High-resolution ab initio three-dimensional x-ray diffraction microscopy

Journal of the Optical Society of America A: Optics and Image Science, and Vision

Volumn 23, Issue 5, 2006, Pages 1179-1200

  Chapman, Henry N ^a   Barty, Anton ^a   Marchesini, Stefano ^a   Noy, Aleksandr ^a   Hau Riege, Stefan P ^a   Cui, Congwu ^b   Howells, Malcolm R ^b   Rosen, Rachel ^b   He, Haifeng ^c   Spence, John C H ^c   Weierstall, Uwe ^c   Beetz, Tobias ^d   Jacobsen, Chris ^d   Shapiro, David ^d  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

^d STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COHERENT LIGHT; DIFFRACTION; LIGHT SCATTERING; OPTICAL RESOLVING POWER; X RAY DIFFRACTION; X RAY MICROSCOPES;

AB INITIO; COHERENT MICROSCOPY; DIFFRACTION IMAGING; HIGH-RESOLUTION IMAGING; X-RAY DIFFRACTION MICROSCOPY;

IMAGING TECHNIQUES;

ALGORITHM; ARTICLE; COMPUTER ASSISTED DIAGNOSIS; EVALUATION; IMAGE ENHANCEMENT; INFORMATION RETRIEVAL; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; THREE DIMENSIONAL IMAGING; TRANSMISSION ELECTRON MICROSCOPY; X RAY DIFFRACTION;

ALGORITHMS; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; INFORMATION STORAGE AND RETRIEVAL; MICROSCOPY, ELECTRON, TRANSMISSION; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; X-RAY DIFFRACTION;

EID: 33745245608     PISSN: 10847529     EISSN: None     Source Type: Journal    
DOI: 10.1364/JOSAA.23.001179     Document Type: Article

References (60)

1. D. Sayre and H. N. Chapman, "X-ray microscopy," Acta Crystallogr., Sect. A: Found. Crystallogr. 51, 237-252 (1995).
2. D. Sayre, H. N. Chapman, and J. Miao, "On the extendibility of x-ray crystallography to noncrystals," Acta Crystallogr., Sect. A: Found. Crystallogr. 54, 232-239 (1998).
3. J. Miao, P. Charalambous, J. Kirz, and D. Sayre, "Extending the methodology of x-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens," Nature (London) 400, 342-344 (1999).
4. I. K. Robinson, I. A. Vartanyants, G. J. Williams, M. A. Pfeifer, and J. A. Pitney, "Reconstruction of the shapes of gold nanocrystals using coherent x-ray diffraction," Phys. Rev. Lett. 87, 195505 (2001).
5. G. J. Williams, M. A. Pfeifer, I. A. Vartanyants, and I. K. Robinson, "Three-dimensional imaging of microstructure in Au nanocrystals," Phys. Rev. Lett. 90, 175501 (2003).
6. S. Marchesini, H. He, H. N. Chapman, S. P. Hau-Riege, A. Noy, M. R. Howells, U. Weierstall, and J. C. H. Spence, "X-ray image reconstruction from a diffraction pattern alone," Phys. Rev. B 68, 140101 (2003).
7. S. Marchesini, H. N. Chapman, S. P. Hau-Riege, R. A. London, A. Szoke, H. He, M. R. Howells, H. Padmore, R. Rosen, J. C. H. Spence, and U. Weierstall, "Coherent x-ray diffractive imaging: applications and limitations," Opt. Express 11, 2344-2353 (2003).
8. H. He, S. Marchesini, M. Howells, U. Weierstall, H. Chapman, S. Hau-Riege, A. Noy, and J. C. H. Spence, "Inversion of x-ray diffuse scattering to images using prepared objects," Phys. Rev. B 67, 174114 (2003).
9. M. R. Howells, T. Beetz, H. N. Chapman, C. Cui, J. M. Holton, C. J. Jacobsen, J. Kirz, E. Lima, S. Marchesini, H. Miao, D. Sayre, D. A. Shapiro, and J. C. H. Spence, "An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy," arxiv.org e-print archive, physics/0502059, February 11, 2005, http://arxiv.org/pdf/physics/0502059.
10. R. Neutze, R. Wouts, D. van der Spoel, E. Weckert, and J. Hajdu, "Potential for biomolecular imaging with femtosecond x-ray pulses," Nature (London) 406, 753-757 (2000).
11. J. Miao, K. O. Hodgson, and D. Sayre, "An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images," Proc. Natl. Acad. Sci. U.S.A. 98, 6641-6645 (2001).
12. J. C. H. Spence and R. B. Doak, "Single molecule diffraction," Phys. Rev. Lett. 92, 198102 (2004).
13. W. S. Haddad, I. McNulty, J. Trebes, E. Anderson, R. Levesque, and L. Yang, "Ultrahigh-resolution x-ray tomography," Science 266, 1213-1215 (1994).
14. D. Weiss, G. Schneider, B. Niemann, P. Guttmann, D. Rudolph, and G. Schmahl, "Computed tomography of cryogenic biological specimens based on x-ray microscopic images," Ultramicroscopy 84, 185-197 (2000).
15. C. A. Larabell and M. A. Le Gros, "X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution," Mol. Biol. Cell 15, 957-962 (2004).
16. N. Streibl, "Three-dimensional imaging by a microscope," J. Opt. Soc. Am. A 2, 121-127 (1985).
17. T. Beetz, M. Howells, C. Jacobsen, C. Kao, J. Kirz, E. Lima, T. Mentes, H. Miao, C. Sanchez-Hanke, D. Sayre, and D. Shapiro, "Apparatus for x-ray diffraction microscopy and tomography of cryo specimens," Nucl. Instrum. Methods Phys. Res. A 545, 459-468 (2005).
18. M. R. Howells, P. Charalambous, H. He, S. Marchesini, and J. C. H. Spence, "An off-axis zone-plate monochromator for high-power undulator radiation," in Design and Microfabrication of Novel X-Ray Optics, D. C. Mancini, ed., Proc. SPIE 4783, 65-73 (2002).
19. C. Giacovazzo, Direct Phasing in Crystallography (Oxford U. Press, 1998), p. 468.
20. R. Crandall, E. Jones, J. Klivington, and D. Kramer, "Gigaelement FFTs on Apple G5 clusters," Advanced Computation Group, Apple Computer (2004), http://images.apple.com/acg/pdf/20040827_GigaFFT.pdf.
21. M. Born and E. Wolf, Principles of Optics, 7th ed. (Cambridge U. Press, 2002).
22. R. W. James, The Optical Principles of the Diffraction of X-Rays (Bell, 1962).
23. E. Wolf, "Three-dimensional structure determination of semi-transparent objects from holographic data," Opt. Commun. 1, 153-156 (1969).
24. J. Kirz, C. Jacobsen, and M. Howells, "Soft x-ray microscopes and their biological applications," Q. Rev. Biophys. 28, 33-130 (1995).
25. F. Natterer, "An error bound for the Born approximation," Inverse Probl. 20, 447-452 (2004).
26. R. N. Bracewell, The Fourier Transform and Its Applications, 2nd ed. (McGraw-Hill, 1986).
27. J. Miao, T. Ishikawa, E. H. Anderson, and K. O. Hodgson, "Phase retrieval of diffraction patterns from noncrystalline samples using the oversampling method," Phys. Rev. B 67, 174104 (2003).
28. J. Miao, D. Sayre, and H. N. Chapman, "Phase retrieval from the magnitude of the Fourier transforms of nonperiodic objects," J. Opt. Soc. Am. A 15, 1662-1669 (1998).
29. J. W. Goodman, Introduction to Fourier Optics, 2nd ed. (McGraw-Hill, 1996).
30. J. C. H. Spence, U. Weierstall, and M. Howells, "Coherence and sampling requirements for diffractive imaging," Ultramicroscopy 101, 149-152 (2004).
31. R. Crowther, D. DeRosier, and A. Klug, "The reconstruction of a three-dimensional structure from its projections and its applications to electron microscopy," Proc. R. Soc. London A317, 319-340 (1970).
32. E. Salerno, "Superresolution capabilities of the Gerchberg method in the band-pass case: an eigenvalue analysis," Int. J. Imaging Syst. Technol. 90, 181-188 (1998).
33. Y. Nishino, J. Miao, and T. Ishikawa, "Image reconstruction of nanostructured nonperiodic objects only from oversampled hard x-ray diffraction intensities," Phys. Rev. B 68, 220101 (2003).
34. T. Sato, S. J. Norton, M. Linzer, O. Ikeda, and M. Hirama, "Tomographic image reconstruction from limited projections using iterative revisions in image and transform spaces," Appl. Opt. 20, 395-399 (1981).
35. M. Bertero and E. R. Pike, "Resolution in diffraction-limited imaging, a singular value analysis. I. The case of coherent illumination," Opt. Acta 29, 727-746 (1982).
36. D. Shapiro, P. Thibault, T. Beetz, V. Elser, M. Howells, C. Jacobsen, J. Kirz, E. Lima, H. Miao, A. M. Neimann, and D. Sayre, "Biological imaging by soft x-ray diffraction microscopy," Proc. Natl. Acad. Sci. U.S.A. 102, 15343-15346 (2005).
37. A. Szoke, H. Szoke, and J. R. Somoza, "Holographic methods in x-ray crystallography. V. Multiple isomorphous replacement, multiple anomalous dispersion and noncrystallographic symmetry," Acta Crystallogr., Sect. A: Found. Crystallogr. 53, 291-313 (1997).
38. S. P. Hau-Riege, H. Szoke, H. N. Chapman, A. Szoke, S. Marchesini, A. Noy, H. He, M. Howells, U. Weierstall, and J. C. H. Spence, "SPEDEN: reconstructing single particles from their diffraction patterns," Acta Crystallogr., Sect. A: Found. Crystallogr. 60, 294-305 (2004).
39. D. Potts, G. Steidl, and M. Tasche, "Fast Fourier transforms for nonequispaced data: a tutorial," in Modern Sampling Theory: Mathematics and Applications, J. J. Benedetto and P. Ferreira, eds. (Springer, 2001), Chap. 12, pp. 249-274.
40. H. Choi and D. C. Munson, Jr., "Direct-Fourier reconstruction in tomography and synthetic aperture radar," Int. J. Imaging Syst. Technol. 9, 1-13 (1998).
41. F. Natterer, The Mathematics of Computerized Tomography (SIAM, 2001).
42. A. J. Devaney, "A filtered backpropagation algorithm for diffraction tomography," Ultrason. Imaging 4, 336-350 (1982).
43. S. Pan and A. Kak, "A computational study of reconstruction algorithms for diffraction tomography: interpolation versus filtered-backpropagation," IEEE Trans. Acoust., Speech, Signal Process. SP-31, 1262-1275 (1983).
44. H. He, S. Marchesini, M. Howells, U. Weierstall, G. Hembree, and J. C. H. Spence, "Experimental lensless soft-x-ray imaging using iterative algorithms: phasing diffuse scattering," Acta Crystallogr., Sect. A: Found. Crystallogr. 59, 143-152 (2003).
45. J. R. Fienup, "Reconstruction of a complex-valued object from the modulus of its Fourier transform using a support constraint," J. Opt. Soc. Am. A 4, 118-123 (1987).
46. J. R. Fienup, "Phase retrieval and support estimation in x-ray diffraction," in Coherence 2005: International Workshop on Phase Retrieval and Coherent Scattering (ESRF, 2005), http://www.esrf.fr/ NewsAndEvents/Conferences/Coherence2005/Proceedings/files/Talks/ Fienup.pdf.
47. T. R. Crimmins, J. Fienup, and B. J. Thelen, "Improved bounds on object support from autocorrelation support and application to phase retrieval," J. Opt. Soc. Am. A 7, 3-13 (1990).
48. J. R. Fienup, "Phase retrieval algorithms: a comparison," Appl. Opt. 21, 2758-2769 (1982).
49. V. Elser, "Phase retrieval by iterated projections," J. Opt. Soc. Am. A 20, 40-55 (2003).
50. D. R. Luke, "Relaxed averaged alternating reflections for diffraction imaging," Inverse Probl. 21, 37-50 (2005).
51. M. Frigo and S. G. Johnson, "The design and implementation of FFTW3," Proc. IEEE 93, 216-231 (2005). (Special issue on "Program Generation, Optimization, and Platform Adaptation").
52. "The message passing interface (MPI) standard," http://www-unix.mcs.anl.gov/mpi/.
53. A. J. Ladd, J. H. Kinney, D. L. Haupt, and S. A. Goldstein, "Finite-element modeling of trabecular bone: comparison with mechanical testing and determination of tissue modulus," J. Orthop. Res. 16, 622-628 (1998).
54. "Movies of three-dimensional diffraction data and reconstruction of the pyramid test object," http://als.lbl.gov/esg_beamlines/cxdi.
55. J. M. Cowley, Diffraction Physics (North-Holland, 1981).
56. J. C. H. Spence, U. Weierstall, and M. Howells, "Phase recovery and lensless imaging by iterative methods in optical, x-ray and electron diffraction," Philos. Trans. R. Soc. London, Ser. A 360, 875-895 (2002).
57. G. Huldt, Biomedical Centre, Uppsala Universitet (personal communication, 2005).
58. J. Frank, Three-Dimensional Electron Microscopy of Macromolecular Assemblies (Academic, 1996).
59. J. R. Fienup and C. Wackerman, "Phase-retrieval stagnation problems and solutions," J. Opt. Soc. Am. A 3, 1897-1907 (1986).
60. J. R. Fienup, "Invariant error metrics for image reconstruction," Appl. Opt. 36, 8352-8357 (1997).