognition, Wiley, New Delhi, 1997.
59. P. Penczek, R.A. Grassucci, and J. Frank, The ribosome at improved resolution - New techniques for merging and orientation refinement in 3D cryoelectron microscopy of biological particles, Ultramicroscopy 53 (1994). 251-270.
60. G.A. Perkins, C.W. Renken, J.Y. Song, T.G. Frey, S.J. Young, S. Lamont, M.E. Martone, S. Lindsey, and M.H. Ellisman, Electron tomography of large, multicomponent biological structure, J Struct Biol 120 (1997), 219-227.
61. M. Radermacher, V. Rao, R. Grassucci, J. Frank, A.P. Timerman, S. Fleischer, and T.A. Wagenknecht. Cryoelectron microscopy and 3-dimensional reconstruction of the calcium release channel ryanodine receptor from skeletal-muscle, J Cell Biol 127 (1994), 411-423.
62. M.C. San Martin, C. Gruss, and J.M. Carazo, Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel, J Mol Biol 268 (1997), 15-20.
63. M.C. San Martin, M. Radermacher, B. Wolpensinger, A. Engel, and C.S. Miles, Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC, Structure 6 (1998), 501-509.
64. M.R. Sawaya, S. Guo, S. Tabor, C.C. Richardson, and T. Ellenberger, Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7, Cell 99 (1999), 167-177.
65. G. Sharma and H.J. Trussell, Set theoretic signal restoration using an error in variables criterion, IEEE Trans Image Process 6 (1997), 1692-1697.
66. U. Skoglund, L.G. Ofverstedt, R. Burnett, and G. Bricogne, Maximum-entropy three-dimensional reconstruction with deconvolution of the contrast transfer function: A test application with adenovirus. J Struct Biol 117 (1996), 173-188.
67. P.R. Smith and J. Kistler, Surface reliefs computed from micrographs of heavy metal-shadowed specimens, J Ultrastruct Res 61 (1977), 124-133.
68. P.R. Smith and J. Kistler, Surface reliefs computed from micrographs of isolated heavy metal shadowed particles. J Ultrastruct Res 71 (1980), 25-36.
69. C.O.S. Sorzano, R. Marabini, J.M. Carazo, E. Rietzel, R. Schröder, G.T. Herman, and N. Boisset, Effects of uneven sampling in 3D reconstructions, Proc 13th Int Cong on Electron Microscopy, vol. I, 1998, pp. 771-772.
70. M. Stewart, Introduction to the computer image processing of electron micrographs of two-dimensionally ordered biological structures, J Electron Microsc Tech 9 (1988), 301-324.
71. R.M. Stroud and D.A. Agard, Structure determination of asymmetric membrane profiles using an iterative Fourier method. Biophys J 25 (1979), 495-512.
72. Y.Z. Tao, N.H. Olson, W. Xu, D.L. Anderson, M.G. Rossmann, and T.S. Baker, Assembly of a tailed bacterial virus and its genome release studied in three dimensions, Cell 95 (1998), 431-437.
73. J.K. Udupa and G.T. Herman (Editors), 3D imaging in medicine (2nd ed.), CRC Press, Boca Raton, FL, 2000.
74. J.K. Udupa, H. Hung, and K. Chuang, Surface and volume rendering in three-dimensional imaging: A comparison, J Digit Imaging 4 (1991), 159-168.
75. J.K. Udupa and D. Odhner, Shell rendering, IEEE Computer Graph Appl 13 (1993), 58-67.
76. J.K. Udupa and S. Samarasekera, Fuzzy connectedness and object definition: Theory, algorithms, and applications in image segmentation, Graphical Model Image Process 58 (1996), 246-261.
77. J.M. Valpuesta, J.J. Fernández, J.M. Carazo, and J.L. Carrascosa, The three-dimensional structure of a DNA translocating machine at 10 angstrom resolution, Struct Fold Design 7 (1999), 289-296.
78. M. van Heel, Angular reconstitution: A posteriori assignment of projection directions for 3D reconstruction, Ultramicroscopy 21 (1987), 111-124.
79. S. Van Huffel (Editor), Recent advances in total least squares techniques and errors-in-variables modeling, SIAM, Philadelphia, 1997.
80. S. Van Huffel and J. Vandewalle, The total least squares problem: Computational aspects and analysis, SIAM, Philadelphia, 1991.
81. T. Walz, T. Hirai, K. Murata, J.B. Heymann, K. Mitsuoka, Y. Fujiyoshi, B.L. Smith, P. Agre, and A. Engel, The three-dimensional structure of aquaporin-1, Nature 387 (1997), 624-627.
82. A.H. Watt, 3D computer graphics (3rd ed.), Addison-Wesley, Reading, MA, 1999.
83. J. Weigelt, S.E. Brown, C.S. Miles, N. Dixon, and G. Otting, NMR structure of the N-terminal domain of the Escherichia coli DnaB helicase: Implications for structure rearrangements in the helicase hexamer. Struct Fold Design 7 (1999), 681-690.
84. J. Zhu, P.A. Penczek, R. Schröder, and J. Frank, Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: Procedure and application to the 70S Escherichia coli rihosome, J Struct Biol 118 (1997a), 197-219.
85. W. Zhu, Y. Wang, Y. Yao, J. Chang, H.L. Graber, and R.L. Barbour, Iterative total least-squares image reconstruction algorithm for optical tomography by the conjugate gradient method, J Opt Soc Am [A] 14 (1997b), 799-807.