Abstract

Coherent X-ray ptychography is a tool for highly dose efficient lensless nano-imaging of biological samples. We have used partially coherent soft X-ray synchrotron radiation to obtain a quantitative image of a laterally extended, dried, and unstained fibroblast cell by ptychography. We used data with and without a beam stop that allowed us to measure coherent diffraction with a high-dynamic range of 1.7·106. As a quantitative result, we obtained the refractive index values for two regions of the cell with respect to a reference area. Due to the photon energy in the water window we obtained an extremely high contrast of 53% at 71 nm half-period resolution. The dose applied in our experiment was 9.5·104 Gy and is well below the radiation damage threshold. The concept for dynamic range improvement for low dynamic range detectors with a beam stop opens the path for high resolution nano-imaging of a variety of samples including cryo-preserved, hydrated and unstained biological cells.

© 2018 Optical Society of America

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2017 (5)

S. H. Shahmoradian, E. H. R. Tsai, A. Diaz, M. Guizar-Sicairos, J. Raabe, L. Spycher, M. Britschgi, A. Ruf, H. Stahlberg, and M. Holler, “Three-dimensional imaging of biological tissue by cryo x-ray ptychography,” Sci. Rep. 7, 6291 (2017).
[Crossref] [PubMed]

J. Reinhardt, R. Hoppe, G. Hofmann, C. D. Damsgaard, J. Patommel, C. Baumbach, S. Baier, A. Rochet, J.-D. Grunwaldt, G. Falkenberg, and C. Schroer, “Beamstop-based low-background ptychography to image weakly scattering objects,” Ultramicroscopy 173, 52–57 (2017).
[Crossref]

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
[Crossref] [PubMed]

M. Rose, D. Dzhigaev, T. Senkbeil, A. R. von Gundlach, S. Stuhr, C. Rumancev, I. Besedin, P. Skopintsev, J. Viefhaus, A. Rosenhahn, and I. A. Vartanyants, “High-dynamic-range water window ptychography,” J. Phys: Conf. Ser. 849, 012027 (2017).

Recently it was claimed that although the ePIE algorithm exhibits improved reconstruction speed, it is easy to come across situations when the difficulties of experimental nature may render certain data more difficult to reconstruct. SeeA. Maiden, D. Johnson, and Peng Li, “Further improvements to the ptychographical iterative engine,” Optica 4, 736 (2017).
[Crossref]

2016 (3)

C. Y. J. Hémonnot, J. Reinhardt, O. Saldanha, J. Patommel, R. Graceffa, B. Weinhausen, M. Burghammer, C. G. Schroer, and S. Köster, “X-rays reveal the internal structure of keratin bundles in whole cells,” ACS Nano 10, 3553–3561 (2016).
[Crossref] [PubMed]

A. Khromova, G. Cautero, D. Giuressi, R. Menk, G. Pinaroli, L. Stebel, J. Correa, A. Marras, C. Wunderer, S. Lange, M. Tennert, M. Niemann, H. Hirsemann, S. Smoljanin, S. Reza, H. Graafsma, P. Göttlicher, I. Shevyakov, J. Supra, Q. Xia, M. Zimmer, N. Guerrini, B. Marsh, I. Sedgwick, T. Nicholls, R. Turchetta, U. Pedersen, N. Tartoni, H. Hyun, K. Kim, S. Rah, M. Hoenk, A. Jewell, T. Jones, and S. Nikzad, “Report on recent results of the PERCIVAL soft x-ray imager,” J. Instrum. 11, C11020 (2016).
[Crossref]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
[Crossref] [PubMed]

2015 (8)

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J. A. Rodriguez, R. Xu, C.-C. Chen, Z. Huang, H. Jiang, A. L. Chen, K. S. Raines, A. Pryor, D. Nam, L. Wiegart, C. Song, A. Madsen, Y. Chushkin, F. Zontone, P. J. Bradley, and J. Miao, “Three-dimensional coherent x-ray diffractive imaging of whole frozen-hydrated cells,” IUCrJ 2, 575–583 (2015).
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K. Giewekemeyer, C. Hackenberg, A. Aquila, R. Wilke, M. Groves, R. Jordanova, V. Lamzin, G. Borchers, K. Saksl, A. Zozulya, M. Sprung, and A. Mancuso, “Tomography of a cryo-immobilized yeast cell using ptychographic coherent x-ray diffractive imaging,” Biophys. J. 109, 1986–1995 (2015).
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S. Chen, J. Deng, D. J. Vine, Y. S. G. Nashed, Q. Jin, T. Peterka, C. Jacobsen, and S. Vogt, “Simultaneous x-ray nano-ptychographic and fluorescence microscopy at the bionanoprobe,” Proc. SPIE 9592, 95920I (2015).
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A. Diaz, B. Malkova, M. Holler, M. Guizar-Sicairos, E. Lima, V. Panneels, G. Pigino, A. G. Bittermann, L. Wettstein, T. Tomizaki, O. Bunk, G. Schertler, T. Ishikawa, R. Wepf, and A. Menzel, “Three-dimensional mass density mapping of cellular ultrastructure by ptychographic x-ray nanotomography,” J. Struct. Biol. 192, 461–469 (2015).
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2014 (3)

C. B. Wunderer, A. Marras, M. Bayer, L. Glaser, P. Göttlicher, S. Lange, F. Pithan, F. Scholz, J. Seltmann, I. Shevyakov, S. Smoljanin, J. Viefhaus, M. Viti, Q. Xia, M. Zimmer, S. Klumpp, P. Gasiorek, N. Guerrini, B. Marsh, I. Sedgwick, R. Turchetta, G. Cautero, S. Farina, D. Giuressi, R. Menk, L. Stebel, H. Yousef, J. Marchal, T. Nicholls, N. Tartoni, and H. Graafsma, “The PERCIVAL soft x-ray imager,” J. Instrum. 9, C03056 (2014).
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T. Gorniak and A. Rosenhahn, “Ptychographic x-ray microscopy with the vacuum imaging apparatus HORST,” Z. Phys. Chem. 228, 1089(2014).
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2013 (5)

J. Viefhaus, F. Scholz, S. Deinert, L. Glaser, M. Ilchen, J. Seltmann, P. Walter, and F. Siewert, “The variable polarization XUV beamline p04 at PETRA III: Optics, mechanics and their performance,” Nucl. Instrum. Methods Phys. Res., Sect. A 710, 151–154 (2013).
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R. N. Wilke, M. Vassholz, and T. Salditt, “Semi-transparent central stop in high-resolution x-ray ptychography using kirkpatrick-baez focusing,” Acta Crystallogr., Sect. A: Found. Crystallogr. 69, 490–497 (2013).
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P. Thibault and A. Menzel, “Reconstructing state mixtures from diffraction measurements,” Nature 494, 68–71 (2013).
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A. Maiden, G. Morrison, B. Kaulich, A. Gianoncelli, and J. Rodenburg, “Soft x-ray spectromicroscopy using ptychography with randomly phased illumination,” Nat. Commun. 4, 1669 (2013).
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2012 (1)

2011 (2)

M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S.-C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft x-ray ptychography,” Phys. Rev. Lett. 107, 208101 (2011).
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K. Giewekemeyer, M. Beckers, T. Gorniak, M. Grunze, T. Salditt, and A. Rosenhahn, “Ptychographic coherent x-ray diffractive imaging in the water window,” Opt. Express 19, 1037–1050 (2011).
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2010 (3)

I. A. Vartanyants and A. Singer, “Coherence properties of hard x-ray synchrotron sources and x-ray free-electron lasers,” New J. Phys. 12, 035004 (2010).
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C. A. Larabell and K. A. Nugent, “Imaging cellular architecture with x-rays,” Curr. Opin. Struc. Biol. 20, 623–631 (2010).
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J. Steinbrener, J. Nelson, X. Huang, S. Marchesini, D. Shapiro, J. J. Turner, and C. Jacobsen, “Data preparation and evaluation techniques for x-ray diffraction microscopy,” Opt. Express 18, 18598–18614 (2010).
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2009 (4)

P. Thibault, M. Dierolf, O. Bunk, A. Menzel, and F. Pfeiffer, “Probe retrieval in ptychographic coherent diffractive imaging,” Ultramicroscopy 109, 338–343 (2009).
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M. Howells, T. Beetz, H. Chapman, C. Cui, J. Holton, C. Jacobsen, J. Kirz, E. Lima, S. Marchesini, H. Miao, D. Sayre, D. Shapiro, J. Spence, and D. Starodub, “An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy,” J. Electron Spectrosc. Relat. Phenom. 170, 4–12 (2009).
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X. Huang, H. Miao, J. Steinbrener, J. Nelson, D. Shapiro, A. Stewart, J. Turner, and C. Jacobsen, “Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy,” Opt. Express 17, 13541–13553 (2009).
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A. M. Maiden and J. M. Rodenburg, “An improved ptychographical phase retrieval algorithm for diffractive imaging,” Ultramicroscopy 109, 1256–1262 (2009).
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2008 (2)

P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, and F. Pfeiffer, “High-resolution scanning x-ray diffraction microscopy,” Science 321, 379–382 (2008).
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O. Bunk, M. Dierolf, S. Kynde, I. Johnson, O. Marti, and F. Pfeiffer, “Influence of the overlap parameter on the convergence of the ptychographical iterative engine,” Ultramicroscopy 108, 481–487 (2008).
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2007 (3)

G. J. Williams, H. M. Quiney, A. G. Peele, and K. A. Nugent, “Coherent diffractive imaging and partial coherence,” Phys. Rev. B 75, 104102 (2007).
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S. Marchesini, “Invited article: A unified evaluation of iterative projection algorithms for phase retrieval,” Rev. Sci. Instrum. 78, 011301 (2007).
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J. M. Rodenburg, A. C. Hurst, A. G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs, and I. Johnson, “Hard-x-ray lensless imaging of extended objects,” Phys. Rev. Lett. 98, 034801 (2007).
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2006 (2)

G. Williams, M. Pfeifer, I. Vartanyants, and I. Robinson, “Effectiveness of iterative algorithms in recovering phase in the presence of noise,” Acta Crystallogr., Sect. A: Found. Crystallogr. 63, 36–42 (2006).
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H. N. Chapman, A. Barty, S. Marchesini, A. Noy, S. P. Hau-Riege, C. Cui, M. R. Howells, R. Rosen, H. He, J. C. H. Spence, U. Weierstall, T. Beetz, C. Jacobsen, and D. Shapiro, “High-resolution ab initio three-dimensional x-ray diffraction microscopy,” J. Opt. Soc. Am. A 23, 1179–1200 (2006).
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2005 (1)

D. Shapiro, P. Thibault, T. Beetz, V. Elser, M. Howells, C. Jacobsen, J. Kirz, E. Lima, H. Miao, A. M. Neiman, and D. Sayre, “Biological imaging by soft x-ray diffraction microscopy,” Proc. Natl. Acad. Sci. U.S.A. 102, 15343–15346 (2005).
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2003 (2)

V. Elser, “Phase retrieval by iterated projections,” J. Opt. Soc. Am. A 20, 40 (2003).
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2002 (2)

2000 (1)

R. Neutze, R. Wouts, D. van der Spoel, E. Weckert, and J. Hajdu, “Potential for biomolecular imaging with femtosecond x-ray pulses,” Nature 406, 752–757 (2000).
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1999 (1)

J. Miao, P. Charalambous, J. Kirz, and D. Sayre, “Extending the methodology of x-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens,” Nature 400, 342–344 (1999).
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1998 (2)

G. Schneider, “Cryo x-ray microscopy with high spatial resolution in amplitude and phase contrast,” Ultramicroscopy 75, 85–104 (1998).
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1995 (1)

J. Kirz, C. Jacobsen, and M. Howells, “Soft x-ray microscopes and their biological applications,” Q. Rev. Biophys. 28, 33–130 (1995).
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1993 (1)

B. Henke, E. Gullikson, and J. Davis, “X-ray interactions: Photoabsorption, scattering, transmission, and reflection at e = 50–30,000 eV, z = 1–92,” Atom. Data Nucl. Data 54, 181–342 (1993).
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1983 (1)

1952 (1)

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Alaimo, G.

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Als-Nielsen, J.

J. Als-Nielsen and D. McMorrow, Elements of Modern X-ray Physics (Wiley, 2001).

Ames, B.

R. Horstmeyer, R. Y. Chen, X. Ou, B. Ames, J. A. Tropp, and C. Yang, “Solving ptychography with a convex relaxation,” New J. Phys. 17, 053044 (2015).
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Andreasson, J.

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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Aquila, A.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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A. Aquila, A. Barty, C. Bostedt, S. Boutet, G. Carini, D. dePonte, P. Drell, S. Doniach, K. H. Downing, T. Earnest, H. Elmlund, V. Elser, M. Gühr, J. Hajdu, J. Hastings, S. P. Hau-Riege, Z. Huang, E. E. Lattman, F. R. N. C. Maia, S. Marchesini, A. Ourmazd, C. Pellegrini, R. Santra, I. Schlichting, C. Schroer, J. C. H. Spence, I. A. Vartanyants, S. Wakatsuki, W. I. Weis, and G. J. Williams, “The linac coherent light source single particle imaging road map,” Struct. Dyn. 2, 041701 (2015).
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K. Giewekemeyer, C. Hackenberg, A. Aquila, R. Wilke, M. Groves, R. Jordanova, V. Lamzin, G. Borchers, K. Saksl, A. Zozulya, M. Sprung, and A. Mancuso, “Tomography of a cryo-immobilized yeast cell using ptychographic coherent x-ray diffractive imaging,” Biophys. J. 109, 1986–1995 (2015).
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Awel, S.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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Ayyer, K.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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Bach, J.

P. Skopintsev, A. Singer, J. Bach, L. Müller, B. Beyersdorff, S. Schleitzer, O. Gorobtsov, A. Shabalin, R. P. Kurta, D. Dzhigaev, O. M. Yefanov, L. Glaser, A. Sakdinawat, G. Grübel, R. Frömter, H. P. Oepen, J. Viefhaus, and I. A. Vartanyants, “Characterization of spatial coherence of synchrotron radiation with non-redundant arrays of apertures,” J. Synchrotron Radiat. 21, 722–728 (2014).
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Baier, S.

J. Reinhardt, R. Hoppe, G. Hofmann, C. D. Damsgaard, J. Patommel, C. Baumbach, S. Baier, A. Rochet, J.-D. Grunwaldt, G. Falkenberg, and C. Schroer, “Beamstop-based low-background ptychography to image weakly scattering objects,” Ultramicroscopy 173, 52–57 (2017).
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Bartels, M.

Barty, A.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
[Crossref] [PubMed]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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R. Carzaniga, M.-C. Domart, L. M. Collinson, and E. Duke, “Cryo-soft x-ray tomography: a journey into the world of the native-state cell,” Protoplasma 251, 449–458 (2013).
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Seibert, M.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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Seibert, M. M.

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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Sellberg, J. A.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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Seltmann, J.

C. B. Wunderer, A. Marras, M. Bayer, L. Glaser, P. Göttlicher, S. Lange, F. Pithan, F. Scholz, J. Seltmann, I. Shevyakov, S. Smoljanin, J. Viefhaus, M. Viti, Q. Xia, M. Zimmer, S. Klumpp, P. Gasiorek, N. Guerrini, B. Marsh, I. Sedgwick, R. Turchetta, G. Cautero, S. Farina, D. Giuressi, R. Menk, L. Stebel, H. Yousef, J. Marchal, T. Nicholls, N. Tartoni, and H. Graafsma, “The PERCIVAL soft x-ray imager,” J. Instrum. 9, C03056 (2014).
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J. Viefhaus, F. Scholz, S. Deinert, L. Glaser, M. Ilchen, J. Seltmann, P. Walter, and F. Siewert, “The variable polarization XUV beamline p04 at PETRA III: Optics, mechanics and their performance,” Nucl. Instrum. Methods Phys. Res., Sect. A 710, 151–154 (2013).
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Senkbeil, T.

M. Rose, D. Dzhigaev, T. Senkbeil, A. R. von Gundlach, S. Stuhr, C. Rumancev, I. Besedin, P. Skopintsev, J. Viefhaus, A. Rosenhahn, and I. A. Vartanyants, “High-dynamic-range water window ptychography,” J. Phys: Conf. Ser. 849, 012027 (2017).

M. Rose, P. Skopintsev, D. Dzhigaev, O. Gorobtsov, T. Senkbeil, A. von Gundlach, T. Gorniak, A. Shabalin, J. Viefhaus, A. Rosenhahn, and I. Vartanyants, “Water window ptychographic imaging with characterized coherent x-rays,” J. Synchrotron Radiat. 22, 819–827 (2015).
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M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S.-C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft x-ray ptychography,” Phys. Rev. Lett. 107, 208101 (2011).
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Shabalin, A.

M. Rose, P. Skopintsev, D. Dzhigaev, O. Gorobtsov, T. Senkbeil, A. von Gundlach, T. Gorniak, A. Shabalin, J. Viefhaus, A. Rosenhahn, and I. Vartanyants, “Water window ptychographic imaging with characterized coherent x-rays,” J. Synchrotron Radiat. 22, 819–827 (2015).
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P. Skopintsev, A. Singer, J. Bach, L. Müller, B. Beyersdorff, S. Schleitzer, O. Gorobtsov, A. Shabalin, R. P. Kurta, D. Dzhigaev, O. M. Yefanov, L. Glaser, A. Sakdinawat, G. Grübel, R. Frömter, H. P. Oepen, J. Viefhaus, and I. A. Vartanyants, “Characterization of spatial coherence of synchrotron radiation with non-redundant arrays of apertures,” J. Synchrotron Radiat. 21, 722–728 (2014).
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Shahmoradian, S. H.

S. H. Shahmoradian, E. H. R. Tsai, A. Diaz, M. Guizar-Sicairos, J. Raabe, L. Spycher, M. Britschgi, A. Ruf, H. Stahlberg, and M. Holler, “Three-dimensional imaging of biological tissue by cryo x-ray ptychography,” Sci. Rep. 7, 6291 (2017).
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Shapiro, D.

J. Steinbrener, J. Nelson, X. Huang, S. Marchesini, D. Shapiro, J. J. Turner, and C. Jacobsen, “Data preparation and evaluation techniques for x-ray diffraction microscopy,” Opt. Express 18, 18598–18614 (2010).
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X. Huang, H. Miao, J. Steinbrener, J. Nelson, D. Shapiro, A. Stewart, J. Turner, and C. Jacobsen, “Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy,” Opt. Express 17, 13541–13553 (2009).
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M. Howells, T. Beetz, H. Chapman, C. Cui, J. Holton, C. Jacobsen, J. Kirz, E. Lima, S. Marchesini, H. Miao, D. Sayre, D. Shapiro, J. Spence, and D. Starodub, “An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy,” J. Electron Spectrosc. Relat. Phenom. 170, 4–12 (2009).
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H. N. Chapman, A. Barty, S. Marchesini, A. Noy, S. P. Hau-Riege, C. Cui, M. R. Howells, R. Rosen, H. He, J. C. H. Spence, U. Weierstall, T. Beetz, C. Jacobsen, and D. Shapiro, “High-resolution ab initio three-dimensional x-ray diffraction microscopy,” J. Opt. Soc. Am. A 23, 1179–1200 (2006).
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D. Shapiro, P. Thibault, T. Beetz, V. Elser, M. Howells, C. Jacobsen, J. Kirz, E. Lima, H. Miao, A. M. Neiman, and D. Sayre, “Biological imaging by soft x-ray diffraction microscopy,” Proc. Natl. Acad. Sci. U.S.A. 102, 15343–15346 (2005).
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Shevyakov, I.

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C. B. Wunderer, A. Marras, M. Bayer, L. Glaser, P. Göttlicher, S. Lange, F. Pithan, F. Scholz, J. Seltmann, I. Shevyakov, S. Smoljanin, J. Viefhaus, M. Viti, Q. Xia, M. Zimmer, S. Klumpp, P. Gasiorek, N. Guerrini, B. Marsh, I. Sedgwick, R. Turchetta, G. Cautero, S. Farina, D. Giuressi, R. Menk, L. Stebel, H. Yousef, J. Marchal, T. Nicholls, N. Tartoni, and H. Graafsma, “The PERCIVAL soft x-ray imager,” J. Instrum. 9, C03056 (2014).
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Sierra, R. G.

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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Siewert, F.

J. Viefhaus, F. Scholz, S. Deinert, L. Glaser, M. Ilchen, J. Seltmann, P. Walter, and F. Siewert, “The variable polarization XUV beamline p04 at PETRA III: Optics, mechanics and their performance,” Nucl. Instrum. Methods Phys. Res., Sect. A 710, 151–154 (2013).
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Singer, A.

P. Skopintsev, A. Singer, J. Bach, L. Müller, B. Beyersdorff, S. Schleitzer, O. Gorobtsov, A. Shabalin, R. P. Kurta, D. Dzhigaev, O. M. Yefanov, L. Glaser, A. Sakdinawat, G. Grübel, R. Frömter, H. P. Oepen, J. Viefhaus, and I. A. Vartanyants, “Characterization of spatial coherence of synchrotron radiation with non-redundant arrays of apertures,” J. Synchrotron Radiat. 21, 722–728 (2014).
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I. A. Vartanyants and A. Singer, “Coherence properties of hard x-ray synchrotron sources and x-ray free-electron lasers,” New J. Phys. 12, 035004 (2010).
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I. A. Vartanyants and A. Singer, “Coherence properties of third-generation synchrotron sources and free-electron lasers,” in Synchrotron Light Sources and Free-Electron Lasers, E. Jaeschke, S. Khan, J. R. Schneider, and J. B. Hastings, eds. (Springer International Publishing, 2016), pp. 821–863.

Skopintsev, P.

M. Rose, D. Dzhigaev, T. Senkbeil, A. R. von Gundlach, S. Stuhr, C. Rumancev, I. Besedin, P. Skopintsev, J. Viefhaus, A. Rosenhahn, and I. A. Vartanyants, “High-dynamic-range water window ptychography,” J. Phys: Conf. Ser. 849, 012027 (2017).

M. Rose, P. Skopintsev, D. Dzhigaev, O. Gorobtsov, T. Senkbeil, A. von Gundlach, T. Gorniak, A. Shabalin, J. Viefhaus, A. Rosenhahn, and I. Vartanyants, “Water window ptychographic imaging with characterized coherent x-rays,” J. Synchrotron Radiat. 22, 819–827 (2015).
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P. Skopintsev, A. Singer, J. Bach, L. Müller, B. Beyersdorff, S. Schleitzer, O. Gorobtsov, A. Shabalin, R. P. Kurta, D. Dzhigaev, O. M. Yefanov, L. Glaser, A. Sakdinawat, G. Grübel, R. Frömter, H. P. Oepen, J. Viefhaus, and I. A. Vartanyants, “Characterization of spatial coherence of synchrotron radiation with non-redundant arrays of apertures,” J. Synchrotron Radiat. 21, 722–728 (2014).
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Smoljanin, S.

A. Khromova, G. Cautero, D. Giuressi, R. Menk, G. Pinaroli, L. Stebel, J. Correa, A. Marras, C. Wunderer, S. Lange, M. Tennert, M. Niemann, H. Hirsemann, S. Smoljanin, S. Reza, H. Graafsma, P. Göttlicher, I. Shevyakov, J. Supra, Q. Xia, M. Zimmer, N. Guerrini, B. Marsh, I. Sedgwick, T. Nicholls, R. Turchetta, U. Pedersen, N. Tartoni, H. Hyun, K. Kim, S. Rah, M. Hoenk, A. Jewell, T. Jones, and S. Nikzad, “Report on recent results of the PERCIVAL soft x-ray imager,” J. Instrum. 11, C11020 (2016).
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C. B. Wunderer, A. Marras, M. Bayer, L. Glaser, P. Göttlicher, S. Lange, F. Pithan, F. Scholz, J. Seltmann, I. Shevyakov, S. Smoljanin, J. Viefhaus, M. Viti, Q. Xia, M. Zimmer, S. Klumpp, P. Gasiorek, N. Guerrini, B. Marsh, I. Sedgwick, R. Turchetta, G. Cautero, S. Farina, D. Giuressi, R. Menk, L. Stebel, H. Yousef, J. Marchal, T. Nicholls, N. Tartoni, and H. Graafsma, “The PERCIVAL soft x-ray imager,” J. Instrum. 9, C03056 (2014).
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Song, C.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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J. A. Rodriguez, R. Xu, C.-C. Chen, Z. Huang, H. Jiang, A. L. Chen, K. S. Raines, A. Pryor, D. Nam, L. Wiegart, C. Song, A. Madsen, Y. Chushkin, F. Zontone, P. J. Bradley, and J. Miao, “Three-dimensional coherent x-ray diffractive imaging of whole frozen-hydrated cells,” IUCrJ 2, 575–583 (2015).
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Spence, J.

M. Howells, T. Beetz, H. Chapman, C. Cui, J. Holton, C. Jacobsen, J. Kirz, E. Lima, S. Marchesini, H. Miao, D. Sayre, D. Shapiro, J. Spence, and D. Starodub, “An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy,” J. Electron Spectrosc. Relat. Phenom. 170, 4–12 (2009).
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Spence, J. C.

H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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Spence, J. C. H.

A. Aquila, A. Barty, C. Bostedt, S. Boutet, G. Carini, D. dePonte, P. Drell, S. Doniach, K. H. Downing, T. Earnest, H. Elmlund, V. Elser, M. Gühr, J. Hajdu, J. Hastings, S. P. Hau-Riege, Z. Huang, E. E. Lattman, F. R. N. C. Maia, S. Marchesini, A. Ourmazd, C. Pellegrini, R. Santra, I. Schlichting, C. Schroer, J. C. H. Spence, I. A. Vartanyants, S. Wakatsuki, W. I. Weis, and G. J. Williams, “The linac coherent light source single particle imaging road map,” Struct. Dyn. 2, 041701 (2015).
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H. N. Chapman, A. Barty, S. Marchesini, A. Noy, S. P. Hau-Riege, C. Cui, M. R. Howells, R. Rosen, H. He, J. C. H. Spence, U. Weierstall, T. Beetz, C. Jacobsen, and D. Shapiro, “High-resolution ab initio three-dimensional x-ray diffraction microscopy,” J. Opt. Soc. Am. A 23, 1179–1200 (2006).
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S. Marchesini, H. N. Chapman, A. Barty, C. Cui, M. R. Howells, J. C. H. Spence, U. Weierstall, and A. M. Minor, “Phase Aberrations in Diffraction Microscopy,” ArXiv Physics e-prints (2005).

Sprung, M.

K. Giewekemeyer, C. Hackenberg, A. Aquila, R. Wilke, M. Groves, R. Jordanova, V. Lamzin, G. Borchers, K. Saksl, A. Zozulya, M. Sprung, and A. Mancuso, “Tomography of a cryo-immobilized yeast cell using ptychographic coherent x-ray diffractive imaging,” Biophys. J. 109, 1986–1995 (2015).
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Spycher, L.

S. H. Shahmoradian, E. H. R. Tsai, A. Diaz, M. Guizar-Sicairos, J. Raabe, L. Spycher, M. Britschgi, A. Ruf, H. Stahlberg, and M. Holler, “Three-dimensional imaging of biological tissue by cryo x-ray ptychography,” Sci. Rep. 7, 6291 (2017).
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Stahlberg, H.

S. H. Shahmoradian, E. H. R. Tsai, A. Diaz, M. Guizar-Sicairos, J. Raabe, L. Spycher, M. Britschgi, A. Ruf, H. Stahlberg, and M. Holler, “Three-dimensional imaging of biological tissue by cryo x-ray ptychography,” Sci. Rep. 7, 6291 (2017).
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Starodub, D.

M. Howells, T. Beetz, H. Chapman, C. Cui, J. Holton, C. Jacobsen, J. Kirz, E. Lima, S. Marchesini, H. Miao, D. Sayre, D. Shapiro, J. Spence, and D. Starodub, “An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy,” J. Electron Spectrosc. Relat. Phenom. 170, 4–12 (2009).
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Stebel, L.

A. Khromova, G. Cautero, D. Giuressi, R. Menk, G. Pinaroli, L. Stebel, J. Correa, A. Marras, C. Wunderer, S. Lange, M. Tennert, M. Niemann, H. Hirsemann, S. Smoljanin, S. Reza, H. Graafsma, P. Göttlicher, I. Shevyakov, J. Supra, Q. Xia, M. Zimmer, N. Guerrini, B. Marsh, I. Sedgwick, T. Nicholls, R. Turchetta, U. Pedersen, N. Tartoni, H. Hyun, K. Kim, S. Rah, M. Hoenk, A. Jewell, T. Jones, and S. Nikzad, “Report on recent results of the PERCIVAL soft x-ray imager,” J. Instrum. 11, C11020 (2016).
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C. B. Wunderer, A. Marras, M. Bayer, L. Glaser, P. Göttlicher, S. Lange, F. Pithan, F. Scholz, J. Seltmann, I. Shevyakov, S. Smoljanin, J. Viefhaus, M. Viti, Q. Xia, M. Zimmer, S. Klumpp, P. Gasiorek, N. Guerrini, B. Marsh, I. Sedgwick, R. Turchetta, G. Cautero, S. Farina, D. Giuressi, R. Menk, L. Stebel, H. Yousef, J. Marchal, T. Nicholls, N. Tartoni, and H. Graafsma, “The PERCIVAL soft x-ray imager,” J. Instrum. 9, C03056 (2014).
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Steinbrener, J.

Stewart, A.

Stuhr, S.

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M. Rose, D. Dzhigaev, T. Senkbeil, A. R. von Gundlach, S. Stuhr, C. Rumancev, I. Besedin, P. Skopintsev, J. Viefhaus, A. Rosenhahn, and I. A. Vartanyants, “High-dynamic-range water window ptychography,” J. Phys: Conf. Ser. 849, 012027 (2017).

J. Struct. Biol. (1)

A. Diaz, B. Malkova, M. Holler, M. Guizar-Sicairos, E. Lima, V. Panneels, G. Pigino, A. G. Bittermann, L. Wettstein, T. Tomizaki, O. Bunk, G. Schertler, T. Ishikawa, R. Wepf, and A. Menzel, “Three-dimensional mass density mapping of cellular ultrastructure by ptychographic x-ray nanotomography,” J. Struct. Biol. 192, 461–469 (2015).
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J. Synchrotron Radiat. (2)

P. Skopintsev, A. Singer, J. Bach, L. Müller, B. Beyersdorff, S. Schleitzer, O. Gorobtsov, A. Shabalin, R. P. Kurta, D. Dzhigaev, O. M. Yefanov, L. Glaser, A. Sakdinawat, G. Grübel, R. Frömter, H. P. Oepen, J. Viefhaus, and I. A. Vartanyants, “Characterization of spatial coherence of synchrotron radiation with non-redundant arrays of apertures,” J. Synchrotron Radiat. 21, 722–728 (2014).
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M. Rose, P. Skopintsev, D. Dzhigaev, O. Gorobtsov, T. Senkbeil, A. von Gundlach, T. Gorniak, A. Shabalin, J. Viefhaus, A. Rosenhahn, and I. Vartanyants, “Water window ptychographic imaging with characterized coherent x-rays,” J. Synchrotron Radiat. 22, 819–827 (2015).
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Nat. Commun. (1)

A. Maiden, G. Morrison, B. Kaulich, A. Gianoncelli, and J. Rodenburg, “Soft x-ray spectromicroscopy using ptychography with randomly phased illumination,” Nat. Commun. 4, 1669 (2013).
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Nature (3)

P. Thibault and A. Menzel, “Reconstructing state mixtures from diffraction measurements,” Nature 494, 68–71 (2013).
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R. Neutze, R. Wouts, D. van der Spoel, E. Weckert, and J. Hajdu, “Potential for biomolecular imaging with femtosecond x-ray pulses,” Nature 406, 752–757 (2000).
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J. Miao, P. Charalambous, J. Kirz, and D. Sayre, “Extending the methodology of x-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens,” Nature 400, 342–344 (1999).
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New J. Phys. (2)

I. A. Vartanyants and A. Singer, “Coherence properties of hard x-ray synchrotron sources and x-ray free-electron lasers,” New J. Phys. 12, 035004 (2010).
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R. Horstmeyer, R. Y. Chen, X. Ou, B. Ames, J. A. Tropp, and C. Yang, “Solving ptychography with a convex relaxation,” New J. Phys. 17, 053044 (2015).
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Nucl. Instrum. Methods Phys. Res., Sect. A (1)

J. Viefhaus, F. Scholz, S. Deinert, L. Glaser, M. Ilchen, J. Seltmann, P. Walter, and F. Siewert, “The variable polarization XUV beamline p04 at PETRA III: Optics, mechanics and their performance,” Nucl. Instrum. Methods Phys. Res., Sect. A 710, 151–154 (2013).
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Opt. Express (4)

Optica (1)

Phys. Rev. B (1)

G. J. Williams, H. M. Quiney, A. G. Peele, and K. A. Nugent, “Coherent diffractive imaging and partial coherence,” Phys. Rev. B 75, 104102 (2007).
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Phys. Rev. Lett. (2)

J. M. Rodenburg, A. C. Hurst, A. G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs, and I. Johnson, “Hard-x-ray lensless imaging of extended objects,” Phys. Rev. Lett. 98, 034801 (2007).
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M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S.-C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft x-ray ptychography,” Phys. Rev. Lett. 107, 208101 (2011).
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Proc. Natl. Acad. Sci. U.S.A. (2)

D. Shapiro, P. Thibault, T. Beetz, V. Elser, M. Howells, C. Jacobsen, J. Kirz, E. Lima, H. Miao, A. M. Neiman, and D. Sayre, “Biological imaging by soft x-ray diffraction microscopy,” Proc. Natl. Acad. Sci. U.S.A. 102, 15343–15346 (2005).
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J. Deng, D. J. Vine, S. Chen, Y. S. G. Nashed, Q. Jin, N. W. Phillips, T. Peterka, R. Ross, S. Vogt, and C. J. Jacobsen, “Simultaneous cryo x-ray ptychographic and fluorescence microscopy of green algae,” Proc. Natl. Acad. Sci. U.S.A. 112, 2314–2319 (2015).
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Proc. SPIE (1)

S. Chen, J. Deng, D. J. Vine, Y. S. G. Nashed, Q. Jin, T. Peterka, C. Jacobsen, and S. Vogt, “Simultaneous x-ray nano-ptychographic and fluorescence microscopy at the bionanoprobe,” Proc. SPIE 9592, 95920I (2015).
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Protoplasma (1)

R. Carzaniga, M.-C. Domart, L. M. Collinson, and E. Duke, “Cryo-soft x-ray tomography: a journey into the world of the native-state cell,” Protoplasma 251, 449–458 (2013).
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Q. Rev. Biophys. (1)

J. Kirz, C. Jacobsen, and M. Howells, “Soft x-ray microscopes and their biological applications,” Q. Rev. Biophys. 28, 33–130 (1995).
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Rev. Sci. Instrum. (1)

S. Marchesini, “Invited article: A unified evaluation of iterative projection algorithms for phase retrieval,” Rev. Sci. Instrum. 78, 011301 (2007).
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Sci. Data (2)

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. J. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. N. Chapman, B. J. Daurer, H. DeMirci, V. Elser, P. Fromme, J. Hajdu, M. F. Hantke, A. Higashiura, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, H. K. Reddy, T.-Y. Lan, D. S. Larsson, H. Liu, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Nakagawa, D. Nam, G. Nelson, C. Nettelblad, K. Okamoto, A. Ourmazd, M. Rose, G. van der Schot, P. Schwander, M. M. Seibert, J. A. Sellberg, R. G. Sierra, C. Song, M. Svenda, N. Timneanu, I. A. Vartanyants, D. Westphal, M. O. Wiedorn, G. J. Williams, P. L. Xavier, C. H. Yoon, and J. Zook, “Coherent diffraction of single rice dwarf virus particles using hard x-rays at the linac coherent light source,” Sci. Data 3, 160064 (2016).
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H. K. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. A. Carini, S. Carron, H. Chapman, B. Daurer, H. DeMirci, T. Ekeberg, P. Fromme, J. Hajdu, M. F. Hanke, P. Hart, B. G. Hogue, A. Hosseinizadeh, Y. Kim, R. A. Kirian, R. P. Kurta, D. S. Larsson, N. D. Loh, F. R. Maia, A. P. Mancuso, K. Mühlig, A. Munke, D. Nam, C. Nettelblad, A. Ourmazd, M. Rose, P. Schwander, M. Seibert, J. A. Sellberg, C. Song, J. C. Spence, M. Svenda, G. V. der Schot, I. A. Vartanyants, G. J. Williams, and P. L. Xavier, “Coherent soft x-ray diffraction imaging of coliphage pr772 at the linac coherent light source,” Sci. Data 4, 170079 (2017).
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Sci. Rep. (1)

S. H. Shahmoradian, E. H. R. Tsai, A. Diaz, M. Guizar-Sicairos, J. Raabe, L. Spycher, M. Britschgi, A. Ruf, H. Stahlberg, and M. Holler, “Three-dimensional imaging of biological tissue by cryo x-ray ptychography,” Sci. Rep. 7, 6291 (2017).
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Science (1)

P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, and F. Pfeiffer, “High-resolution scanning x-ray diffraction microscopy,” Science 321, 379–382 (2008).
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Struct. Dyn. (1)

A. Aquila, A. Barty, C. Bostedt, S. Boutet, G. Carini, D. dePonte, P. Drell, S. Doniach, K. H. Downing, T. Earnest, H. Elmlund, V. Elser, M. Gühr, J. Hajdu, J. Hastings, S. P. Hau-Riege, Z. Huang, E. E. Lattman, F. R. N. C. Maia, S. Marchesini, A. Ourmazd, C. Pellegrini, R. Santra, I. Schlichting, C. Schroer, J. C. H. Spence, I. A. Vartanyants, S. Wakatsuki, W. I. Weis, and G. J. Williams, “The linac coherent light source single particle imaging road map,” Struct. Dyn. 2, 041701 (2015).
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Ultramicroscopy (5)

G. Schneider, “Cryo x-ray microscopy with high spatial resolution in amplitude and phase contrast,” Ultramicroscopy 75, 85–104 (1998).
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J. Reinhardt, R. Hoppe, G. Hofmann, C. D. Damsgaard, J. Patommel, C. Baumbach, S. Baier, A. Rochet, J.-D. Grunwaldt, G. Falkenberg, and C. Schroer, “Beamstop-based low-background ptychography to image weakly scattering objects,” Ultramicroscopy 173, 52–57 (2017).
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A. M. Maiden and J. M. Rodenburg, “An improved ptychographical phase retrieval algorithm for diffractive imaging,” Ultramicroscopy 109, 1256–1262 (2009).
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P. Thibault, M. Dierolf, O. Bunk, A. Menzel, and F. Pfeiffer, “Probe retrieval in ptychographic coherent diffractive imaging,” Ultramicroscopy 109, 338–343 (2009).
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Z. Phys. Chem. (1)

T. Gorniak and A. Rosenhahn, “Ptychographic x-ray microscopy with the vacuum imaging apparatus HORST,” Z. Phys. Chem. 228, 1089(2014).
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J. Als-Nielsen and D. McMorrow, Elements of Modern X-ray Physics (Wiley, 2001).

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I. A. Vartanyants and A. Singer, “Coherence properties of third-generation synchrotron sources and free-electron lasers,” in Synchrotron Light Sources and Free-Electron Lasers, E. Jaeschke, S. Khan, J. R. Schneider, and J. B. Hastings, eds. (Springer International Publishing, 2016), pp. 821–863.

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Figures (10)

Fig. 1
Fig. 1 Experimental geometry inside the HORST chamber for the ptychographic imaging experiment. A beam stop is located on a Si3N4 membrane (transparent layer) in front of the detector for dynamic range improvement.
Fig. 2
Fig. 2 Diffraction pattern of a single position of the fibroblast cell without beam stop a) and with semitransparent beam stop b). The white circles mark the effective signal cut-off with the corresponding spatial frequency. The diffraction patterns are shown on the same logarithmic scale.
Fig. 3
Fig. 3 Fibroblast cell images. a) Visible light image with the ptychography scan area marked by the white rectangle. b) Reconstructed fibroblast cell phase of the double exposure HDR data. Regions N (nucleus) and Nu (nucleolus) are quantitatively analyzed with respect to a reference area outside the cell marked by R. c) An enlarged view of the region shown by the black square in b) shows the cells fibrous cytoskeleton and dot structures. The red line denotes a profile used for contrast evaluation.
Fig. 4
Fig. 4 Contrast profile line perpendicular to several aligned filament bundles along the red line in Fig. 3(c). Red and blue markers denote the maximum and minimum phase shift between the filament bundles.
Fig. 5
Fig. 5 Histograms of quantitatively measured transmission a) and phase values b) from two regions. The ratio of the refraction and absorption coefficient is given in c). Mean values of the measurements are indicated by black dashed and solid lines and the literature value for a typical protein compound is indicated by the red line.
Fig. 6
Fig. 6 wPRTF for the ptychographic fibroblast cell reconstructions. The reconstruction yielded 250 nm half-period resolution from single exposure data and 54 nm from HDR data.
Fig. 7
Fig. 7 Power spectral density for both measured data sets and the HDR data set. The dynamic range was improved by roughly two orders of magnitude as indicated by the inset number to the right.
Fig. 8
Fig. 8 Probe modes and corresponding energies εl. Hue encodes the phase and brightness the modulus as indicated by the color wheel in the lower right corner.
Fig. 9
Fig. 9 Reconstructed and propagated illumination intensity as the sum over all modes a). Intensity distribution in the pinhole b) and the sample plane c).
Fig. 10
Fig. 10 Reconstructed fibroblast cell phase of the single exposure data without beam stop a). Unwrapping artifacts arise due to the low SNR. The magnified view without unwrapping artifacts show only low resolution without the cell details b).

Tables (1)

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Table 1 Quantitative transmission and phase values for cell regions.

Equations (21)

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W ( r 1 , r 2 ) = l β l P l * ( r 1 ) P l ( r 2 ) ,
ψ i , l = β l P l O i .
I i = l | F { ψ i , l } | 2
= l β l 2 | F { P l O i } | 2 ,
O ( r ) = e 1 2 μ Δ z ( r ) e i Δ φ ( r ) ,
C = φ m a x φ m i n φ m a x + φ m i n .
ψ j ( r ) = P ( r r j ) O j ( r ) , j
I j = | F { ψ j } | 2 , j
O n + 1 ( r ) = j P n ¯ ( r r j ) ψ j n + 1 ( r ) j | P n ( r r j ) | 2
P n + 1 ( r ) = j O n ¯ ( r + r j ) ψ j n + 1 ( r + r j ) j | O n ( r r j ) | 2 ,
ψ j n + 1 ( r ) = ψ j n + π F [ 2 π O ( ψ j n ) ψ j n ] π O [ ψ j n ]
π O [ ψ j n ( r ) ] = P n ( r r j ) O j n ( r )
π F [ ψ j n ] = F 1 ( I j F ψ j | F ψ j | ) .
O n + 1 ( r ) = O n ( r ) + β O P n ¯ max | P n ¯ | 2 ( ψ j n + 1 ψ j n )
P n + 1 = P n + β P O n ¯ max | O n ¯ | 2 ( ψ j n + 1 ψ j n ) ,
ψ j n + 1 = π F [ P n ( r r j ) O ( r ) ]
ψ j n = P n ( r r j ) O ( r ) .
O n + 1 ( r ) = O n ( r ) + β O P n ¯ max | P n ¯ | 2 ( ψ j n + 1 ψ j n )
P n + 1 = P n + β P O n ¯ max | O n ¯ | 2 ( ψ j n + 1 ψ j n ) .
ψ j n + 1 = π M [ P n O j n ] + π M [ 2 P n O j n π M ( P n O j n ) ] P n O j n ,
e ~ j ( | ψ j n + 1 | | π M [ P n O j n ] | ) 2 .

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