Image restoration in cryo-electron microscopy

Methods in Enzymology

Volumn 482, Issue C, 2010, Pages 35-72

  Penczek, Pawel A ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOOK; CHI SQUARE DISTRIBUTION; COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; DENSITY GRADIENT; ELECTRON MICROSCOPY; EXPERIMENTAL STUDY; IMAGE ANALYSIS; IMAGE PROCESSING; MACROMOLECULE; PRIORITY JOURNAL; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 77957305562     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)82002-6     Document Type: Chapter

References (57)

1. Akey C.W., Radermacher M. Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 1993, 122:1-19.
2. Angert I., Majorovits E., Schröder R. Zero-loss image formation and modified contrast transfer theory in EFTEM. Ultramicroscopy 2000, 81:203-222.
3. Baldwin P.R., Penczek P.A. Estimating alignment errors in sets of 2-D images. J. Struct. Biol. 2005, 150:211-225.
4. Baldwin P.R., Penczek P.A. The transform class in SPARX and EMAN2. J. Struct. Biol. 2007, 157:250-261.
5. Böttcher B., Crowther R.A. Difference imaging reveals ordered regions of RNA in turnip yellow mosaic virus. Structure 1996, 4:387-394.
6. Carazo J.M. The fidelity of 3D reconstruction from incomplete data and the use of restoration methods. Electron Tomography 1992, 117-166. Plenum, New York. J. Frank (Ed.).
7. Carazo J.M., Carrascosa J.L. Information recovery in missing angular data cases: An approach by the convex projections method in three dimensions. J. Microsc. 1987, 145:23-43.
8. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 1996, 116:190-199.
9. Gabashvili I.S., Agrawal R.K., Spahn C.M., Grassucci R.A., Svergun D.I., Frank J., Penczek P. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 2000, 100:537-549.
10. Gerchberg W.O. Super resolution through energy reduction. Opt. Acta 1974, 21:709-720.
11. Gonzalez R.F., Woods R.E. Digital Image Processing. 2002, Prentice Hall, Upper Saddle River, NJ.
12. Grigorieff N. Three-dimensional structure of bovine NADH: Ubiquinone oxidoreductase (complex I) at 22 Å in ice. J. Mol. Biol. 1998, 277:1033-1046.
13. Guinier A., Fournet G. Small-angle Scattering of X-rays 1955, Wiley, New York.
14. Hohn M., Tang G., Goodyear G., Baldwin P.R., Huang Z., Penczek P.A., Yang C., Glaeser R.M., Adams P.D., Ludtke S.J. SPARX, a new environment for cryo-EM image processing. J. Struct. Biol. 2007, 157:47-55.
15. Huang Z., Penczek P.A. Application of template matching technique to particle detection in electron micrographs. J. Struct. Biol. 2004, 145:29-40.
16. Huang Z., Baldwin P.R., Mullapudi S.R., Penczek P.A. Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biol. 2003, 144:79-94.
17. Jain A.K. Fundamentals of Digital Image Processing. 1989, Prentince Hall, Englewood Cliffs.
18. Jensen G.J. Alignment error envelopes for single particle analysis. J. Struct. Biol. 2001, 133:143-155.
19. Langmore J.P., Smith M.F. Quantitative energy-filtered electron microscopy of biological molecules in ice. Ultramicroscopy 1992, 46:349-373.
20. Ludtke S.J, Jakana J., Song J.L., Chuang D.T., Chiu W. A 11.5 Å single particle reconstruction of GroEL using EMAN. J. Mol. Biol. 2001, 314:253-262.
21. Ludtke S.J., Chiu W. Image restoration in sets of noisy electron micrographs. Proceedings of the IEEE Symposium on Biomedical Imaging, Washington, DC 2002, 745-748.
22. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: Semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 1999, 128:82-97.
23. Ludtke S.J., Jakana J., Song J.L., Chuang D.T., Chiu W. A 11.5 Å single particle reconstruction of GroEL using EMAN. J. Mol. Biol. 2001, 314:253-262.
24. Mallick S.P., Carragher B., Potter C.S., Kriegman D.J. ACE: Automated CTF estimation. Ultramicroscopy 2005, 104:8-29.
25. Marabini R., Carazo J.M. On a new computationally fast image invariant based on bispectral projections. Pattern Recognit. Lett. 1996, 17:959-967.
26. Mindell J.A., Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 2003, 142:334-347.
27. Papoulis A. A new algorithm in spectral analysis and band-limited extrapolation. IEEE Trans. Circuits Syst. 1975, CAS-22.
28. Penczek P.A. Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms. J. Struct. Biol. 2002, 138:34-46.
29. Penczek P.A. Single particle reconstruction. Reciprocal Space 2008, B:375-388. Springer, New York. U. Shmueli (Ed.).
30. Penczek P., Radermacher M., Frank J. Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 1992, 40:33-53.
31. Penczek P.A., Zhu J., Schröder R., Frank J. Three-dimensional reconstruction with contrast transfer function compensation from defocus series. Scanning Microsc. Suppl. 1997, 11:1-10.
32. Pratt W.K. Digital Image Processing. 1992, Wiley, New York.
33. Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 1987, 146:113-136.
34. Radermacher M., Rao V., Grassucci R., Frank J., Timerman A.P., Fleischer S., Wagenknecht T. Cryo-electron microscopy and three-dimensional reconstruction of the calcium release channel/ryanodine receptor from skeletal muscle. J. Cell Biol. 1994, 127:411-423.
35. Richardson L.F. The approximate arithmetical solution by finite diff erences of physical problems involving diff erential equations with an application to the stresses to a masonry dam. Philos. Trans. R. Soc. Lond. A. 1910, 210:307-357.
36. Saad A., Ludtke S.J., Jakana J., Rixon F.J., Tsuruta H., Chiu W. Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 2001, 133:32-42.
37. Sander B., Golas M.M., Stark H. Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. J. Struct. Biol. 2003, 142:392-401.
38. Schatz M., van Heel M. Invariant classification of molecular views in electron micrographs. Ultramicroscopy 1990, 32:255-264.
39. Schatz M., van Heel M. Invariant recognition of molecular projections in vitreous ice preparations. Ultramicroscopy 1992, 45:15-22.
40. Scherzer O. The theoretical resolution limit of the electron microscope. J. Appl. Phys. 1949, 20:20-29.
41. Sezan M.I. An overview of convex projections theory and its application to image recovery problems. Ultramicroscopy 1992, 40:55-67.
42. Sorzano C.O., Jonic S., Nunez-Ramirez R., Boisset N., Carazo J.M. Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. J. Struct. Biol. 2007, 160:249-262.
43. Sorzano C.O.S., Velazquez-Muriel J.A., Marabini R., Herman G.T., Carazo J.M. Volumetric restrictions in single particle 3DEM reconstruction. Pattern Recognit. 2008, 41:616-626.
44. Stark H., Yang Y. Vector Space Projections: A Numerical Approach to Signal and Image Processing, Neural Nets, and Optics. 1998, Wiley, New York.
45. Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., Rees I., Ludtke S.J. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 2007, 157:38-46.
46. van Heel M., Harauz G., Orlova E.V. A new generation of the IMAGIC image processing system. J. Struct. Biol. 1996, 116:17-24.
47. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., Patwardhan A. Single-particle electron cryo-microscopy: Towards atomic resolution. Quart. Rev. Biophys. 2000, 33:307-369.
48. Velazquez-Muriel J.A., Sorzano C.O., Fernandez J.J., Carazo J.M. A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment. Ultramicroscopy 2003, 96:17-35.
49. Volkmann N., Hanein D. Docking of atomic models into reconstructions from electron microscopy. Methods Enzymol. 2003, 374:204-225.
50. Wade R.H. A brief look at imaging and contrast transfer. Ultramicroscopy 1992, 46:145-156.
51. Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymology: Diffraction Methods in Biology, Part B 1985, 115. Academic Press, Orlando, FL. C. Wyckoff, H.W. Hirs, S.N. Timasheff (Eds.).
52. Yang C., Ng E.G., Penczek P.A. Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm. J. Struct. Biol. 2005, 149:53-64.
53. Yang C., Jiang W., Chen D.H., Adiga U., Ng E.G., Chiu W. Estimating contrast transfer function and associated parameters by constrained non-linear optimization. J. Microsc. 2009, 233:391-403.
54. Zhang W., Kimmel M., Spahn C.M., Penczek P.A. Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis. Structure 2008, 16:1770-1776.
55. Zheng Y.B., Doerschuk P.C., Johnson J.E. Symmetry-constrained 3-D interpolation of viral X-ray crystallography data. IEEE Trans. Signal Process. 2000, 48:214-222.
56. Zhou Z.H., Hardt S., Wang B., Sherman M.B., Jakana J., Chiu W. CTF determination of images of ice-embedded single particles using a graphics interface. J. Struct. Biol. 1996, 116:216-222.
57. Zhu J., Penczek P.A., Schröder R., Frank J. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. J. Struct. Biol. 1997, 118:197-219.