Abstract

Focal stack (FS) is an effective technique for fast 3D imaging in high-resolution scanning transmission X-ray microscopy. Its crucial issue is to assign each object within the sample to the correct position along the optical axis according to a proper focus measure. There is probably information loss with previous algorithms for FS reconstruction because the old algorithms can only detect one focused object along each optical-axial pixel line (OAPL). In this study, we present an improved FS algorithm, which utilizes an elaborately calculated threshold for normalized local variances to extract multiple focused objects in each OAPL. Simulation and experimental results show its feasibility and high efficiency for 3D imaging of high contrast, sparse samples. It is expected that our advanced approach has potential applications in 3D X-ray microscopy for more complex samples.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Full Article  |  PDF Article
OSA Recommended Articles
Three-dimensional iterative multislice reconstruction for ptychographic X-ray computed tomography

Kei Shimomura, Makoto Hirose, Takaya Higashino, and Yukio Takahashi
Opt. Express 26(24) 31199-31208 (2018)

Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection

Mårten Selin, Emelie Fogelqvist, Stephan Werner, and Hans M. Hertz
Opt. Lett. 40(10) 2201-2204 (2015)

Method for extending the depth of focus in X-ray microscopy

Fahu Li, Yong Guan, Ying Xiong, Xiaobo Zhang, Gang Liu, and Yangchao Tian
Opt. Express 25(7) 7657-7667 (2017)

References

  • View by:
  • |
  • |
  • |

  1. D. Attwood, “Microscopy: nanotomography comes of age,” Nature 442(7103), 642–643 (2006).
    [Crossref] [PubMed]
  2. J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
    [Crossref] [PubMed]
  3. B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
    [Crossref] [PubMed]
  4. M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
    [Crossref] [PubMed]
  5. G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
    [Crossref] [PubMed]
  6. J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
    [Crossref]
  7. L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
    [Crossref] [PubMed]
  8. M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
    [Crossref] [PubMed]
  9. S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
    [Crossref] [PubMed]
  10. I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
    [Crossref] [PubMed]
  11. M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
    [Crossref] [PubMed]
  12. G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
    [Crossref] [PubMed]
  13. M. A. Le Gros, G. McDermott, and C. A. Larabell, “X-ray tomography of whole cells,” Curr. Opin. Struct. Biol. 15(5), 593–600 (2005).
    [Crossref] [PubMed]
  14. M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
    [Crossref] [PubMed]
  15. A. Späth, J. Raabe, and R. H. Fink, “Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations,” J. Synchrotron Radiat. 22(1), 113–118 (2015).
    [Crossref] [PubMed]
  16. J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
    [Crossref] [PubMed]
  17. X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
    [Crossref] [PubMed]
  18. G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
    [Crossref]
  19. 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(1), 15 (2016).
    [Crossref] [PubMed]
  20. A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
    [Crossref]
  21. Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
    [Crossref] [PubMed]
  22. A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
    [Crossref]
  23. J. B. Pawley and B. R. Masters, Handbook of Biological Confocal Microscopy, Third Edition (Plenum Press, 2006).
  24. N. Streibl, “Three-dimensional imaging by a microscope,” J. Opt. Soc. Am. A 2(2), 121–127 (1985).
    [Crossref]
  25. L. Jochum, “Imaging X-Ray Microscopy with Extended Depth of Focus by Use of a Digital Image Processing System,” in Proceedings of X-Ray Microscopy II, (Acdemic, 1988), pp.292–295.
    [Crossref]
  26. J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
    [Crossref] [PubMed]
  27. M. Selin, E. Fogelqvist, S. Werner, and H. M. Hertz, “Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection,” Opt. Lett. 40(10), 2201–2204 (2015).
    [Crossref] [PubMed]
  28. Y. Liu, J. Wang, Y. Hong, Z. Wang, K. Zhang, P. A. Williams, P. Zhu, J. C. Andrews, P. Pianetta, and Z. Wu, “Extended depth of focus for transmission x-ray microscope,” Opt. Lett. 37(17), 3708–3710 (2012).
    [Crossref] [PubMed]
  29. T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
    [Crossref]
  30. K. N. Kutulakos and S. W. Hasinoff, “Focal Stack Photography: High-Performance Photography with a Conventional Camera,” in Procedings of Iapr Machine Vision Applications, (Academic,2013).
  31. A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
    [Crossref] [PubMed]
  32. F. Li, Y. Guan, Y. Xiong, X. Zhang, G. Liu, and Y. Tian, “Method for extending the depth of focus in X-ray microscopy,” Opt. Express 25(7), 7657–7667 (2017).
    [Crossref] [PubMed]
  33. D. Attwood, Soft X-rays and Extreme Ultraviolet Radiation: Principles and Applications (Cambridge University, 2017).
  34. Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
    [Crossref]
  35. W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
    [Crossref] [PubMed]
  36. W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
    [Crossref] [PubMed]
  37. Q. Wu, F. Merchant. K. R. Castleman, Microscope Image Processing (Elsevier, 2008).
  38. J. M. Cowley and A. F. Moodie, “The Scattering of Electrons by Atoms and Crystals. III. Single-Crystal Diffraction Patterns,” Acta Crystallogr. 12(5), 360–367 (1959).
    [Crossref]
  39. A. M. Maiden, M. J. Humphry, and J. M. Rodenburg, “Ptychographic transmission microscopy in three dimensions using a multi-slice approach,” J. Opt. Soc. Am. A 29(8), 1606–1614 (2012).
    [Crossref] [PubMed]
  40. J. D. Schmidt, Numerical Simulation of Optical Wave Propagation with Examples in MATLAB (SPIE, 2010).
  41. A. Thompson, D. Attwood, E. Gullikson, M. Howells, K.-J. Kim, I. Lindau, Y. liu, P. Pianetta, A. Robinson, J. Scofield, J. Underwood, and G. Williams, X-ray Data Booklet. (Berkeley, California, 2009).
  42. K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).
  43. J. W. Goodman, Introduction to Fourier Optics. (Stanford University, 2004).
  44. D. Attwood, Soft X-rays and Extreme Ultraviolet Radiation: Principles and Applications (Cambridge University, 1999), Chap. 9.

2018 (1)

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

2017 (3)

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

F. Li, Y. Guan, Y. Xiong, X. Zhang, G. Liu, and Y. Tian, “Method for extending the depth of focus in X-ray microscopy,” Opt. Express 25(7), 7657–7667 (2017).
[Crossref] [PubMed]

2016 (3)

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(1), 15 (2016).
[Crossref] [PubMed]

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

2015 (5)

A. Späth, J. Raabe, and R. H. Fink, “Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations,” J. Synchrotron Radiat. 22(1), 113–118 (2015).
[Crossref] [PubMed]

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

M. Selin, E. Fogelqvist, S. Werner, and H. M. Hertz, “Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection,” Opt. Lett. 40(10), 2201–2204 (2015).
[Crossref] [PubMed]

2014 (1)

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

2013 (3)

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
[Crossref]

2012 (3)

2010 (2)

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

2009 (1)

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

2008 (4)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

2007 (2)

W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
[Crossref] [PubMed]

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

2006 (1)

D. Attwood, “Microscopy: nanotomography comes of age,” Nature 442(7103), 642–643 (2006).
[Crossref] [PubMed]

2005 (2)

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

M. A. Le Gros, G. McDermott, and C. A. Larabell, “X-ray tomography of whole cells,” Curr. Opin. Struct. Biol. 15(5), 593–600 (2005).
[Crossref] [PubMed]

2001 (1)

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

2000 (1)

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

1985 (1)

1959 (1)

J. M. Cowley and A. F. Moodie, “The Scattering of Electrons by Atoms and Crystals. III. Single-Crystal Diffraction Patterns,” Acta Crystallogr. 12(5), 360–367 (1959).
[Crossref]

Allner, S.

Andrews, J. C.

Attwood, D.

D. Attwood, “Microscopy: nanotomography comes of age,” Nature 442(7103), 642–643 (2006).
[Crossref] [PubMed]

Bai, R.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Bates, M.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Bazylinski, D. A.

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Belakhovsky, M.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Belden, J.

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

Bennett, B. T.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Bewersdorf, J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Bleuet, P.

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Bunk, O.

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Cabana, J.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Calvayrac, Y.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Carazo, J. M.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Carrascosa, J. L.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[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(1), 15 (2016).
[Crossref] [PubMed]

Celestre, R.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Chen, C.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Chevrier, J.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Chiappi, M.

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(1), 15 (2016).
[Crossref] [PubMed]

Chichón, F. J.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[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(1), 15 (2016).
[Crossref] [PubMed]

Chien, C. C.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Chu, Y. S.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Clare, R.

Cloetens, P.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Conchello, J. A.

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

Conesa, J. J.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[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(1), 15 (2016).
[Crossref] [PubMed]

Cowley, J. M.

J. M. Cowley and A. F. Moodie, “The Scattering of Electrons by Atoms and Crystals. III. Single-Crystal Diffraction Patterns,” Acta Crystallogr. 12(5), 360–367 (1959).
[Crossref]

Cram, D. S.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Davidson, M. W.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

De Carlo, F.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Delette, G.

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Denbeaux, G.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Denes, P.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Dierolf, M.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Enders, B.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

Englich, U.

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

Etkin, L. D.

W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
[Crossref] [PubMed]

Faigel, G.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Farmand, M.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Fehringer, A.

Feser, M.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Fetter, R. D.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Fink, R. H.

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

A. Späth, J. Raabe, and R. H. Fink, “Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations,” J. Synchrotron Radiat. 22(1), 113–118 (2015).
[Crossref] [PubMed]

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Fogelqvist, E.

Galbraith, C. G.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Galbraith, J. A.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Ghugare, S.

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

Gillette, J. M.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Gillilan, R.

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

Gould, T. J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Graf-Zeiler, B. A.

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

Grey, C. P.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Gu, W.

W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
[Crossref] [PubMed]

Guan, Y.

Guttmann, P.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Hamamoto, D.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Heim, S.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Henzler, K.

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(1), 15 (2016).
[Crossref] [PubMed]

Heraud, P.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Herman, G. T.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Hertz, H. M.

Hess, H. F.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Hess, S. T.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Heymann, J. B.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Hitchcock, A. P.

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Hong, Y.

Hornegger, J.

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Huang, B.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Huang, W.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Hubert, M.

Humphry, M. J.

Hwu, Y.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Je, J. H.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Johansson, G. A.

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

Johnson, L.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Joseph, J.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Juette, M. F.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Junker, M.

G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
[Crossref]

Kanchanawong, P.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Karunakaran, C.

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Kaznatcheev, K. V.

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Keefe, M. H.

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

Kewish, C. M.

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Khan, I.

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

Kilcoyne, A. L. D.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Kim, C.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Klukowska, J.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Kriksunov, I.

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

Krishnan, H.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Lanke, U. D.

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Larabell, C. A.

W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
[Crossref] [PubMed]

M. A. Le Gros, G. McDermott, and C. A. Larabell, “X-ray tomography of whole cells,” Curr. Opin. Struct. Biol. 15(5), 593–600 (2005).
[Crossref] [PubMed]

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Laurencin, J.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Le Gros, M. A.

W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
[Crossref] [PubMed]

M. A. Le Gros, G. McDermott, and C. A. Larabell, “X-ray tomography of whole cells,” Curr. Opin. Struct. Biol. 15(5), 593–600 (2005).
[Crossref] [PubMed]

Lee, W. K.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Legros, M. A.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Leite, T. P. C.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Lelièvre, S. A.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Lessard, M. D.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Li, B.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Li, F.

Li, P.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Liang, K. S.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Lichtman, J. W.

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

Lins, U.

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Liu, C. J.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Liu, G.

Liu, J.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Liu, Y.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Y. Liu, J. Wang, Y. Hong, Z. Wang, K. Zhang, P. A. Williams, P. Zhu, J. C. Andrews, P. Pianetta, and Z. Wu, “Extended depth of focus for transmission x-ray microscope,” Opt. Lett. 37(17), 3708–3710 (2012).
[Crossref] [PubMed]

Luque, D.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Maia, F. R. N. C.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Maiden, A. M.

Manley, S.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Marabini, R.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Marchesini, S.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Margaritondo, G.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

McDermott, G.

M. A. Le Gros, G. McDermott, and C. A. Larabell, “X-ray tomography of whole cells,” Curr. Opin. Struct. Biol. 15(5), 593–600 (2005).
[Crossref] [PubMed]

McEwen, B.

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

McNally, J. G.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Menzel, A.

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Meyer-Ilse, W.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Mitchell, G. E.

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

Mlodzianoski, M. J.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Moodie, A. F.

J. M. Cowley and A. F. Moodie, “The Scattering of Electrons by Atoms and Crystals. III. Single-Crystal Diffraction Patterns,” Acta Crystallogr. 12(5), 360–367 (1959).
[Crossref]

Mueller, F.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Müller, W. G.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Murphy, S. V.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Nagashima, K.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Nagpure, B. S.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Nair, A.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Ni, R.

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

Niclis, J. C.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Obst, M.

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Otón, J.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Padmore, H.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Paradossi, G.

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Parkinson, D. Y.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Pearson, A. L.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Peele, A. G.

G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
[Crossref]

Pendlebury, J.

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

Pereiro, E.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[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(1), 15 (2016).
[Crossref] [PubMed]

Pérez-Berná, A. J.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Pfeiffer, F.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Phillips, N. W.

G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
[Crossref]

Pianetta, P.

Raabe, J.

A. Späth, J. Raabe, and R. H. Fink, “Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations,” J. Synchrotron Radiat. 22(1), 113–118 (2015).
[Crossref] [PubMed]

Raabe, J. R.

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Rehbein, S.

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Riess, C.

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Riessen, G. A.

G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
[Crossref]

Rodenburg, J. M.

Rodríguez, J. M.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Rodríguez, M. J.

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(1), 15 (2016).
[Crossref] [PubMed]

Sathananthan, A. H.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Schmidtel, D.

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Schmithusen, F.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

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(1), 15 (2016).
[Crossref] [PubMed]

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

Schneider, P.

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Schö Ll, S.

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Selin, M.

Shapiro, D. A.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Shen, Q.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Shiu, H. W.

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Shtengel, G.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Simionovici, A. S.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Sorzano, C. O.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Sorzano, C. O. S.

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(1), 15 (2016).
[Crossref] [PubMed]

Sougrat, R.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Späth, A.

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

A. Späth, J. Raabe, and R. H. Fink, “Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations,” J. Synchrotron Radiat. 22(1), 113–118 (2015).
[Crossref] [PubMed]

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Stockmar, M.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

Streibl, N.

Strobridge, F. C.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Suhonen, H.

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Tang, J.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Tegze, M.

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Thibault, P.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Tian, Y.

Tkachuk, A.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Truscott, T. T.

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

Tyliszcak, T.

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

Tyliszczak, T.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Tzvetkov, G.

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

Urquhart, S. G.

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Usseglio-Viretta, F.

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Vargas, J.

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

Villanova, J.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

Wang, C. H.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Wang, C. L.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Wang, J.

Wang, J. Y.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Wang, L.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Wang, P.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Wang, W.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Wang, Z.

Warwick, T.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Waterman, C. M.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Wepf, R.

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Werner, S.

Williams, P. A.

Williams, R.

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

Wu, H. J.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Wu, S. R.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Wu, Z.

Xiong, Y.

Yager, D.

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

Yang, C. S.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Yi, J. M.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Yu, Y. S.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Yuan, Q.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Yun, W.

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Zanette, I.

M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23(10), 12720–12731 (2015).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

Zedan, A.

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

Zhang, K.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Y. Liu, J. Wang, Y. Hong, Z. Wang, K. Zhang, P. A. Williams, P. Zhu, J. C. Andrews, P. Pianetta, and Z. Wu, “Extended depth of focus for transmission x-ray microscope,” Opt. Lett. 37(17), 3708–3710 (2012).
[Crossref] [PubMed]

Zhang, T.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Zhang, X.

Zhao, Y.

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Zhu, P.

Zhu, X.

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

Zhuang, X.

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Zipfel, W. R.

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

ACS Nano (1)

L. Wang, T. Zhang, P. Li, W. Huang, J. Tang, P. Wang, J. Liu, Q. Yuan, R. Bai, B. Li, K. Zhang, Y. Zhao, and C. Chen, “Use of Synchrotron Radiation-Analytical Techniques To Reveal Chemical Origin of Silver-Nanoparticle Cytotoxicity,” ACS Nano 9(6), 6532–6547 (2015).
[Crossref] [PubMed]

Acta Crystallogr. (1)

J. M. Cowley and A. F. Moodie, “The Scattering of Electrons by Atoms and Crystals. III. Single-Crystal Diffraction Patterns,” Acta Crystallogr. 12(5), 360–367 (1959).
[Crossref]

Appl. Phys. Lett. (1)

Y. S. Chu, J. M. Yi, F. De Carlo, Q. Shen, W. K. Lee, H. J. Wu, C. L. Wang, J. Y. Wang, C. J. Liu, C. H. 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(10), 103119 (2008).
[Crossref]

Appl. Phys., A Mater. Sci. Process. (1)

A. P. Hitchcock, G. A. Johansson, G. E. Mitchell, M. H. Keefe, and T. Tyliszcak, “3-d chemical imaging using angle-scan nanotomography in a soft X-ray scanning transmission X-ray microscope,” Appl. Phys., A Mater. Sci. Process. 92(3), 447–452 (2008).
[Crossref]

Curr. Opin. Struct. Biol. (1)

M. A. Le Gros, G. McDermott, and C. A. Larabell, “X-ray tomography of whole cells,” Curr. Opin. Struct. Biol. 15(5), 593–600 (2005).
[Crossref] [PubMed]

Differentiation (1)

W. Gu, L. D. Etkin, M. A. Le Gros, and C. A. Larabell, “X-ray tomography of Schizosaccharomyces pombe,” Differentiation 75(6), 529–535 (2007).
[Crossref] [PubMed]

Exp. Fluids (1)

T. T. Truscott, J. Belden, R. Ni, J. Pendlebury, and B. McEwen, “Three-dimensional microscopic light field particle image velocimetry,” Exp. Fluids 58(3), 16 (2017).
[Crossref]

J. Appl. Cryst. (1)

I. Khan, R. Gillilan, I. Kriksunov, R. Williams, W. R. Zipfel, and U. Englich, “Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning,” J. Appl. Cryst. 45(Pt 5), 936–943 (2012).
[Crossref] [PubMed]

J. Microsc. (1)

W. Meyer-Ilse, D. Hamamoto, A. Nair, S. A. Lelièvre, G. Denbeaux, L. Johnson, A. L. Pearson, D. Yager, M. A. Legros, and C. A. Larabell, “High resolution protein localization using soft X-ray microscopy,” J. Microsc. 201(Pt 3), 395–403 (2001).
[Crossref] [PubMed]

J. Nanobiotechnology (1)

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(1), 15 (2016).
[Crossref] [PubMed]

J. Opt. Soc. Am. A (2)

J. Pow. Sour. (1)

J. Villanova, J. Laurencin, P. Cloetens, P. Bleuet, G. Delette, H. Suhonen, and F. Usseglio-Viretta, “3D phase mapping of solid oxide fuel cell YSZ/Ni cermet at the nanoscale by holographic X-ray nanotomography,” J. Pow. Sour. 243, 841–849 (2013).
[Crossref]

J. R. Soc. Interface (1)

J. C. Niclis, S. V. Murphy, D. Y. Parkinson, A. Zedan, A. H. Sathananthan, D. S. Cram, and P. Heraud, “Three-dimensional imaging of human stem cells using soft X-ray tomography,” J. R. Soc. Interface 12(108), 20150252 (2015).
[Crossref] [PubMed]

J. Synchrotron Radiat. (1)

A. Späth, J. Raabe, and R. H. Fink, “Confocal soft X-ray scanning transmission microscopy: setup, alignment procedure and limitations,” J. Synchrotron Radiat. 22(1), 113–118 (2015).
[Crossref] [PubMed]

Nat. Commun. (1)

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. N. C. Maia, A. L. D. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9(1), 921 (2018).
[Crossref] [PubMed]

Nat. Methods (3)

G. Schneider, P. Guttmann, S. Heim, S. Rehbein, F. Mueller, K. Nagashima, J. B. Heymann, W. G. Müller, and J. G. McNally, “Three-dimensional cellular ultrastructure resolved by X-ray microscopy,” Nat. Methods 7(12), 985–987 (2010).
[Crossref] [PubMed]

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure, B. T. Bennett, S. T. Hess, and J. Bewersdorf, “Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples,” Nat. Methods 5(6), 527–529 (2008).
[Crossref] [PubMed]

Nature (2)

D. Attwood, “Microscopy: nanotomography comes of age,” Nature 442(7103), 642–643 (2006).
[Crossref] [PubMed]

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467(7314), 436–439 (2010).
[Crossref] [PubMed]

Nuclear Inst. &. Methods in Physics Research A (1)

K. V. Kaznatcheev, C. Karunakaran, U. D. Lanke, S. G. Urquhart, M. Obst, and A. P. Hitchcock, “Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results,” Nuclear Inst. &. Methods in Physics Research A 582, 96–99 (2007).

Opt. Express (2)

Opt. Lett. (2)

Phys. Rev. Lett. (1)

S. Marchesini, F. Schmithusen, M. Tegze, G. Faigel, Y. Calvayrac, M. Belakhovsky, J. Chevrier, and A. S. Simionovici, “Direct 3D imaging of Al70.4Pd21Mn8.6 quasicrystal local atomic structure by X-ray holography,” Phys. Rev. Lett. 85(22), 4723–4726 (2000).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (2)

X. Zhu, A. P. Hitchcock, D. A. Bazylinski, P. Denes, J. Joseph, U. Lins, S. Marchesini, H. W. Shiu, T. Tyliszczak, and D. A. Shapiro, “Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography,” Proc. Natl. Acad. Sci. U.S.A. 113(51), E8219–E8227 (2016).
[Crossref] [PubMed]

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-Schwartz, J. M. Gillette, S. Manley, R. Sougrat, C. M. Waterman, P. Kanchanawong, M. W. Davidson, R. D. Fetter, and H. F. Hess, “Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure,” Proc. Natl. Acad. Sci. U.S.A. 106(9), 3125–3130 (2009).
[Crossref] [PubMed]

Proc. SPIE (1)

G. A. Riessen, M. Junker, N. W. Phillips, and A. G. Peele, “A soft x-ray beamline for quantitative nanotomography using ptychography,” Proc. SPIE 8851, 885117 (2013).
[Crossref]

RSC Advances (1)

A. Späth, B. A. Graf-Zeiler, G. Paradossi, S. Ghugare, G. Tzvetkov, and R. H. Fink, “Quantitative X-ray microscopic analysis of individual thermoresponsive microgel particles in aqueous solution,” RSC Advances 6(100), 98228–98233 (2016).
[Crossref]

Sci. Rep. (2)

J. Otón, E. Pereiro, J. J. Conesa, F. J. Chichón, D. Luque, J. M. Rodríguez, A. J. Pérez-Berná, C. O. Sorzano, J. Klukowska, G. T. Herman, J. Vargas, R. Marabini, J. L. Carrascosa, and J. M. Carazo, “XTEND: Extending the depth of field in cryo soft X-ray tomography,” Sci. Rep. 7(1), 45808 (2017).
[Crossref] [PubMed]

M. Stockmar, P. Cloetens, I. Zanette, B. Enders, M. Dierolf, F. Pfeiffer, and P. Thibault, “Near-field ptychography: phase retrieval for inline holography using a structured illumination,” Sci. Rep. 3(1), 1927 (2013).
[Crossref] [PubMed]

Science (1)

B. Huang, W. Wang, M. Bates, and X. Zhuang, “Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy,” Science 319(5864), 810–813 (2008).
[Crossref] [PubMed]

Ultramicroscopy (1)

A. Späth, S. Schö Ll, C. Riess, D. Schmidtel, G. Paradossi, J. R. Raabe, J. Hornegger, and R. H. Fink, “STXM goes 3D: digital reconstruction of focal stacks as novel approach towards confocal soft x-ray microscopy,” Ultramicroscopy 144, 19–25 (2014).
[Crossref] [PubMed]

Other (9)

D. Attwood, Soft X-rays and Extreme Ultraviolet Radiation: Principles and Applications (Cambridge University, 2017).

K. N. Kutulakos and S. W. Hasinoff, “Focal Stack Photography: High-Performance Photography with a Conventional Camera,” in Procedings of Iapr Machine Vision Applications, (Academic,2013).

L. Jochum, “Imaging X-Ray Microscopy with Extended Depth of Focus by Use of a Digital Image Processing System,” in Proceedings of X-Ray Microscopy II, (Acdemic, 1988), pp.292–295.
[Crossref]

J. B. Pawley and B. R. Masters, Handbook of Biological Confocal Microscopy, Third Edition (Plenum Press, 2006).

J. W. Goodman, Introduction to Fourier Optics. (Stanford University, 2004).

D. Attwood, Soft X-rays and Extreme Ultraviolet Radiation: Principles and Applications (Cambridge University, 1999), Chap. 9.

J. D. Schmidt, Numerical Simulation of Optical Wave Propagation with Examples in MATLAB (SPIE, 2010).

A. Thompson, D. Attwood, E. Gullikson, M. Howells, K.-J. Kim, I. Lindau, Y. liu, P. Pianetta, A. Robinson, J. Scofield, J. Underwood, and G. Williams, X-ray Data Booklet. (Berkeley, California, 2009).

Q. Wu, F. Merchant. K. R. Castleman, Microscope Image Processing (Elsevier, 2008).

Supplementary Material (4)

NameDescription
» Visualization 1       The focal stack imaging process with the corresponding STXM setup.
» Visualization 2       The 3D reconstructed image for the simulated sample using our improved algorithm
» Visualization 3       The reconstructed image by our improved algorithm.
» Visualization 4       3D reconstructed image of the CNF/Fe3O4 film with our improved algorithm.

Cited By

OSA participates in Crossref's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (11)

Fig. 1
Fig. 1 Illustrations of a scanning image and its corresponding beam propagation map. (a) Schematic diagram of a scanning image by STXM. (b) The corresponding light focusing map for the three circular spots marked by boxes in (a); z1, z2, z3: focused positions of the particles marked with the same colors in (a).
Fig. 2
Fig. 2 Schematic of obtaining 3D image voxel values by thresholding local variances. (a) The relationship between the normalized local variances rn along one of the OAPLs and the thresholding value Tn. The red circled points indicate the positions of the features to be extracted. (b) According to the analysis from (a), the voxel values along an OAPL are obtained as follows: for the positions with rnTn, the voxel values are the measured 2D image intensity or optical density while for the other positions the voxel values are zero.
Fig. 3
Fig. 3 Schematic of the improved focal stack approach. (a) The improved FS algorithm flow-chart that details each step including the calculation of the threshold Tn for the normalized local variances. (b) The focal stack imaging process with the corresponding STXM setup (see Visualization 1).
Fig. 4
Fig. 4 (a) Schematic 3D representation of the sample model with randomly distributed two kinds of elements. The green and blue cubes represent the particles of Fe and Mn, respectively. (b) The sample model with a side length of 3 μm that is thicker than the DOF, and z1, z2 and z3 are three different focused positions in the sample for 2D imaging. (c-d) Two 2D micrographs with a focal distance of 1 μm (Δz = 1 μm) between them. The marked regions demonstrated the sharp or the defocused features. The enlarged views on the left side of each graph show clear details.
Fig. 5
Fig. 5 3D reconstructed images of the sample model with two different algorithms. (a) The 3D reconstructed image using our algorithm (see Visualization 2). (b) The 3D reconstructed image using the algorithm reported in the literature [31]. The unit of colorbar is in g/cm3.
Fig. 6
Fig. 6 Comparison between the reconstructed images by the previous algorithm and the improved one. (a-b) The reconstructed images by our improved algorithm (Visualization 3) and the previous one, respectively. The part marked by a white circle in (b) has fewer particles than that in (a). (c-d) Details comparison between the two enlarged reconstructed half microballoons by the two algorithms.
Fig. 7
Fig. 7 Four representative STXM images of the CNF/Fe3O4 film collected at different optical -axis positions. The film is thicker than the DOF of the used FZP, and the imaged area is 7 × 7 μm2. (a) An STXM image of the specimen which is completely off-focus. (b-c) Two micrographs for the film with part of the particles are in-focus. Each graph has two magnified views of details. (d) The image of the specimen which is off-focus again. Scale bars: 1 μm.
Fig. 8
Fig. 8 3D reconstructed image of the CNF/Fe3O4 film with two algorithms. (a) Reconstruction with our improved algorithm. The distribution of the Fe3O4 nanoparticles can be seen clearly (see Visualization 4). (b) The 3D image reconstructed with the reported algorithm.
Fig. 9
Fig. 9 Resolution estimations for the reconstructed 3D image of the simulated sample model (section 3). (a-b) Two slices of the reconstructed image perpendicular to each other were picked out for resolution estimations. Red-solid lines are the line scans across targeted edges used for Gaussian fitting. (c-e) Blue short-dashed lines are the image intensity profiles across the edges of a particle, corresponding to the red-solid lines in (a) and (b). The black dashed-dot lines are the derivatives of the blue short-dashed lines, which are fitted by Gaussian curves (red solid lines) and the FWHMs of the Gaussians give resolutions in the x, y and z dimensions as 11 nm, 14 nm and 95 nm, respectively.
Fig. 10
Fig. 10 Estimation of the 3D resolutions for the first experimental data reconstruction (section 4.1) with our improved algorithm. (a) Picking out two slices perpendicular to each other and selecting three line-scans across edges of a Fe3O4 particle along the x, y and z axes for resolution estimation. (b-d) Line profiles taken across the edges of an Fe3O4 particle are shown as the blue short-dashed lines. Fitting the derivative of the line profiles (black dashed-dot lines) to Gaussian curves (red solid lines), gives the spatial resolutions of 35 nm in the x and y directions and 496 nm in the z-direction.
Fig. 11
Fig. 11 The thickness of the second experimental specimen and the analysis of the 3D spatial resolutions for its reconstructed image. (a) Scanning electron micrograph of CNF/Fe3O4 film cross-section. (b) Picking out two slices which are perpendicular to each other and cutting through an Fe3O4 particle. The edge line-profile fitting method was used to estimate the resolutions of the 3D reconstructed image. (c-d) Resolutions of 80 nm in the x- and y- dimensions were achieved by fitting the gradient of the edge line-profiles of a particle to Gaussian curves. (e) A resolution of 214 nm in the optical axis direction was obtained.

Equations (10)

Equations on this page are rendered with MathJax. Learn more.

DOF= 4Δ r n 2 λ
R n (x,y)= i=a a j=a a ( I n (x+i,y+i) I ¯ (x,y)) 2 I ¯ (x,y) 2
I ¯ (x,y)= 1 (2a+1) 2 i=a a j=a a I(x+i,y+j)
r n (x,y)= R n (x,y) R n (x,y) max
U(Q)= 1 jλ U 0 (p) e jkr r ds
U(r)= 2j E 0 λ f e jk f e jk r 2 2f r in r zp J 0 (kρθ)ρ d ρ
χ (r) ex,j =P(r r j )O(r)
ψ j (r)= F 1 [ F( χ ex,j (r) ) D z ]
D Z = e 2πjz λ 1 q 2 λ 2
I= | ψ ex,j (r) | 2 = | F 1 { { F{ F 1 { F[ P(r r j ) O 1 (r) ] D z 1,2 } O 2 (r) } D z 2,3 } D z n1,n } O n (r) | 2

Metrics