Image formation in cellular X-ray microscopy

Journal of Structural Biology

Volumn 178, Issue 1, 2012, Pages 29-37

  Oton, Joaquin ^a   Sorzano, C O S ^a   Pereiro, Eva ^b   Cuenca Alba, Jesús ^a   Navarro, Rafael ^c   Carazo, Jose M ^a   Marabini, Roberto ^d  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b ALBA SYNCHROTRON LIGHT SOURCE   (Spain)

^c CSIC   (Spain)

^d Calle Francisco Tomás y Valiente   (Spain)

Author keywords

3D reconstruction; Image formation model; Point spread function; X ray microscopy

Indexed keywords

ARTICLE; CELL ORGANELLE; CELL STRUCTURE; CONFOCAL MICROSCOPY; ELECTRON MICROSCOPY; IMAGE PROCESSING; IMAGE RECONSTRUCTION; MICROSCOPE; MICROSCOPE IMAGE; MICROSCOPY; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION; SOFT X RAY TOMOGRAPHIC MICROSCOPY; THREE DIMENSIONAL IMAGING; X RAY ANALYSIS;

CANDIDA ALBICANS; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MODELS, THEORETICAL; PHANTOMS, IMAGING; X-RAY MICROTOMOGRAPHY;

EID: 84859428449     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2012.01.006     Document Type: Article

References (33)

1. Agard D., Hiraoka Y., Shaw P., Sedat J. Fluorescence microscopy in three dimensions. Fluorescence microscopy of living cells in culture. Methods Cell Biol. 1989, 30:353-377.
2. Attwood D. Soft X-Rays and Extreme Ultraviolet Radiation: Principles and Applications 2007, Cambridge University Press, New York, NY, USA. first ed.
3. Bertilson M., von Hofsten O., Hertz H.M., Vogt U. Numerical model for tomographic image formation in transmission X-ray microscopy. Optics Express 2011, 19:11578-11583.
4. Carrascosa J.L., Chichon F.J., Pereiro E., Rodriguez M.J., Fernandez J.J., Esteban M., Heim S., Guttmann P., Schneider G. Cryo-X-ray tomography of vaccinia virus membranes and inner compartments. J. Struct. Biol. 2009, 168:234-239.
5. Dey, N., Boucher, A., Thonnat, M., 2002. Image formation model of a 3D translucent object observed in light microscopy. In: Proceedings. International Conference on Image Processing, Rochester, NY, USA. pp. II-469-II-472.
6. Frank J. Three Dimensional Electron Microscopy of Macromolecular Assemblies 2006, Oxford University Press, New York.
7. 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.
8. Goodman J.W. Introduction to Fourier Optics 1996, McGraw-Hill, New York.
9. Gu W., Etkin L.D., Le Gros M.A., Larabell C.A. X-ray tomography of Schizosaccharomyces pombe. Differentiation 2007, 75:529-535.
10. Hanssen E., Knoechel C., Dearnley M., Dixon M.W., Le Gros M., Larabell C., Tilley L. Soft X-ray microscopy analysis of cell volume and hemoglobin content in erythrocytes infected with asexual and sexual stages of Plasmodium falciparum. J. Struct. Biol. 2011.
11. von Hofsten O., Takman P.A.C., Vogt U. Simulation of partially coherent image formation in a compact soft X-ray microscope. Ultramicroscopy 2007, 107:604-609. PMID: 17261350.
12. Howells, M., Jacobsen, C., Warwick, T., 2007. Principles and applications of zone plate X-ray microscopes. In: Hawkes, P., Spence, J. (Eds.), Science in Microscopy, pp. 835-926.
13. Jacobsen, C., 1992. Making soft X-ray microscopy harder: considerations for sub-0.1 micron resolution imaging at 4a° wavelengths, In: Michette, A.G., Morrison, G.R., Buckley, C.J. (Eds.), X-ray Microscopy III. Volume 67 of Springer Series in Optical Sciences. Springer-Verlag, Berlin, pp. 274-277.
14. Kirz J., Jacobsen C., Howells M. Soft X-ray microscopes and their biological applications. Q. Rev. Biophys. 1995, 28:33-130.
15. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996, 116:71-76.
16. Larabell C.A., Le Gros M.A. X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution. Mol. Biol. Cell 2004, 15:957-962.
17. Le Gros M.A., McDermott G., Larabell C.A. X-ray tomography of whole cells. Curr. Opin. Struct. Biol. 2005, 15:593-600.
18. Mendoza-Yero, O., Mínguez-Vega, G., Navarro, R., Lancis, J., Climent, V., 2010. PSF analysis of nanometric fresnel zone plates. In: Proceeding of the EOS Topical Meeting on Diffractive Optics, Koli, Finland.
19. Mielenz K.D. On the diffraction limit for lensless imaging. J. Res. NIST 1999, 104:479-485.
20. Parkinson D.Y., McDermott G., Etkin L.D., Le Gros M.A., Larabell C.A. Quantitative 3-D imaging of eukaryotic cells using soft X-ray tomography. J. Struct. Biol. 2008, 162:380-386.
21. Rosenthal P.B., Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 2003, 333:721-745.
22. Rudolph D., Schmahl G., Niemann B. Amplitude and phase contrast in X-ray microscopy. Mod. Microsc. 1990, 59-67. Plenum, New York. P.J. Duke, A.G. Michette (Eds.).
23. Schmahl G., Rudolph D. Proposal for a phase contrast X-ray microscope. X-ray Microscopy 1987, 231-238. Springer-Verlag, Berlin. P. Cheng, G. Jan (Eds.).
24. Schneider G. Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast. Ultramicroscopy 1998, 75:85-104.
25. Schneider G., Guttmann P., Heim S., Rehbein S., Mueller F., Nagashima K., Heymann J.B., Muller W.G., McNally J.G. Three-dimensional cellular ultrastructure resolved by X-ray microscopy. Nat. Methods 2010, 7:985-987.
26. Sorzano C.O.S., Marabini R., Boisset N., Rietzel E., Schröder R., Herman G.T., Carazo J.M. The effect of overabundant projection directions on 3D reconstruction algorithms. J. Struct. Biol. 2001, 113:108-118.
27. Sorzano C.O.S., Marabini R., Velázquez-Muriel J., Bilbao-Castro J.R., Scheres S.H.W., Carazo J.M., Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 2004, 148:194-204.
28. Sypek, M., Makowski, M., Kolodziejczyk, A., Navarro, R., 2010. Calculations of PSF functions for X-ray zone plates with high number of zones. In: Proceeding of the EOS Topical Meeting on Diffractive Optics, Koli, Finland.
29. Thieme J., Schneider G., Knochel C. X-ray tomography of a microhabitat of bacteria and other soil colloids with sub-100nm resolution. Micron 2003, 34:339-344.
30. Uchida M., McDermott G., Wetzler M., Le Gros M.A., Myllys M., Knoechel C., Barron A.E., Larabell C.A. Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans. Proc. Natl. Acad. Sci. USA 2009, 106:19375-19380.
31. Weiss D., Schneider G., Niemann B., Guttmann P., Rudolph D., Schmahl G. Computed tomography of cryogenic biological specimens based on X-ray microscopic images. Ultramicroscopy 2000, 84:185-197.
32. Weiss D., Schneider G., Niemann B., Guttmann P., Rudolph D., Schmahl G. Computed tomography of cryogenic biological specimens based on X-ray microscopic images. Ultramicroscopy 2000, 84:185-197. (PMID: 10945329).
33. Wolter H. Spiegelsysteme streifenden Einfalls als abbildende Optiken für Röntgenstrahlen. Ann. Phys. 1952, 445:94-114.