Abstract

Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells preserved under cryo conditions. Images obtained in these X-ray microscopes can be combined by tomographic reconstruction to quantitatively estimate the three-dimensional (3D) distribution of absorption coefficients inside the cell. The impulse response of an imaging system is one of the factors that limits the quality of the X-ray microscope reconstructions. The main goal of this work is to experimentally measure the 3D impulse response and to assess the optical resolution and depth of field of the Mistral microscope at ALBA synchrotron (Barcelona, Spain). To this end we measure the microscope apparent transfer function (ATF) and we use it to design a deblurring Wiener filter, obtaining an increase in the image quality when applied to experimental datasets collected at ALBA.

© 2016 Optical Society of America

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2016 (3)

J. J. Conesa, J. Otón, M. Chiappi, J. M. Carazo, E. Pereiro, F. J. Chichón, and J. L. Carrascosa, “Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography,” Sci. Rep. 6, 22354 (2016).
[Crossref] [PubMed]

A. J. Pérez-Berná, M. J. Rodríguez, F. J. Chichón, M. F. Friesland, A. Sorrentino, J. L. Carrascosa, E. Pereiro, and P. Gastaminza, “Structural Changes In Cells Imaged by Soft X-Ray Cryo-Tomography During Hepatitis C Virus Infection,” ACS Nano 10 (7), 6597–6611 (2016).
[Crossref] [PubMed]

M. Chiappi, J. J. Conesa, E. Pereiro, C. O. S. Sorzano, M. J. Rodríguez, K. Henzler, G. Schneider, F. J. Chichón, and J. L. Carrascosa, “Cryo-soft X-ray tomography as a quantitative three-dimensional tool to model nanoparticle:cell interaction,” J. Nanobiotechnology 14, 15 (2016).
[Crossref] [PubMed]

2015 (2)

A. Sorrentino, J. Nicolás, R. Valcárcel, F. J. Chichón, M. Rosanes, J. Avila, A. Tkachuk, J. Irwin, S. Ferrer, and E. Pereiro, “MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging,” J. Synchrotron Radiat. 22, 1112–1117 (2015).
[Crossref] [PubMed]

J. Otón, C. O. S. Sorzano, R. Marabini, E. Pereiro, and J. M. Carazo, “Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star,” Opt. Express 23, 9567 (2015).
[Crossref] [PubMed]

2014 (3)

E. M. H. Duke, M. Razi, A. Weston, P. Guttmann, S. Werner, K. Henzler, G. Schneider, S. A. Tooze, and L. M. Collinson, “Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM),” Ultramicroscopy 143, 77–87 (2014).
[Crossref]

C. Hagen, S. Werner, and S. Carregal-Romero, “Multimodal nanoparticles as alignment and correlation markers in fluorescence/soft X-ray cryo-microscopy/tomography of nucleoplasmic reticulum and apoptosis in mammalian cells,” Ultramicroscopy 146, 46–54 (2014).
[Crossref] [PubMed]

K. C. Dent, C. Hagen, and K. Grünewald, “Critical step-by-step approaches toward correlative fluorescence/soft X-ray cryo-microscopy of adherent mammalian cells,” Methods Cell Biol. 124, 179–216 (2014).
[Crossref] [PubMed]

2013 (2)

J. Chen, K. Gao, X. Ge, Z. Wang, K. Zhang, Y. Hong, Z. Pan, Z. Wu, P. Zhu, W. Yun, and Z. Wu, “Scattering imaging method in transmission X-ray microscopy,” Opt. Lett. 38, 2068–2070 (2013).
[Crossref] [PubMed]

D. B. Carlson, J. Gelb, V. Palshin, and J. E. Evans, “Laboratory-based cryogenic soft X-ray tomography with correlative cryo-light and electron microscopy,” Microsc. Microanal. 19, 22–29 (2013).
[Crossref] [PubMed]

2012 (4)

W. Chao, P. Fischer, T. Tyliszczak, S. Rekawa, E. Anderson, and P. Naulleau, “Real space soft X-ray imaging at 10 nm spatial resolution,” Opt. Express 20, 9777–9783 (2012).
[Crossref] [PubMed]

S. Rehbein, P. Guttmann, S. Werner, and G. Schneider, “Characterization of the resolving power and contrast transfer function of a transmission X-ray microscope with partially coherent illumination,” Opt. Express 20, 1–3 (2012).
[Crossref]

Q. Yuan, K. Zhang, Y. Hong, W. Huang, K. Gao, Z. Wang, P. Zhu, J. Gelb, A. Tkachuk, B. Hornberger, M. Feser, W. Yun, and Z. Wu, “A 30 nm-resolution hard X-ray microscope with X-ray fluorescence mapping capability at BSRF,” J. Synchrotron Radiat. 19, 1021–1028 (2012).
[Crossref] [PubMed]

J. Oton, C. O. S. Sorzano, E. Pereiro, J. Cuenca-Alba, R. Navarro, J. M. Carazo, and R. Marabini, “Image formation in cellular X-ray microscopy,” J. Struct. Biol. 178, 29–37 (2012).
[Crossref] [PubMed]

2010 (2)

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Muller, J. G. McNally, and W. G. Müller, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7, 985–987 (2010).
[Crossref] [PubMed]

I. G. Kazantsev, J. Klukowska, G. T. Herman, and L. Cernetic, “Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy,” Ultramicroscopy 110, 1128–1142 (2010).
[Crossref] [PubMed]

2009 (4)

E. Pereiro, J. Nicolás, S. Ferrer, and M. R. Howells, “A soft X-ray beamline for transmission X-ray microscopy at ALBA,” J. Synchrotron Radiat. 16, 505–512 (2009).
[Crossref] [PubMed]

M. Bertilson, O. von Hofsten, U. Vogt, A. Holmberg, and H. M. Hertz, “High-resolution computed tomography with a compact soft X-ray microscope,” Opt. Express 17, 11057–11065 (2009).
[Crossref] [PubMed]

D. Schäfer, M. Benk, K. Bergmann, T. Nisius, U. Wiesemann, and T. Wilhein, “Optical setup for tabletop soft X-ray microscopy using electrical discharge sources,” Journal of Physics: Conference Series 186, 012033 (2009).

M. Uchida, G. McDermott, M. Wetzler, M. a. Le Gros, M. Myllys, C. Knoechel, A. E. Barron, and C. a. Larabell, “Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans,” P. Natl. Acad. Sci. USA 106, 19375–19380 (2009).
[Crossref]

2008 (2)

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W.-K. Lee, H. J. Wu, C. H. L. H. L. Wang, J. Y. Wang, C. J. Liu, C. H. L. H. L. Wang, S. R. Wu, C. C. Chien, Y. Hwu, A. Tkachuk, W. Yun, M. Feser, K. S. Liang, C. S. Yang, J. H. Je, and G. Margaritondo, “Hard-X-ray microscopy with Fresnel zone plates reaches 40 nm Rayleigh resolution,” Appl. Phys. Lett. 92, 103119 (2008).
[Crossref]

X. Zeng, F. Duewer, M. Feser, and C. Huang, “Ellipsoidal and parabolic glass capillaries as condensers for X-ray microscopes,” Appl. Opt. 47, 2376–2381 (2008).
[Crossref] [PubMed]

2007 (1)

S. Gabarda and G. Cristóbal, “Blind image quality assessment through anisotropy,” J. Opt. Soc. Am. A Op.t Image Sci. Vis. 24, B42–B51 (2007).
[Crossref] [PubMed]

2005 (1)

W. Chao, B. D. Harteneck, J. A. Liddle, E. H. Anderson, and D. T. Attwood, “Soft X-ray microscopy at a spatial resolution better than 15 nm,” Nature 435, 1210–1213 (2005).
[Crossref] [PubMed]

2000 (1)

R. Burge, X.-C. Yuan, G. Morrison, P. Charalambous, M. Browne, and Z. An, “Incoherent imaging with the soft X-ray microscope,” Ultramicroscopy 83, 75–92 (2000).
[Crossref] [PubMed]

1998 (1)

J. Lehr, J. B. Sibarita, and J. M. Chassery, “Image restoration in X-ray microscopy: PSF determination and biological applications,” IEEE transactions on image processing 7, 258–263 (1998).
[Crossref]

1996 (1)

H. N. Chapman, “Phase-retrieval X-ray microscopy by Wigner-distribution deconvolution,” Ultramicroscopy 66, 153–172 (1996).
[Crossref]

1995 (1)

J. Kirz, C. Jacobsen, and M. Howells, “Soft X-ray microscopes and their biological applications,” Q. Rev. Biophys. 28, 33–130 (1995).
[Crossref] [PubMed]

1950 (1)

H. Hopkins and P. Barham, “The influence of the condenser on microscopic resolution,” Proceedings of the Physical Society Section B 63, 737 (1950).
[Crossref]

An, Z.

R. Burge, X.-C. Yuan, G. Morrison, P. Charalambous, M. Browne, and Z. An, “Incoherent imaging with the soft X-ray microscope,” Ultramicroscopy 83, 75–92 (2000).
[Crossref] [PubMed]

Anderson, E.

Anderson, E. H.

W. Chao, B. D. Harteneck, J. A. Liddle, E. H. Anderson, and D. T. Attwood, “Soft X-ray microscopy at a spatial resolution better than 15 nm,” Nature 435, 1210–1213 (2005).
[Crossref] [PubMed]

Attwood, D.

D. Attwood, Soft X-Rays and Extreme Ultraviolet Radiation: Principles and Applications (Cambridge University, 2000).

Attwood, D. T.

W. Chao, B. D. Harteneck, J. A. Liddle, E. H. Anderson, and D. T. Attwood, “Soft X-ray microscopy at a spatial resolution better than 15 nm,” Nature 435, 1210–1213 (2005).
[Crossref] [PubMed]

Avila, J.

A. Sorrentino, J. Nicolás, R. Valcárcel, F. J. Chichón, M. Rosanes, J. Avila, A. Tkachuk, J. Irwin, S. Ferrer, and E. Pereiro, “MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging,” J. Synchrotron Radiat. 22, 1112–1117 (2015).
[Crossref] [PubMed]

Barham, P.

H. Hopkins and P. Barham, “The influence of the condenser on microscopic resolution,” Proceedings of the Physical Society Section B 63, 737 (1950).
[Crossref]

Barron, A. E.

M. Uchida, G. McDermott, M. Wetzler, M. a. Le Gros, M. Myllys, C. Knoechel, A. E. Barron, and C. a. Larabell, “Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans,” P. Natl. Acad. Sci. USA 106, 19375–19380 (2009).
[Crossref]

Benk, M.

D. Schäfer, M. Benk, K. Bergmann, T. Nisius, U. Wiesemann, and T. Wilhein, “Optical setup for tabletop soft X-ray microscopy using electrical discharge sources,” Journal of Physics: Conference Series 186, 012033 (2009).

Bergmann, K.

D. Schäfer, M. Benk, K. Bergmann, T. Nisius, U. Wiesemann, and T. Wilhein, “Optical setup for tabletop soft X-ray microscopy using electrical discharge sources,” Journal of Physics: Conference Series 186, 012033 (2009).

Bertilson, M.

Born, M.

M. Born and E. Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light (Cambridge University, 1999).
[Crossref]

Browne, M.

R. Burge, X.-C. Yuan, G. Morrison, P. Charalambous, M. Browne, and Z. An, “Incoherent imaging with the soft X-ray microscope,” Ultramicroscopy 83, 75–92 (2000).
[Crossref] [PubMed]

Burge, R.

R. Burge, X.-C. Yuan, G. Morrison, P. Charalambous, M. Browne, and Z. An, “Incoherent imaging with the soft X-ray microscope,” Ultramicroscopy 83, 75–92 (2000).
[Crossref] [PubMed]

Carazo, J. M.

J. J. Conesa, J. Otón, M. Chiappi, J. M. Carazo, E. Pereiro, F. J. Chichón, and J. L. Carrascosa, “Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography,” Sci. Rep. 6, 22354 (2016).
[Crossref] [PubMed]

J. Otón, C. O. S. Sorzano, R. Marabini, E. Pereiro, and J. M. Carazo, “Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star,” Opt. Express 23, 9567 (2015).
[Crossref] [PubMed]

J. Oton, C. O. S. Sorzano, E. Pereiro, J. Cuenca-Alba, R. Navarro, J. M. Carazo, and R. Marabini, “Image formation in cellular X-ray microscopy,” J. Struct. Biol. 178, 29–37 (2012).
[Crossref] [PubMed]

J. Oton, C. O. S. Sorzano, F. J. Chichón, J. L. Carrascosa, J. M. Carazo, and R. Marabini, “Soft X-ray Tomography Imaging for Biological Samples,” in “Computational Methods for Three-Dimensional Microscopy Reconstruction,” (2014), Chap. 8, p. 260.

Carlson, D. B.

D. B. Carlson, J. Gelb, V. Palshin, and J. E. Evans, “Laboratory-based cryogenic soft X-ray tomography with correlative cryo-light and electron microscopy,” Microsc. Microanal. 19, 22–29 (2013).
[Crossref] [PubMed]

Carrascosa, J. L.

M. Chiappi, J. J. Conesa, E. Pereiro, C. O. S. Sorzano, M. J. Rodríguez, K. Henzler, G. Schneider, F. J. Chichón, and J. L. Carrascosa, “Cryo-soft X-ray tomography as a quantitative three-dimensional tool to model nanoparticle:cell interaction,” J. Nanobiotechnology 14, 15 (2016).
[Crossref] [PubMed]

J. J. Conesa, J. Otón, M. Chiappi, J. M. Carazo, E. Pereiro, F. J. Chichón, and J. L. Carrascosa, “Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography,” Sci. Rep. 6, 22354 (2016).
[Crossref] [PubMed]

A. J. Pérez-Berná, M. J. Rodríguez, F. J. Chichón, M. F. Friesland, A. Sorrentino, J. L. Carrascosa, E. Pereiro, and P. Gastaminza, “Structural Changes In Cells Imaged by Soft X-Ray Cryo-Tomography During Hepatitis C Virus Infection,” ACS Nano 10 (7), 6597–6611 (2016).
[Crossref] [PubMed]

J. Oton, C. O. S. Sorzano, F. J. Chichón, J. L. Carrascosa, J. M. Carazo, and R. Marabini, “Soft X-ray Tomography Imaging for Biological Samples,” in “Computational Methods for Three-Dimensional Microscopy Reconstruction,” (2014), Chap. 8, p. 260.

Carregal-Romero, S.

C. Hagen, S. Werner, and S. Carregal-Romero, “Multimodal nanoparticles as alignment and correlation markers in fluorescence/soft X-ray cryo-microscopy/tomography of nucleoplasmic reticulum and apoptosis in mammalian cells,” Ultramicroscopy 146, 46–54 (2014).
[Crossref] [PubMed]

Cernetic, L.

I. G. Kazantsev, J. Klukowska, G. T. Herman, and L. Cernetic, “Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy,” Ultramicroscopy 110, 1128–1142 (2010).
[Crossref] [PubMed]

Chang, C.

C. Chang and T. Nakamura, “Partially coherent image formation theory for X-ray microscopy,” in “Microscopy: Science, Technology, Applications and Education,” 4th ed. A. Mav and J. Da, eds. (Formatex Research Center, 2010), Chap. 3, pp. 1897–1904.

Chao, W.

W. Chao, P. Fischer, T. Tyliszczak, S. Rekawa, E. Anderson, and P. Naulleau, “Real space soft X-ray imaging at 10 nm spatial resolution,” Opt. Express 20, 9777–9783 (2012).
[Crossref] [PubMed]

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Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W.-K. Lee, H. J. Wu, C. H. L. H. L. Wang, J. Y. Wang, C. J. Liu, C. H. L. H. L. Wang, S. R. Wu, C. C. Chien, Y. Hwu, A. Tkachuk, W. Yun, M. Feser, K. S. Liang, C. S. Yang, J. H. Je, and G. Margaritondo, “Hard-X-ray microscopy with Fresnel zone plates reaches 40 nm Rayleigh resolution,” Appl. Phys. Lett. 92, 103119 (2008).
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Muller, W. G.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Muller, J. G. McNally, and W. G. Müller, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7, 985–987 (2010).
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Müller, W. G.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Muller, J. G. McNally, and W. G. Müller, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7, 985–987 (2010).
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M. Uchida, G. McDermott, M. Wetzler, M. a. Le Gros, M. Myllys, C. Knoechel, A. E. Barron, and C. a. Larabell, “Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans,” P. Natl. Acad. Sci. USA 106, 19375–19380 (2009).
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G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Muller, J. G. McNally, and W. G. Müller, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7, 985–987 (2010).
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Navarro, R.

J. Oton, C. O. S. Sorzano, E. Pereiro, J. Cuenca-Alba, R. Navarro, J. M. Carazo, and R. Marabini, “Image formation in cellular X-ray microscopy,” J. Struct. Biol. 178, 29–37 (2012).
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D. Schäfer, M. Benk, K. Bergmann, T. Nisius, U. Wiesemann, and T. Wilhein, “Optical setup for tabletop soft X-ray microscopy using electrical discharge sources,” Journal of Physics: Conference Series 186, 012033 (2009).

Oton, J.

J. Oton, C. O. S. Sorzano, E. Pereiro, J. Cuenca-Alba, R. Navarro, J. M. Carazo, and R. Marabini, “Image formation in cellular X-ray microscopy,” J. Struct. Biol. 178, 29–37 (2012).
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J. J. Conesa, J. Otón, M. Chiappi, J. M. Carazo, E. Pereiro, F. J. Chichón, and J. L. Carrascosa, “Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography,” Sci. Rep. 6, 22354 (2016).
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Pereiro, E.

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J. J. Conesa, J. Otón, M. Chiappi, J. M. Carazo, E. Pereiro, F. J. Chichón, and J. L. Carrascosa, “Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography,” Sci. Rep. 6, 22354 (2016).
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A. Sorrentino, J. Nicolás, R. Valcárcel, F. J. Chichón, M. Rosanes, J. Avila, A. Tkachuk, J. Irwin, S. Ferrer, and E. Pereiro, “MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging,” J. Synchrotron Radiat. 22, 1112–1117 (2015).
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J. Otón, C. O. S. Sorzano, R. Marabini, E. Pereiro, and J. M. Carazo, “Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star,” Opt. Express 23, 9567 (2015).
[Crossref] [PubMed]

J. Oton, C. O. S. Sorzano, E. Pereiro, J. Cuenca-Alba, R. Navarro, J. M. Carazo, and R. Marabini, “Image formation in cellular X-ray microscopy,” J. Struct. Biol. 178, 29–37 (2012).
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E. Pereiro, J. Nicolás, S. Ferrer, and M. R. Howells, “A soft X-ray beamline for transmission X-ray microscopy at ALBA,” J. Synchrotron Radiat. 16, 505–512 (2009).
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A. J. Pérez-Berná, M. J. Rodríguez, F. J. Chichón, M. F. Friesland, A. Sorrentino, J. L. Carrascosa, E. Pereiro, and P. Gastaminza, “Structural Changes In Cells Imaged by Soft X-Ray Cryo-Tomography During Hepatitis C Virus Infection,” ACS Nano 10 (7), 6597–6611 (2016).
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S. Rehbein, P. Guttmann, S. Werner, and G. Schneider, “Characterization of the resolving power and contrast transfer function of a transmission X-ray microscope with partially coherent illumination,” Opt. Express 20, 1–3 (2012).
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G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Muller, J. G. McNally, and W. G. Müller, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7, 985–987 (2010).
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Rodríguez, M. J.

A. J. Pérez-Berná, M. J. Rodríguez, F. J. Chichón, M. F. Friesland, A. Sorrentino, J. L. Carrascosa, E. Pereiro, and P. Gastaminza, “Structural Changes In Cells Imaged by Soft X-Ray Cryo-Tomography During Hepatitis C Virus Infection,” ACS Nano 10 (7), 6597–6611 (2016).
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[Crossref] [PubMed]

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Schneider, G.

M. Chiappi, J. J. Conesa, E. Pereiro, C. O. S. Sorzano, M. J. Rodríguez, K. Henzler, G. Schneider, F. J. Chichón, and J. L. Carrascosa, “Cryo-soft X-ray tomography as a quantitative three-dimensional tool to model nanoparticle:cell interaction,” J. Nanobiotechnology 14, 15 (2016).
[Crossref] [PubMed]

E. M. H. Duke, M. Razi, A. Weston, P. Guttmann, S. Werner, K. Henzler, G. Schneider, S. A. Tooze, and L. M. Collinson, “Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM),” Ultramicroscopy 143, 77–87 (2014).
[Crossref]

S. Rehbein, P. Guttmann, S. Werner, and G. Schneider, “Characterization of the resolving power and contrast transfer function of a transmission X-ray microscope with partially coherent illumination,” Opt. Express 20, 1–3 (2012).
[Crossref]

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Muller, J. G. McNally, and W. G. Müller, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7, 985–987 (2010).
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A. Sorrentino, J. Nicolás, R. Valcárcel, F. J. Chichón, M. Rosanes, J. Avila, A. Tkachuk, J. Irwin, S. Ferrer, and E. Pereiro, “MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging,” J. Synchrotron Radiat. 22, 1112–1117 (2015).
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J. Otón, C. O. S. Sorzano, R. Marabini, E. Pereiro, and J. M. Carazo, “Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star,” Opt. Express 23, 9567 (2015).
[Crossref] [PubMed]

J. Oton, C. O. S. Sorzano, E. Pereiro, J. Cuenca-Alba, R. Navarro, J. M. Carazo, and R. Marabini, “Image formation in cellular X-ray microscopy,” J. Struct. Biol. 178, 29–37 (2012).
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J. Oton, C. O. S. Sorzano, F. J. Chichón, J. L. Carrascosa, J. M. Carazo, and R. Marabini, “Soft X-ray Tomography Imaging for Biological Samples,” in “Computational Methods for Three-Dimensional Microscopy Reconstruction,” (2014), Chap. 8, p. 260.

Tkachuk, A.

A. Sorrentino, J. Nicolás, R. Valcárcel, F. J. Chichón, M. Rosanes, J. Avila, A. Tkachuk, J. Irwin, S. Ferrer, and E. Pereiro, “MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging,” J. Synchrotron Radiat. 22, 1112–1117 (2015).
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Tooze, S. A.

E. M. H. Duke, M. Razi, A. Weston, P. Guttmann, S. Werner, K. Henzler, G. Schneider, S. A. Tooze, and L. M. Collinson, “Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM),” Ultramicroscopy 143, 77–87 (2014).
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Tyliszczak, T.

Uchida, M.

M. Uchida, G. McDermott, M. Wetzler, M. a. Le Gros, M. Myllys, C. Knoechel, A. E. Barron, and C. a. Larabell, “Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans,” P. Natl. Acad. Sci. USA 106, 19375–19380 (2009).
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A. Sorrentino, J. Nicolás, R. Valcárcel, F. J. Chichón, M. Rosanes, J. Avila, A. Tkachuk, J. Irwin, S. Ferrer, and E. Pereiro, “MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging,” J. Synchrotron Radiat. 22, 1112–1117 (2015).
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von Hofsten, O.

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E. M. H. Duke, M. Razi, A. Weston, P. Guttmann, S. Werner, K. Henzler, G. Schneider, S. A. Tooze, and L. M. Collinson, “Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM),” Ultramicroscopy 143, 77–87 (2014).
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E. M. H. Duke, M. Razi, A. Weston, P. Guttmann, S. Werner, K. Henzler, G. Schneider, S. A. Tooze, and L. M. Collinson, “Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM),” Ultramicroscopy 143, 77–87 (2014).
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M. Uchida, G. McDermott, M. Wetzler, M. a. Le Gros, M. Myllys, C. Knoechel, A. E. Barron, and C. a. Larabell, “Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans,” P. Natl. Acad. Sci. USA 106, 19375–19380 (2009).
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D. Schäfer, M. Benk, K. Bergmann, T. Nisius, U. Wiesemann, and T. Wilhein, “Optical setup for tabletop soft X-ray microscopy using electrical discharge sources,” Journal of Physics: Conference Series 186, 012033 (2009).

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D. Schäfer, M. Benk, K. Bergmann, T. Nisius, U. Wiesemann, and T. Wilhein, “Optical setup for tabletop soft X-ray microscopy using electrical discharge sources,” Journal of Physics: Conference Series 186, 012033 (2009).

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Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W.-K. Lee, H. J. Wu, C. H. L. H. L. Wang, J. Y. Wang, C. J. Liu, C. H. L. H. L. Wang, S. R. Wu, C. C. Chien, Y. Hwu, A. Tkachuk, W. Yun, M. Feser, K. S. Liang, C. S. Yang, J. H. Je, and G. Margaritondo, “Hard-X-ray microscopy with Fresnel zone plates reaches 40 nm Rayleigh resolution,” Appl. Phys. Lett. 92, 103119 (2008).
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Yang, C. S.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W.-K. Lee, H. J. Wu, C. H. L. H. L. Wang, J. Y. Wang, C. J. Liu, C. H. L. H. L. Wang, S. R. Wu, C. C. Chien, Y. Hwu, A. Tkachuk, W. Yun, M. Feser, K. S. Liang, C. S. Yang, J. H. Je, and G. Margaritondo, “Hard-X-ray microscopy with Fresnel zone plates reaches 40 nm Rayleigh resolution,” Appl. Phys. Lett. 92, 103119 (2008).
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Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W.-K. Lee, H. J. Wu, C. H. L. H. L. Wang, J. Y. Wang, C. J. Liu, C. H. L. H. L. Wang, S. R. Wu, C. C. Chien, Y. Hwu, A. Tkachuk, W. Yun, M. Feser, K. S. Liang, C. S. Yang, J. H. Je, and G. Margaritondo, “Hard-X-ray microscopy with Fresnel zone plates reaches 40 nm Rayleigh resolution,” Appl. Phys. Lett. 92, 103119 (2008).
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Figures (6)

Fig. 1
Fig. 1

Optical system scheme of a full field transmission X-ray microscope. The exit slit of a monochromator used to select the proper photon energy acts as light source. Beam is then condensed by an ellipsoidal glass capillary onto the sample plane, while a central stopper blocks the center part of the beam that is not reflected by the capillary. Finally, images are obtained by FZP objective lens.

Fig. 2
Fig. 2

Transverse profiles of the APSF and PAPSF calculated for different numerical apertures ratio m values. Axial units has been normalized to λ NA O.

Fig. 3
Fig. 3

Axial profiles of the APSF and PAPSF calculated for different numerical apertures ratio m values. Axial units has been normalized to λ NA O 2.

Fig. 4
Fig. 4

Experimental characterization of the Mistral microscope when using: ZP40, 937 zones, 2.52 mm theoretical focal length (blue); and ZP25, 1,500 zones, 1.57 mm theoretical focal length (red). Profiles have been calculated for 520 eV. (a) Apparent transfer function profiles; (b) Pseudo apparent transfer function profile calculated at in-focus plane. Applying Rayleigh criteria results in critical resolution values of 61.9 and 51.8 nm for ZP40 and ZP25 lenses, respectively; (c) Axial apparent transfer function profiles. Experimental DOF are 3.3 and 1.6 μm for ZP40 and ZP25, respectively.

Fig. 5
Fig. 5

Comparison of Scenedesmus cells tomograms obtained using ZP40. The first row shows standard tomographic results (non-deconvolved), while the second row presents the reconstruction from deconvolved tilt series tomogram. (a, e) Sections perpendicular to the tilt axis where three dashed lines are drawn, corresponding to slices in x–y plane at different distances in z: (b, f) z=−1.3 μm, (c, g) z=0.7 μm and (d, h) z=2 μm. Scale bars = 1 μm; (i) Density profile along the dashed red line marked in (b) compared to the same profile, dashed blue line, in (f); (j) Anisotropic quality index (AQI) comparison of slice pairs (b,f), (c,g) and (d,h). In all the cases the visibility of the slices is enhanced in the case when deconvolution is applied.

Fig. 6
Fig. 6

Comparison of Huh-7 cells tomograms obtained using ZP25. The first row shows standard tomographic results (non-deconvolved), while the second row presents the reconstruction from deconvolved tilt series tomogram. (a, e) Sections perpendicular to the tilt axis where three dashed lines are drawn, corresponding to slices in x–y plane at different distances in z: (b, f) z=−0.3 μm, (c, g) z=0 μm and (d, h) z=0.84 μm. Scale bars = 1 μm; (i) Density profile along the dashed red line marked in (c) compared to the same profile, dashed blue line, in (g); Anisotropic quality index (AQI) comparison of slice pairs (b,f), (c,g) and (d,h). In all the cases the visibility of the slices is enhanced in the case when deconvolution is applied.

Equations (7)

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A ( f x ) = I ˜ out ( f x ) I ˜ in ( f x ) ,
h A ( x ) = 1 { A ( f x ) } ,
h PA ( x ) = 1 { | A ( f x ) | } .
I s ( x ) = [ I 0 ( x ) e z 0 z s μ ( x , z ) d z ] h A ( x ) ,
z 0 z s μ ( x , z ) d z = ln [ I s ( x ) h A 1 ( x ) I 0 ( x ) h A 1 ( x ) ] ,
I ˜ s e ( f x ) = W ( f x ) I ˜ s ( f x ) ,
W ( f x ) = A * ( f x ) | A ( f x ) | 2 + S n ( f x ) S I ( f x ) ,

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