Tables for
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 9.3, pp. 234-239
doi: 10.1107/97809553602060000826

Chapter 9.3. X-ray diffraction imaging of whole cells

D. Shapiroa*

aAdvanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 2–400, Berkeley, CA 94720, USA
Correspondence e-mail:


Barty, A., Marchesini, S., Chapman, H. N., Cui, C., Howells, M. R., Shapiro, D. A., Minor, A. M., Spence, J. C., Weierstall, U., Ilavsky, J., Noy, A., Hau-Riege, S. P., Artyukhin, A. B., Baumann, T., Willey, T., Stolken, J., van Buuren, T. & Kinney, J. H. (2008). Three-dimensional coherent X-ray diffraction imaging of a ceramic nanofoam: determination of structural deformation mechanisms. Phys. Rev. Lett. 101, 055501.
Bates, R. H. T. (1982). Fourier phase problems are uniquely soluble in more than one dimension. I. Underlying theory. Optik (Stuttgart), 61, 247–262.
Bates, R. H. T. & Fright, W. R. (1983). Composite two-dimensional phase-restoration procedure. J. Opt. Soc. Am. 73, 358–365.
Bergh, M., Huldt, G., Timneanu, N., Maia, F. R. & Hajdu, J. (2008). Feasibility of imaging living cells at subnanometer resolutions by ultrafast X-ray diffraction. Q. Rev. Biophys. 41, 181–204.
Chao, W., Kim, J., Rekawa, S., Fischer, P. & Anderson, E. H. (2009). Demonstration of 12 nm resolution Fresnel zone plate lens based soft X-ray microscopy. Opt. Express, 17, 17669–17677.
Chapman, H. N., Barty, A., Marchesini, S., Noy, A., Hau-Riege, S. P., Cui, C., Howells, M. R., Rosen, R., He, H., Spence, J. C., Weierstall, U., Beetz, T., Jacobsen, C. & Shapiro, D. (2006). High-resolution ab initio three-dimensional X-ray diffraction microscopy. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 23, 1179–1200.
Fienup, J. R. (1978). Reconstruction of an object from the modulus of its Fourier transform. Opt. Lett. 3, 27–29.
Fienup, J. R. (1982). Phase retrieval algorithms: a comparison. Appl. Opt. 21, 2758–2769.
Fienup, J. R. (1987). Reconstruction of a complex-valued object from the modulus of its Fourier transform using a support constraint. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 4, 118–123.
Fienup, J. R., Crimmins, T. R. & Holsztynski, W. (1982). Reconstruction of the support of an object from the support of its autocorrelation. J. Opt. Soc. Am. 72, 610–624.
Gerchberg, R. W. & Saxton, W. O. (1972). A practical algorithm for the determination of phase from image and diffraction plane pictures. Optik (Stuttgart), 35, 237–246.
Hegerl, R. & Hoppe, W. (1976). Influence of electron noise on three-dimensional image reconstruction. Z. Naturforsch. Teil A, 31, 1717–1721.
Howells, M. R., Beetz, T., Chapman, H. N., Cui, C., Holton, J. M., Jacobsen, C. J., Kirz, J., Lima, E., Marchesini, S., Miao, H., Sayre, D., Shapiro, D. A., Spence, J. C. H. & Starodub, D. (2009). An assessment of the resolution limitation due to radiation damage in X-ray diffraction microscopy. J. Electron Spectrosc. Relat. Phenom. 170, 4–12.
Huang, X., Nelson, J., Kirz, J., Lima, E., Marchesini, S., Miao, H., Nieman, A. M., Shapiro, D., Steinbrener, J., Stewart, A., Turner, J. J. & Jacobsen, C. (2009). Soft X-ray diffraction microscopy of a frozen hydrated yeast cell. Phys. Rev. Lett. 103, 198101.
Jearanaikoon, S. & Abraham-Peskir, J. V. (2005). An X-ray microscopy perspective on the effect of glutaraldehyde fixation on cells. J. Microsc. 218, 185–192.
Larabell, C. A. & Le Gros, M. A. (2004). X-ray tomography generates 3-d reconstructions of the yeast, Saccharomyces cerevisiae, at 60 nm resolution. Mol. Biol. Cell, 15, 957–962.
Le Gros, M. A., McDermott, G., Uchida, M., Knoechel, C. G. & Larabell, C. A. (2009). High-aperture cryogenic light microscopy. J. Microsc. 235, 1–8.
Lima, E., Wiegart, L., Pernot, P., Howells, M. R., Timmins, J., Zontone, F. & Madsen, A. (2009). Cryogenic X-ray diffraction microscopy for biological samples. Phys. Rev. Lett. 103, 198102.
Marchesini, S. (2007). A unified evaluation of iterative projection algorithms for phase retrieval. Rev. Sci. Instrum. 78, 011301.
Marchesini, S., He, H., Chapman, H. N., Hau-Riege, S. P., Noy, A., Howells, M. R., Weierstall, U. & Spence, J. C. H. (2003). X-ray image reconstruction from a diffraction pattern alone. Phys. Rev. B, 68, 140101.
Miao, J., Charalambous, P., Kirz, J. & Sayre, D. (1999). Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens. Nature (London), 400, 342–344.
Miao, J., Ishikawa, T., Johnson, B., Anderson, E. H., Lai, B. & Hodgson, K. O. (2002). High resolution 3D X-ray diffraction microscopy. Phys. Rev. Lett. 89, 088303.
Miao, J., Sayre, D. & Chapman, H. N. (1998). Phase retrieval from the magnitude of the Fourier transforms of nonperiodic objects. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 15, 1662–1669.
Nelson, J., Huang, X., Steinbrener, J., Shapiro, D. A., Kirz, J., Marchesini, S., Neiman, A. M., Turner, J. & Jacobsen, C. (2010). High resolution X-ray diffraction microscopy of speciffically labelled yeast cells. Proc. Natl Acad. Sci. USA, 107, 7235–7239.
Nishino, Y., Takahashi, Y., Imamoto, N., Ishikawa, T. & Maeshima, K. (2009). Three-dimensional visualization of a human chromosome using coherent X-ray diffraction. Phys. Rev. Lett. 102, 018101.
Pfeifer, M. A., Williams, G. J., Vartanyants, I. A., Harder, R. & Robinson, I. K. (2006). Three-dimensional mapping of a deformation field inside a nanocrystal. Nature (London), 442, 63–66.
Sayre, D. (1980). Imaging Processes and Coherence in Physics, edited by M. Schlenker, M. Fink, J. P. Goedgebuer, C. Malgrange, J. Ch. Viénot & R. H. Wade, p. 229. Heidelberg: Springer-Verlag.
Sayre, D. (1991). Direct Methods of Solving Crystal Structures, edited by H. Schenk, pp. 353–355. New York: Plenum Press.
Sayre, D. (2008). Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction. Acta Cryst. A64, 33–35.
Sayre, D. & Chapman, H. N. (1995). X-ray microscopy. Acta Cryst. A51, 237–252.
Schroer, C. G., Boye, P., Feldkamp, J. M., Patommel, J., Schropp, A., Schwab, A., Stephan, S., Burghammer, M., Schöder, S. & Riekel, C. (2008). Coherent X-ray diffraction imaging with nanofocused illumination. Phys. Rev. Lett. 101, 090801.
Shapiro, D., Thibault, P., Beetz, T., Elser, V., Howells, M., Jacobsen, C., Kirz, J., Lima, E., Miao, H., Neiman, A. M. & Sayre, D. (2005). Biological imaging by soft X-ray diffraction microscopy. Proc. Natl Acad. Sci. USA, 102, 15343–15346.
Shapiro, D. A. (2004). Biological Imaging by Soft X-ray Diffraction Microscopy. PhD thesis, Stony Brook University.
Thibault, P., Elser, V., Jacobsen, C., Shapiro, D. & Sayre, D. (2006). Reconstruction of a yeast cell from X-ray diffraction data. Acta Cryst. A62, 248–261.
Wang, Y., Jacobsen, C., Maser, J. & Osanna, A. (2000). Soft X-ray microscopy with a cryo scanning transmission X-ray microscope: II. Tomography. J. Microsc. 197, 80–93.
Weiss, D., Schneider, G., Niemann, B., Guttman, P., Rudolph, D. & Schmahl, G. (2000). Computed tomography of cryogenic biological specimens based on X-ray microscopic images. Ultramicroscopy, 84, 185–197.