3-D reconstruction of 2-D crystals in real space

IEEE Transactions on Image Processing

Volumn 13, Issue 4, 2004, Pages 549-561

  Marabini, Roberto ^a   Sorzano, Carlos O S ^b   Matej, Samuel ^c   Fernández, José J ^d   Carazo, Jose M ^a   Herman, Gabor T ^e  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b EPFL   (Switzerland)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d UNIVERSITY OF ALMERÍA   (Spain)

^e CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

3 D reconstruction; Crystals; Electron microscopy; Image reconstruction; Projections

Indexed keywords

ALGORITHMS; CRYSTALS; ITERATIVE METHODS; MACROMOLECULES; MATHEMATICAL MODELS; THREE DIMENSIONAL; TRANSMISSION ELECTRON MICROSCOPY;

THREE DIMENSIONAL RECONSTRUCTION; TWO DIMENSIONAL CRYSTALS;

IMAGE RECONSTRUCTION;

CAPSID PROTEIN;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BACILLUS PHAGE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER ASSISTED DIAGNOSIS; COMPUTER GRAPHICS; CONFORMATION; CRYSTALLOGRAPHY; ELECTRON MICROSCOPY; EVALUATION; IMAGE ENHANCEMENT; IMAGE QUALITY; INFORMATION RETRIEVAL; INSTRUMENTATION; MACROMOLECULE; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE; VALIDATION STUDY;

ALGORITHMS; BACILLUS PHAGES; CAPSID PROTEINS; COMPUTER GRAPHICS; CRYSTALLOGRAPHY; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; INFORMATION STORAGE AND RETRIEVAL; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; MOLECULAR CONFORMATION; PATTERN RECOGNITION, AUTOMATED; PHANTOMS, IMAGING; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 1942468565     PISSN: 10577149     EISSN: None     Source Type: Journal    
DOI: 10.1109/TIP.2003.822620     Document Type: Article

References (40)

1. R. Henderson, J. M. Baldwin, T. A. Ceska, F. Zemlin, E. Beckmann, and K. H. Downing, "Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy," J. Mol. Biol., vol. 213, pp. 899-929, 1990.
2. W. Kühlbrandt, D. N. Wang, and Y. Fujiyoshi, "Atomic model of plant light-harvesting complex by electron crystallography," Nature, vol. 367, pp. 614-621, 199
3. E. Nogales, S. G. Wolf, and K. H. Downing, "Visualizing the secondary structure of tubulin: Three-dimensional map at 4 Å," J. Struct. Biol., vol. 118, pp. 119-127, 1997.
4. K. Mitsuoka, T. Hirai, K. Murata, A. Miyazawa, A. Kidera, Y. Kimura, and Y. Fujiyoshi, "The structure of bacteriorhodopsin at 3.0 Å resolution based on electron crystallography: Implication of the charge distribution," J. Mol. Biol., vol. 286, no. 3, pp. 861-82, 1999.
5. K. Murata, K. Mitsuoka, T. Hirai, T. Walz, P. Agre, J. Heymann, A. Engel, and Y. Fujiyoshi, "Structural determinants of water permeation through aquaporin-1," Nature, vol. 407, pp. 599-605, 2000.
6. G. Ren, A. Cheng, V. Reddy, P. Melnyk, and A. Mitra, "Three-dimensional fold of the human AQP1 water channel determined at 4 Å resolution by electron crystallography of two-dimensional crystals embedded in ice," J. Mol. Biol., vol. 301, no. 2, pp. 369-87, 2000.
7. R. Henderson, J. M. Baldwin, K. H. Downing, J. Lepault, and F. Zemlin, "Structure of purple membrane from halobacterian halobium: Recording, measurement and evaluation of electron micrographs at 3.5 Å resolution," Ultramicroscopy, vol. 19, pp. 147-178, 1986.
8. M. Stewart, "Introduction to the computer image processing of electron micrographs of two-dimensionally ordered biological structures," J. Electron. Micr. Tech., vol. 9, pp. 301-324, 1988.
9. P. R. Smith and J. Kistler, "Surface reliefs computed from micrographs of heavy metal-shadowed specimens," J. Ultrastruc. Res., vol. 61, pp. 124-133, 1977.
10. ____, "Surface reliefs computed from micrographs of isolated heavy metal-shadowed particles," J. Ultrastruc. Res., vol. 71, pp. 25-36, 1980.
11. D. J. Müller, A. Engel, J. L. Carrascosa, and M. Vélez, "The bacteriophage φ29 head-tail connector imaged at high resolution with the atomic force microscope in buffer solution," EMBO J., vol. 16, pp. 2547-2553, 1997.
12. M. T. Chan, G. T. Herman, and E. Levitan, "Bayesian image reconstruction using image-modeling Gibbs priors," Int. J. Imag. Syst. Tech., vol. 9, pp. 85-98, 1998.
13. 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., vol. 39, pp. 183-231, 1982.
14. R. Bracewell, Two-Dimensional Imaging. London, U.K.: Prentice-Hall, 1995.
15. R. A. Crowther, R. Henderson, and J. M. Smith, "MRC image processing programs," J. Struc. Biol., vol. 116, pp. 9-16, 1996.
16. M. Yeager, V. M. Unger, and A. K. Mitra, "Three-dimensional structure of membrane proteins determined by two-dimensional crystallization, electron cryomicroscopy, and image analysis," Methods Enzymol., vol. 294, pp. 135-180, 1999.
17. E. R. Kunji, S. von Gronau, D. Oesterhelt, and R. Henderson, "The three-dimensional structure of halorhodopsin to 5 Å by electron crystallography: A new unbending procedure for two-dimensional crystals by using a global reference structure," in Proc. National Academy of Science, vol. 97, 2000, pp. 4637-4642.
18. M. F. Schmid, R. Dargahi, and M. W. Tam, "SPECTRA: A system for processing electron images of crystals," Ultramicroscopy, vol. 48, pp. 251-264, 1993.
19. D. A. Agard, "A least-squares method for determining structure factors in three-dimensional tilted-view reconstructions," J. Mol. Biol., vol. 167, pp. 849-52, 1983.
20. 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., vol. 39, pp. 355-367, 1994.
21. S. Matej and R. M. Lewitt, "Practical consideration for 3-D image reconstruction using spherically symmetric volume elements." IEEE Trans. Med. Imaging, vol. 15, pp. 68-78, Jan. 1996.
22. 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., vol. 120, pp. 363-371, 1997.
23. R. Marabini, G. T. Herman, and J. M. Carazo, "3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs)," Ultramicroscopy, vol. 72, pp. 53-65, 1998.
24. C. O. S. Sorzano, R. Marabini, N. Boisset, E. Rietzel, R. Schröder, G. T. Herman, and J. M. Carazo, "The effect of overabundant projection directions on 3D reconstruction algorithms," J. Struct. Biol., vol. 113, pp. 108-118, 2001.
25. G. T. Herman, Image Reconstruction From Projections: The Fundamentals of Computerized Tomography. New York: Academic, 1980.
26. ____, "Algebraic reconstruction techniques in medical imaging," in Medical Imaging, Systems Techniques and Applications, C. T. Leondes, Ed. Amsterdam, The Netherlands: Gordon and Breach, 1998, vol. 6, Computational Techniques, pp. 1-42.
27. G. T. Herman, H. Levkowitz, S. McCormick, and H. K. Tuy, "Multilevel image reconstruction," in Multiresolution Image Processing and Analysis, A. Rosenfeld, Ed. New York: Springer-Verlag, 1984.
28. R. M. Lewitt, "Alternatives to voxels for image representation in iterative reconstruction algorithms," Phys. Med. Biol., vol. 37, pp. 705-716, 1992.
29. S. Matej and R. M. Lewitt, "Effcient 3D grids for image reconstruction usign spherically-symmetric volume elements," IEEE Trans. Nucl. Sci., vol. 42, pp. 1361-1370, Oct. 1995.
30. R. M. Lewitt, "Multidimensional digital image representations using generalized Kaiser-Bessel window functions," J. Opt. Soc. Amer. A, vol. 7, pp. 1834-1846, 1990.
31. 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., vol. 39, pp. 341-354, 1994.
32. J. A. Reeds and L. A. Shepp, "Limited angle reconstruction in tomography via squashing," IEEE Trans. Med. Imag., vol. MI-6, pp. 89-97, Feb. 1987.
33. G. T. Herman, R. Marabini, J. M. Carazo, E. Garduño, R. Lewitt, and S. Matej, "Image processing approaches to biological three-dimensional electron microscopy," Int. J. Imag. Syst. Tech., vol. 11, pp. 12-29, 2000.
34. International Tables for Crystallography (Space-Group Symmetry), vol. A, T. H. Hahn, Ed., Kluwer Academic, Dordrecht, The Netherlands, 1996.
35. R. Marabini, I. M. Masegosa, S. M. M. C. San Martín, J. J. Fernández, C. V. L. G. de la Fraga, and J. M. Carazo, "Xmipp: An image processing package for electron microscopy," J. Struct. Biol., vol. 116, pp. 237-240, 1996.
36. 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. & Des., vol. 7, pp. 289-296, 1999.
37. A. A. Simpson, Y. Z. Tao, P. G. Leiman, M. O. Badasso, Y. N. He, P. J. Jardine, N. H. Olson, M. C. Morais, S. Grimes, D. L. Anderson, T. S. Baker, and M. G. Rossmann, "Structure of the bacteriophage φ29 DNA packaging motor," Nature, vol. 408, pp. 745-750, 2000.
38. J. M. Carazo, "The fidelity of 3D reconstructions from incomplete data and the use of restoration methods," in Electron Tomography. Three-Dimensional Imaging With the Transmission Electron Microscope, J. Frank, Ed. New York: Plenum, 1992, pp. 117-166.
39. S. B. Vardeman, Statistics for Engineering Problem Solving. Boston, MA: Academic, 1994.
40. E. Dimmeler, R. Marabini, P. Tittman, and H. Gross, "Correlation of topographic surface and volume data from three-dimensional electron microscopy," J. Struc. Biol., vol. 136, pp. 20-29, 2001.