Abstract

Modern Flash X-ray diffraction Imaging (FXI) acquires diffraction signals from single biomolecules at a high repetition rate from X-ray Free Electron Lasers (XFELs), easily obtaining millions of 2D diffraction patterns from a single experiment. Due to the stochastic nature of FXI experiments and the massive volumes of data, retrieving 3D electron densities from raw 2D diffraction patterns is a challenging and time-consuming task. We propose a semi-automatic data analysis pipeline for FXI experiments, which includes four steps: hit-finding and preliminary filtering, pattern classification, 3D Fourier reconstruction, and post-analysis. We also include a recently developed bootstrap methodology in the post-analysis step for uncertainty analysis and quality control. To achieve the best possible resolution, we further suggest using background subtraction, signal windowing, and convex optimization techniques when retrieving the Fourier phases in the post-analysis step. As an application example, we quantified the 3D electron structure of the PR772 virus using the proposed data analysis pipeline. The retrieved structure was above the detector edge resolution and clearly showed the pseudo-icosahedral capsid of the PR772.

© 2020 Optical Society of America

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2019 (5)

Y. Shi, K. Yin, X. Tai, H. DeMirci, A. Hosseinizadeh, B. G. Hogue, H. Li, A. Ourmazd, P. Schwander, I. A. Vartanyants, C. H. Yoon, A. Aquila, and H. Liu, “Evaluation of the performance of classification algorithms for XFEL single-particle imaging data,” IUCrJ 6, 331–340 (2019).
[Crossref]

K. Ayyer, A. J. Morgan, A. Aquila, H. DeMirci, B. G. Hogue, R. A. Kirian, P. L. Xavier, C. H. Yoon, H. N. Chapman, and A. Barty, “Low-signal limit of X-ray single particle diffractive imaging,” Opt. Express 27, 37816–37833 (2019).
[Crossref]

J. Liu, G. van der Schot, and S. Engblom, “Supervised classification methods for flash X-ray single particle diffraction imaging,” Opt. Express 27, 3884–3899 (2019).
[Crossref]

J. Bielecki, M. Hantke, B. Daurer, H. Reddy, D. Hasse, D. Larsson, L. Gunn, M. Svenda, A. Munke, J. Sellberg, L. Flueckiger, A. Pietrini, C. Nettelblad, I. Lundholm, G. Carlsson, K. Okamoto, N. Timneanu, D. Westphal, O. Kulyk, and F. Maia, “Electrospray sample injection for single-particle imaging with X-ray lasers,” Sci. Adv. 5, eaav8801 (2019).
[Crossref]

H. K. Reddy, M. Carroni, J. Hajdu, and M. Svenda, “Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture,” eLife 8, e48496 (2019).
[Crossref]

2018 (3)

A. Pietrini and C. Nettelblad, “Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy,” Opt. Express 26, 24422–24443 (2018).
[Crossref]

J. Liu, S. Engblom, and C. Nettelblad, “Assessing uncertainties in X-ray single-particle three-dimensional reconstruction,” Phys. Rev. E 98, 013303 (2018).
[Crossref]

M. Rose, S. Bobkov, K. Ayyer, R. Kurta, D. Dzhigaev, Y. Y. Kim, A. Morgan, C. H. Yoon, D. Westphal, J. Bielecki, J. Sellberg, G. Williams, F. Maia, O. Yefanov, V. Ilyin, A. Mancuso, H. Chapman, B. Hogue, A. Aquila, and I. Vartanyants, “Single-particle imaging without symmetry constraints at an X-ray free-electron laser,” IUCrJ 5, 727–736 (2018).
[Crossref]

2017 (5)

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
[Crossref]

A. Hosseinizadeh, G. Mashayekhi, J. Copperman, P. Schwander, A. Dashti, R. Sepehr, R. Fung, M. Schmidt, C. H. Yoon, B. G. Hogue, G. J. Williams, A. Aquila, and A. Ourmazd, “Conformational landscape of a virus by single-particle X-ray scattering,” Nat. Methods 14, 877–881 (2017).
[Crossref]

R. Kurta, J. Donatelli, C. H. Yoon, P. Berntsen, J. Bielecki, B. Daurer, H. Demirci, P. Fromme, M. Hantke, F. Maia, A. Munke, C. Nettelblad, K. Pande, H. Reddy, J. Sellberg, R. Sierra, M. Svenda, G. Schot, I. Vartanyants, and A. Mancuso, “Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses,” Phys. Rev. Lett. 119, 158102 (2017).
[Crossref]

J. Li and T. Zhou, “On relaxed averaged alternating reflections (RAAR) algorithm for phase retrieval with structured illumination,” Inverse Prob. 33, 025012 (2017).
[Crossref]

2016 (2)

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

M. F. Hantke, T. Ekeberg, and F. R. N. C. Maia, “Condor: a simulation tool for flash X-ray imaging,” J. Appl. Crystallogr. 49, 1356–1362 (2016).
[Crossref]

2015 (6)

G. van der Schot, M. Svenda, F. Maia, M. Hantke, D. DePonte, M. Seibert, A. Aquila, J. Schulz, R. Kirian, M. Liang, F. Stellato, B. Iwan, J. Andreasson, N. Timneanu, D. Westphal, F. Nunes de Almeida, D. Odic, D. Hasse, G. Carlsson, and T. Ekeberg, “Imaging single cells in a beam of live cyanobacteria with an X-ray laser,” Nat. Commun. 6, 5704 (2015).
[Crossref]

A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
[Crossref]

T. Ekeberg, M. Svenda, C. Abergel, F. Maia, V. Seltzer, J.-M. Claverie, M. Hantke, O. Jönsson, C. Nettelblad, G. van der Schot, M. Liang, D. DePonte, A. Barty, M. Seibert, B. Iwan, I. Andersson, N. Loh, A. Martin, H. Chapman, and J. Hajdu, “Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser,” Phys. Rev. Lett. 114, 098102 (2015).
[Crossref]

T. Ekeberg, S. Engblom, and J. Liu, “Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters,” Int. J. High Perform. Comput. Appl. 29, 233–243 (2015).
[Crossref]

S. Bobkov, A. Teslyuk, R. Kurta, O. Y. Gorobtsov, O. Yefanov, V. Ilyin, R. Senin, and I. Vartanyants, “Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers,” J. Synchrotron Radiat. 22, 1345–1352 (2015).
[Crossref]

A. Hosseinizadeh, A. Dashti, P. Schwander, R. Fung, and A. Ourmazd, “Single-particle structure determination by X-ray free-electron lasers: possibilities and challenges,” Struct. Dyn. 2, 041601 (2015).
[Crossref]

2014 (2)

M. Hantke, D. Hasse, F. Maia, T. Ekeberg, K. John, M. Svenda, N. Loh, A. Martin, N. Timneanu, D. S. D. Larsson, G. van der Schot, G. Carlsson, M. Ingelman, J. Andreasson, D. Westphal, M. Liang, F. Stellato, D. DePonte, R. Hartmann, and I. Andersson, “High-throughput imaging of heterogeneous cell organelles with an X-ray laser,” Nat. Photonics 8, 943–949 (2014).
[Crossref]

A. Barty, R. A. Kirian, F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White, and H. Chapman, “ Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data,” J. Appl. Crystallogr. 47, 1118–1131 (2014).
[Crossref]

2013 (1)

J. Becker, L. Bianco, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, M. Gronewald, B. Henrich, H. Hirsemann, G. Yu, R. Klanner, A. Klyuev, H. Krüger, S. Lange, A. Marras, A. Mozzanica, B. Schmitt, J. Schwandt, I. Sheviakov, and J. Zhang, “High speed cameras for X-rays: AGIPD and others,” J. Instrum. 8, C01042 (2013).
[Crossref]

2012 (3)

F. R. N. C. Maia, “The coherent X-ray imaging data bank,” Nat. Methods 9, 854–855 (2012).
[Crossref]

C. Yoon, “Novel algorithms in coherent diffraction imaging using X-ray free-electron lasers,” Proc. SPIE 8500, 85000H (2012).
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N. D. Loh, “Effects of extraneous noise in cryptotomography,” Proc. SPIE 8500, 85000K (2012).
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2011 (2)

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
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M. Seibert, T. Ekeberg, F. Maia, M. Svenda, J. Andreasson, O. Jönsson, D. Odić, B. Iwan, A. Rocker, D. Westphal, M. Hantke, D. DePonte, A. Barty, J. Schulz, L. Gumprecht, N. Coppola, A. Aquila, M. Liang, T. White, and J. Hajdu, “Single mimivirus particles intercepted and imaged with an X-ray laser,” Nature 470, 78–81 (2011).
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2010 (2)

L. Strüder, S. Epp, D. Rolles, R. Hartmann, P. Holl, G. Lutz, H. Soltau, R. Eckart, C. Reich, K. Heinzinger, C. Thamm, A. Rudenko, F. Krasniqi, K. Kuehnel, C. Bauer, C. Schroeter, R. Moshammer, S. Techert, D. Miessner, and J. Ullrich, “Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources,” Nucl. Instrum. Methods Phys. Res. A 614, 483–496 (2010).
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N. Miyazaki, B. Wu, K. Hagiwara, C.-Y. Wang, L. Xing, L. Hammar, A. Higashiura, T. Tsukihara, A. Nakagawa, T. Omura, and R. H. Cheng, “The functional organization of the internal components of Rice dwarf virus,” J. Biochem. 147, 843–850 (2010).
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2009 (1)

N. D. Loh and V. Elser, “Reconstruction algorithm for single-particle diffraction imaging experiments,” Phys. Rev. E 80, 026705 (2009).
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2008 (1)

D. DePonte, U. Weierstall, K. Schmidt, J. Warner, D. Starodub, J. Spence, and R. Doak, “Gas dynamic virtual nozzle for generation of microscopic droplet streams,” J. Phys. D 41, 195505 (2008).
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2006 (2)

H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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H. Chapman, A. Barty, S. Marchesini, A. Noy, S. Hau-Riege, C. Cui, M. Howells, R. Rosen, H. He, J. 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. R. Luke, “Relaxed averaged alternating reflections for diffraction imaging,” Inverse Prob. 21, 37–50 (2005).
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2001 (1)

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
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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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1982 (1)

Abbey, A.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
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Abergel, C.

T. Ekeberg, M. Svenda, C. Abergel, F. Maia, V. Seltzer, J.-M. Claverie, M. Hantke, O. Jönsson, C. Nettelblad, G. van der Schot, M. Liang, D. DePonte, A. Barty, M. Seibert, B. Iwan, I. Andersson, N. Loh, A. Martin, H. Chapman, and J. Hajdu, “Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser,” Phys. Rev. Lett. 114, 098102 (2015).
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C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
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Allahgholi, A.

A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
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Andersson, I.

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
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T. Ekeberg, M. Svenda, C. Abergel, F. Maia, V. Seltzer, J.-M. Claverie, M. Hantke, O. Jönsson, C. Nettelblad, G. van der Schot, M. Liang, D. DePonte, A. Barty, M. Seibert, B. Iwan, I. Andersson, N. Loh, A. Martin, H. Chapman, and J. Hajdu, “Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser,” Phys. Rev. Lett. 114, 098102 (2015).
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M. Hantke, D. Hasse, F. Maia, T. Ekeberg, K. John, M. Svenda, N. Loh, A. Martin, N. Timneanu, D. S. D. Larsson, G. van der Schot, G. Carlsson, M. Ingelman, J. Andreasson, D. Westphal, M. Liang, F. Stellato, D. DePonte, R. Hartmann, and I. Andersson, “High-throughput imaging of heterogeneous cell organelles with an X-ray laser,” Nat. Photonics 8, 943–949 (2014).
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C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
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Andreasson, J.

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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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G. van der Schot, M. Svenda, F. Maia, M. Hantke, D. DePonte, M. Seibert, A. Aquila, J. Schulz, R. Kirian, M. Liang, F. Stellato, B. Iwan, J. Andreasson, N. Timneanu, D. Westphal, F. Nunes de Almeida, D. Odic, D. Hasse, G. Carlsson, and T. Ekeberg, “Imaging single cells in a beam of live cyanobacteria with an X-ray laser,” Nat. Commun. 6, 5704 (2015).
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M. Hantke, D. Hasse, F. Maia, T. Ekeberg, K. John, M. Svenda, N. Loh, A. Martin, N. Timneanu, D. S. D. Larsson, G. van der Schot, G. Carlsson, M. Ingelman, J. Andreasson, D. Westphal, M. Liang, F. Stellato, D. DePonte, R. Hartmann, and I. Andersson, “High-throughput imaging of heterogeneous cell organelles with an X-ray laser,” Nat. Photonics 8, 943–949 (2014).
[Crossref]

M. Seibert, T. Ekeberg, F. Maia, M. Svenda, J. Andreasson, O. Jönsson, D. Odić, B. Iwan, A. Rocker, D. Westphal, M. Hantke, D. DePonte, A. Barty, J. Schulz, L. Gumprecht, N. Coppola, A. Aquila, M. Liang, T. White, and J. Hajdu, “Single mimivirus particles intercepted and imaged with an X-ray laser,” Nature 470, 78–81 (2011).
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C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
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Anfinrud, P.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Aquila, A.

Y. Shi, K. Yin, X. Tai, H. DeMirci, A. Hosseinizadeh, B. G. Hogue, H. Li, A. Ourmazd, P. Schwander, I. A. Vartanyants, C. H. Yoon, A. Aquila, and H. Liu, “Evaluation of the performance of classification algorithms for XFEL single-particle imaging data,” IUCrJ 6, 331–340 (2019).
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K. Ayyer, A. J. Morgan, A. Aquila, H. DeMirci, B. G. Hogue, R. A. Kirian, P. L. Xavier, C. H. Yoon, H. N. Chapman, and A. Barty, “Low-signal limit of X-ray single particle diffractive imaging,” Opt. Express 27, 37816–37833 (2019).
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M. Rose, S. Bobkov, K. Ayyer, R. Kurta, D. Dzhigaev, Y. Y. Kim, A. Morgan, C. H. Yoon, D. Westphal, J. Bielecki, J. Sellberg, G. Williams, F. Maia, O. Yefanov, V. Ilyin, A. Mancuso, H. Chapman, B. Hogue, A. Aquila, and I. Vartanyants, “Single-particle imaging without symmetry constraints at an X-ray free-electron laser,” IUCrJ 5, 727–736 (2018).
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H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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. Hosseinizadeh, G. Mashayekhi, J. Copperman, P. Schwander, A. Dashti, R. Sepehr, R. Fung, M. Schmidt, C. H. Yoon, B. G. Hogue, G. J. Williams, A. Aquila, and A. Ourmazd, “Conformational landscape of a virus by single-particle X-ray scattering,” Nat. Methods 14, 877–881 (2017).
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A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

G. van der Schot, M. Svenda, F. Maia, M. Hantke, D. DePonte, M. Seibert, A. Aquila, J. Schulz, R. Kirian, M. Liang, F. Stellato, B. Iwan, J. Andreasson, N. Timneanu, D. Westphal, F. Nunes de Almeida, D. Odic, D. Hasse, G. Carlsson, and T. Ekeberg, “Imaging single cells in a beam of live cyanobacteria with an X-ray laser,” Nat. Commun. 6, 5704 (2015).
[Crossref]

M. Seibert, T. Ekeberg, F. Maia, M. Svenda, J. Andreasson, O. Jönsson, D. Odić, B. Iwan, A. Rocker, D. Westphal, M. Hantke, D. DePonte, A. Barty, J. Schulz, L. Gumprecht, N. Coppola, A. Aquila, M. Liang, T. White, and J. Hajdu, “Single mimivirus particles intercepted and imaged with an X-ray laser,” Nature 470, 78–81 (2011).
[Crossref]

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
[Crossref]

Arnaud, M.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Arthur, J.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Audebert, P.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Awel, S.

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
[Crossref]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

Ayyer, K.

K. Ayyer, A. J. Morgan, A. Aquila, H. DeMirci, B. G. Hogue, R. A. Kirian, P. L. Xavier, C. H. Yoon, H. N. Chapman, and A. Barty, “Low-signal limit of X-ray single particle diffractive imaging,” Opt. Express 27, 37816–37833 (2019).
[Crossref]

M. Rose, S. Bobkov, K. Ayyer, R. Kurta, D. Dzhigaev, Y. Y. Kim, A. Morgan, C. H. Yoon, D. Westphal, J. Bielecki, J. Sellberg, G. Williams, F. Maia, O. Yefanov, V. Ilyin, A. Mancuso, H. Chapman, B. Hogue, A. Aquila, and I. Vartanyants, “Single-particle imaging without symmetry constraints at an X-ray free-electron laser,” IUCrJ 5, 727–736 (2018).
[Crossref]

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

Bajt, S.

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
[Crossref]

H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Balasini, M.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Bane, K.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Barbera, M.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Barthelmess, M.

Barty, A.

K. Ayyer, A. J. Morgan, A. Aquila, H. DeMirci, B. G. Hogue, R. A. Kirian, P. L. Xavier, C. H. Yoon, H. N. Chapman, and A. Barty, “Low-signal limit of X-ray single particle diffractive imaging,” Opt. Express 27, 37816–37833 (2019).
[Crossref]

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
[Crossref]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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. Barty, R. A. Kirian, F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White, and H. Chapman, “ Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data,” J. Appl. Crystallogr. 47, 1118–1131 (2014).
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C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
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M. Seibert, T. Ekeberg, F. Maia, M. Svenda, J. Andreasson, O. Jönsson, D. Odić, B. Iwan, A. Rocker, D. Westphal, M. Hantke, D. DePonte, A. Barty, J. Schulz, L. Gumprecht, N. Coppola, A. Aquila, M. Liang, T. White, and J. Hajdu, “Single mimivirus particles intercepted and imaged with an X-ray laser,” Nature 470, 78–81 (2011).
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H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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H. Chapman, A. Barty, S. Marchesini, A. Noy, S. Hau-Riege, C. Cui, M. Howells, R. Rosen, H. He, J. 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,” in IPAP Conference Series 7 (2006), pp. 380–382.

Bauer, C.

L. Strüder, S. Epp, D. Rolles, R. Hartmann, P. Holl, G. Lutz, H. Soltau, R. Eckart, C. Reich, K. Heinzinger, C. Thamm, A. Rudenko, F. Krasniqi, K. Kuehnel, C. Bauer, C. Schroeter, R. Moshammer, S. Techert, D. Miessner, and J. Ullrich, “Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources,” Nucl. Instrum. Methods Phys. Res. A 614, 483–496 (2010).
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Bean, R.

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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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Becker, J.

A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
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J. Becker, L. Bianco, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, M. Gronewald, B. Henrich, H. Hirsemann, G. Yu, R. Klanner, A. Klyuev, H. Krüger, S. Lange, A. Marras, A. Mozzanica, B. Schmitt, J. Schwandt, I. Sheviakov, and J. Zhang, “High speed cameras for X-rays: AGIPD and others,” J. Instrum. 8, C01042 (2013).
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Beetz, T.

Belsole, E.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
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Benner, H.

H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Benner, W. H.

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
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Bennie, P.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
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Ben-Zvi, I.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Bernard, J.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
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Berntsen, P.

R. Kurta, J. Donatelli, C. H. Yoon, P. Berntsen, J. Bielecki, B. Daurer, H. Demirci, P. Fromme, M. Hantke, F. Maia, A. Munke, C. Nettelblad, K. Pande, H. Reddy, J. Sellberg, R. Sierra, M. Svenda, G. Schot, I. Vartanyants, and A. Mancuso, “Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses,” Phys. Rev. Lett. 119, 158102 (2017).
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H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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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Bharadwaj, V.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Bianco, L.

A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
[Crossref]

J. Becker, L. Bianco, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, M. Gronewald, B. Henrich, H. Hirsemann, G. Yu, R. Klanner, A. Klyuev, H. Krüger, S. Lange, A. Marras, A. Mozzanica, B. Schmitt, J. Schwandt, I. Sheviakov, and J. Zhang, “High speed cameras for X-rays: AGIPD and others,” J. Instrum. 8, C01042 (2013).
[Crossref]

Bielecki, J.

J. Bielecki, M. Hantke, B. Daurer, H. Reddy, D. Hasse, D. Larsson, L. Gunn, M. Svenda, A. Munke, J. Sellberg, L. Flueckiger, A. Pietrini, C. Nettelblad, I. Lundholm, G. Carlsson, K. Okamoto, N. Timneanu, D. Westphal, O. Kulyk, and F. Maia, “Electrospray sample injection for single-particle imaging with X-ray lasers,” Sci. Adv. 5, eaav8801 (2019).
[Crossref]

M. Rose, S. Bobkov, K. Ayyer, R. Kurta, D. Dzhigaev, Y. Y. Kim, A. Morgan, C. H. Yoon, D. Westphal, J. Bielecki, J. Sellberg, G. Williams, F. Maia, O. Yefanov, V. Ilyin, A. Mancuso, H. Chapman, B. Hogue, A. Aquila, and I. Vartanyants, “Single-particle imaging without symmetry constraints at an X-ray free-electron laser,” IUCrJ 5, 727–736 (2018).
[Crossref]

R. Kurta, J. Donatelli, C. H. Yoon, P. Berntsen, J. Bielecki, B. Daurer, H. Demirci, P. Fromme, M. Hantke, F. Maia, A. Munke, C. Nettelblad, K. Pande, H. Reddy, J. Sellberg, R. Sierra, M. Svenda, G. Schot, I. Vartanyants, and A. Mancuso, “Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses,” Phys. Rev. Lett. 119, 158102 (2017).
[Crossref]

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
[Crossref]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

Bignami, G.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Bionta, R.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Bobkov, S.

M. Rose, S. Bobkov, K. Ayyer, R. Kurta, D. Dzhigaev, Y. Y. Kim, A. Morgan, C. H. Yoon, D. Westphal, J. Bielecki, J. Sellberg, G. Williams, F. Maia, O. Yefanov, V. Ilyin, A. Mancuso, H. Chapman, B. Hogue, A. Aquila, and I. Vartanyants, “Single-particle imaging without symmetry constraints at an X-ray free-electron laser,” IUCrJ 5, 727–736 (2018).
[Crossref]

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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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S. Bobkov, A. Teslyuk, R. Kurta, O. Y. Gorobtsov, O. Yefanov, V. Ilyin, R. Senin, and I. Vartanyants, “Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers,” J. Synchrotron Radiat. 22, 1345–1352 (2015).
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Boër, M.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Bogan, M.

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
[Crossref]

H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Bolton, P.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Borland, M.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Bostedt, C.

Boutet, S.

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
[Crossref]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

P. Hart, S. Boutet, G. Carini, A. Dragone, B. Duda, D. Freytag, G. Haller, R. Herbst, S. Herrmann, C. Kenney, J. Morse, M. Nordby, J. Pines, N. van Bakel, M. Weaver, and G. Williams, “The Cornell-SLAC pixel array detector at LCLS,” in IEEE Nuclear Science Symposium and Medical Imaging Conference Record (NSS/MIC) (IEEE, 2012), pp. 538–541.

S. Boutet, P. Fromme, and M. S. Hunter, X-ray Free Electron Lasers: A Revolution in Structural Biology (Springer, 2018), Chap. 14.

Bozek, J.

Briel, U.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Bucher, M.

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

Bucksbaum, P.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Butler, I.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Cara, C.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Carini, G.

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

P. Hart, S. Boutet, G. Carini, A. Dragone, B. Duda, D. Freytag, G. Haller, R. Herbst, S. Herrmann, C. Kenney, J. Morse, M. Nordby, J. Pines, N. van Bakel, M. Weaver, and G. Williams, “The Cornell-SLAC pixel array detector at LCLS,” in IEEE Nuclear Science Symposium and Medical Imaging Conference Record (NSS/MIC) (IEEE, 2012), pp. 538–541.

Carlsson, G.

J. Bielecki, M. Hantke, B. Daurer, H. Reddy, D. Hasse, D. Larsson, L. Gunn, M. Svenda, A. Munke, J. Sellberg, L. Flueckiger, A. Pietrini, C. Nettelblad, I. Lundholm, G. Carlsson, K. Okamoto, N. Timneanu, D. Westphal, O. Kulyk, and F. Maia, “Electrospray sample injection for single-particle imaging with X-ray lasers,” Sci. Adv. 5, eaav8801 (2019).
[Crossref]

G. van der Schot, M. Svenda, F. Maia, M. Hantke, D. DePonte, M. Seibert, A. Aquila, J. Schulz, R. Kirian, M. Liang, F. Stellato, B. Iwan, J. Andreasson, N. Timneanu, D. Westphal, F. Nunes de Almeida, D. Odic, D. Hasse, G. Carlsson, and T. Ekeberg, “Imaging single cells in a beam of live cyanobacteria with an X-ray laser,” Nat. Commun. 6, 5704 (2015).
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M. Hantke, D. Hasse, F. Maia, T. Ekeberg, K. John, M. Svenda, N. Loh, A. Martin, N. Timneanu, D. S. D. Larsson, G. van der Schot, G. Carlsson, M. Ingelman, J. Andreasson, D. Westphal, M. Liang, F. Stellato, D. DePonte, R. Hartmann, and I. Andersson, “High-throughput imaging of heterogeneous cell organelles with an X-ray laser,” Nat. Photonics 8, 943–949 (2014).
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Carlsson, G. H.

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
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Carron, S.

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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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Carroni, M.

H. K. Reddy, M. Carroni, J. Hajdu, and M. Svenda, “Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture,” eLife 8, e48496 (2019).
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Cauble, R.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Chabaud, C.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
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Chapman, H.

M. Rose, S. Bobkov, K. Ayyer, R. Kurta, D. Dzhigaev, Y. Y. Kim, A. Morgan, C. H. Yoon, D. Westphal, J. Bielecki, J. Sellberg, G. Williams, F. Maia, O. Yefanov, V. Ilyin, A. Mancuso, H. Chapman, B. Hogue, A. Aquila, and I. Vartanyants, “Single-particle imaging without symmetry constraints at an X-ray free-electron laser,” IUCrJ 5, 727–736 (2018).
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H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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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T. Ekeberg, M. Svenda, C. Abergel, F. Maia, V. Seltzer, J.-M. Claverie, M. Hantke, O. Jönsson, C. Nettelblad, G. van der Schot, M. Liang, D. DePonte, A. Barty, M. Seibert, B. Iwan, I. Andersson, N. Loh, A. Martin, H. Chapman, and J. Hajdu, “Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser,” Phys. Rev. Lett. 114, 098102 (2015).
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A. Barty, R. A. Kirian, F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White, and H. Chapman, “ Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data,” J. Appl. Crystallogr. 47, 1118–1131 (2014).
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C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
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H. Chapman, A. Barty, S. Marchesini, A. Noy, S. Hau-Riege, C. Cui, M. Howells, R. Rosen, H. He, J. 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).
[Crossref]

H. Chapman, A. Barty, M. Bogan, S. Boutet, M. Frank, S. Hau-Riege, S. Marchesini, B. Woods, S. Bajt, H. Benner, R. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Duesterer, T. Tschentscher, J. Schneider, E. Spiller, T. Möller, and J. Hajdu, “Femtosecond diffractive imaging with a soft-X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Chapman, H. N.

K. Ayyer, A. J. Morgan, A. Aquila, H. DeMirci, B. G. Hogue, R. A. Kirian, P. L. Xavier, C. H. Yoon, H. N. Chapman, and A. Barty, “Low-signal limit of X-ray single particle diffractive imaging,” Opt. Express 27, 37816–37833 (2019).
[Crossref]

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,” in IPAP Conference Series 7 (2006), pp. 380–382.

Cheng, R. H.

N. Miyazaki, B. Wu, K. Hagiwara, C.-Y. Wang, L. Xing, L. Hammar, A. Higashiura, T. Tsukihara, A. Nakagawa, T. Omura, and R. H. Cheng, “The functional organization of the internal components of Rice dwarf virus,” J. Biochem. 147, 843–850 (2010).
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Claverie, J.-M.

T. Ekeberg, M. Svenda, C. Abergel, F. Maia, V. Seltzer, J.-M. Claverie, M. Hantke, O. Jönsson, C. Nettelblad, G. van der Schot, M. Liang, D. DePonte, A. Barty, M. Seibert, B. Iwan, I. Andersson, N. Loh, A. Martin, H. Chapman, and J. Hajdu, “Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser,” Phys. Rev. Lett. 114, 098102 (2015).
[Crossref]

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
[Crossref]

Clendenin, J.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Cole, R.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Collura, A.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Conte, M.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Copperman, J.

A. Hosseinizadeh, G. Mashayekhi, J. Copperman, P. Schwander, A. Dashti, R. Sepehr, R. Fung, M. Schmidt, C. H. Yoon, B. G. Hogue, G. J. Williams, A. Aquila, and A. Ourmazd, “Conformational landscape of a virus by single-particle X-ray scattering,” Nat. Methods 14, 877–881 (2017).
[Crossref]

Coppola, N.

M. Seibert, T. Ekeberg, F. Maia, M. Svenda, J. Andreasson, O. Jönsson, D. Odić, B. Iwan, A. Rocker, D. Westphal, M. Hantke, D. DePonte, A. Barty, J. Schulz, L. Gumprecht, N. Coppola, A. Aquila, M. Liang, T. White, and J. Hajdu, “Single mimivirus particles intercepted and imaged with an X-ray laser,” Nature 470, 78–81 (2011).
[Crossref]

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
[Crossref]

Cornacchia, M.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Cros, A.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

Cui, C.

H. Chapman, A. Barty, S. Marchesini, A. Noy, S. Hau-Riege, C. Cui, M. Howells, R. Rosen, H. He, J. 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).
[Crossref]

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,” in IPAP Conference Series 7 (2006), pp. 380–382.

Dashti, A.

A. Hosseinizadeh, G. Mashayekhi, J. Copperman, P. Schwander, A. Dashti, R. Sepehr, R. Fung, M. Schmidt, C. H. Yoon, B. G. Hogue, G. J. Williams, A. Aquila, and A. Ourmazd, “Conformational landscape of a virus by single-particle X-ray scattering,” Nat. Methods 14, 877–881 (2017).
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A. Hosseinizadeh, A. Dashti, P. Schwander, R. Fung, and A. Ourmazd, “Single-particle structure determination by X-ray free-electron lasers: possibilities and challenges,” Struct. Dyn. 2, 041601 (2015).
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Daurer, B.

J. Bielecki, M. Hantke, B. Daurer, H. Reddy, D. Hasse, D. Larsson, L. Gunn, M. Svenda, A. Munke, J. Sellberg, L. Flueckiger, A. Pietrini, C. Nettelblad, I. Lundholm, G. Carlsson, K. Okamoto, N. Timneanu, D. Westphal, O. Kulyk, and F. Maia, “Electrospray sample injection for single-particle imaging with X-ray lasers,” Sci. Adv. 5, eaav8801 (2019).
[Crossref]

R. Kurta, J. Donatelli, C. H. Yoon, P. Berntsen, J. Bielecki, B. Daurer, H. Demirci, P. Fromme, M. Hantke, F. Maia, A. Munke, C. Nettelblad, K. Pande, H. Reddy, J. Sellberg, R. Sierra, M. Svenda, G. Schot, I. Vartanyants, and A. Mancuso, “Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses,” Phys. Rev. Lett. 119, 158102 (2017).
[Crossref]

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

Daurer, B. J.

B. J. Daurer, K. Okamoto, J. Bielecki, F. R. N. C. Maia, K. Mühlig, M. M. Seibert, M. F. Hantke, C. Nettelblad, W. H. Benner, M. Svenda, N. Tmneanu, T. Ekeberg, N. D. Loh, A. Pietrini, A. Zani, A. D. Rath, D. Westphal, R. A. Kirian, S. Awel, M. O. Wiedorn, G. van der Schot, G. H. Carlsson, D. Hasse, J. A. Sellberg, A. Barty, J. Andreasson, S. Boutet, G. Williams, J. Koglin, I. Andersson, J. Hajdu, and D. S. D. Larsson, “Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses,” IUCrJ 4, 251–262 (2017).
[Crossref]

Decker, G.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Delfs, A.

A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
[Crossref]

DeMirci, H.

Y. Shi, K. Yin, X. Tai, H. DeMirci, A. Hosseinizadeh, B. G. Hogue, H. Li, A. Ourmazd, P. Schwander, I. A. Vartanyants, C. H. Yoon, A. Aquila, and H. Liu, “Evaluation of the performance of classification algorithms for XFEL single-particle imaging data,” IUCrJ 6, 331–340 (2019).
[Crossref]

K. Ayyer, A. J. Morgan, A. Aquila, H. DeMirci, B. G. Hogue, R. A. Kirian, P. L. Xavier, C. H. Yoon, H. N. Chapman, and A. Barty, “Low-signal limit of X-ray single particle diffractive imaging,” Opt. Express 27, 37816–37833 (2019).
[Crossref]

H. Reddy, C. H. Yoon, A. Aquila, S. Awel, K. Ayyer, A. Barty, P. Berntsen, J. Bielecki, S. Bobkov, M. Bucher, G. Carini, S. Carron, H. Chapman, B. Daurer, H. Demirci, T. Ekeberg, P. Fromme, J. Hajdu, M. Hanke, 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]

R. Kurta, J. Donatelli, C. H. Yoon, P. Berntsen, J. Bielecki, B. Daurer, H. Demirci, P. Fromme, M. Hantke, F. Maia, A. Munke, C. Nettelblad, K. Pande, H. Reddy, J. Sellberg, R. Sierra, M. Svenda, G. Schot, I. Vartanyants, and A. Mancuso, “Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses,” Phys. Rev. Lett. 119, 158102 (2017).
[Crossref]

A. Munke, J. Andreasson, A. Aquila, S. Awel, K. Ayyer, A. Barty, R. Bean, P. Berntsen, J. Bielecki, S. Boutet, M. Bucher, H. Chapman, B. Daurer, H. Demirci, V. Elser, P. Fromme, J. Hajdu, M. Hantke, A. Higashiura, 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]

Den Hartog, P.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Denby, M.

M. Turner, A. Abbey, M. Arnaud, M. Balasini, M. Barbera, E. Belsole, P. Bennie, J. Bernard, G. Bignami, M. Boër, U. Briel, I. Butler, C. Cara, C. Chabaud, R. Cole, A. Collura, M. Conte, A. Cros, M. Denby, and E. Zonca, “The European photon imaging camera on XMM-Newton: the MOS cameras,” Astron. Astrophys. 365, L27–L35 (2001).
[Crossref]

DePonte, D.

T. Ekeberg, M. Svenda, C. Abergel, F. Maia, V. Seltzer, J.-M. Claverie, M. Hantke, O. Jönsson, C. Nettelblad, G. van der Schot, M. Liang, D. DePonte, A. Barty, M. Seibert, B. Iwan, I. Andersson, N. Loh, A. Martin, H. Chapman, and J. Hajdu, “Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser,” Phys. Rev. Lett. 114, 098102 (2015).
[Crossref]

G. van der Schot, M. Svenda, F. Maia, M. Hantke, D. DePonte, M. Seibert, A. Aquila, J. Schulz, R. Kirian, M. Liang, F. Stellato, B. Iwan, J. Andreasson, N. Timneanu, D. Westphal, F. Nunes de Almeida, D. Odic, D. Hasse, G. Carlsson, and T. Ekeberg, “Imaging single cells in a beam of live cyanobacteria with an X-ray laser,” Nat. Commun. 6, 5704 (2015).
[Crossref]

M. Hantke, D. Hasse, F. Maia, T. Ekeberg, K. John, M. Svenda, N. Loh, A. Martin, N. Timneanu, D. S. D. Larsson, G. van der Schot, G. Carlsson, M. Ingelman, J. Andreasson, D. Westphal, M. Liang, F. Stellato, D. DePonte, R. Hartmann, and I. Andersson, “High-throughput imaging of heterogeneous cell organelles with an X-ray laser,” Nat. Photonics 8, 943–949 (2014).
[Crossref]

M. Seibert, T. Ekeberg, F. Maia, M. Svenda, J. Andreasson, O. Jönsson, D. Odić, B. Iwan, A. Rocker, D. Westphal, M. Hantke, D. DePonte, A. Barty, J. Schulz, L. Gumprecht, N. Coppola, A. Aquila, M. Liang, T. White, and J. Hajdu, “Single mimivirus particles intercepted and imaged with an X-ray laser,” Nature 470, 78–81 (2011).
[Crossref]

C. H. Yoon, P. Schwander, C. Abergel, I. Andersson, J. Andreasson, A. Aquila, S. Bajt, M. Barthelmess, A. Barty, M. Bogan, C. Bostedt, J. Bozek, H. Chapman, J.-M. Claverie, N. Coppola, D. DePonte, T. Ekeberg, S. Epp, B. Erk, and A. Ourmazd, “Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering,” Opt. Express 19, 16542–16549 (2011).
[Crossref]

D. DePonte, U. Weierstall, K. Schmidt, J. Warner, D. Starodub, J. Spence, and R. Doak, “Gas dynamic virtual nozzle for generation of microscopic droplet streams,” J. Phys. D 41, 195505 (2008).
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Dierker, S.

J. Arthur, P. Anfinrud, P. Audebert, K. Bane, I. Ben-Zvi, V. Bharadwaj, R. Bionta, P. Bolton, M. Borland, P. Bucksbaum, R. Cauble, J. Clendenin, M. Cornacchia, G. Decker, P. Den Hartog, S. Dierker, D. Dowell, D. Dungan, P. Emma, and D. Waltz, “Linac coherent light source (LCLS) conceptual design report,” Technical Report SLAC-R-593 (SLAC, 2002).

Dinapoli, R.

A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
[Crossref]

J. Becker, L. Bianco, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, M. Gronewald, B. Henrich, H. Hirsemann, G. Yu, R. Klanner, A. Klyuev, H. Krüger, S. Lange, A. Marras, A. Mozzanica, B. Schmitt, J. Schwandt, I. Sheviakov, and J. Zhang, “High speed cameras for X-rays: AGIPD and others,” J. Instrum. 8, C01042 (2013).
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A. Klyuev, A. Allahgholi, J. Becker, L. Bianco, A. Delfs, R. Dinapoli, P. Göttlicher, H. Graafsma, D. Greiffenberg, H. Hirsemann, G. Yu, R. Klanner, H. Krueger, S. Lange, A. Marras, D. Mezza, A. Mozzanica, S. Rah, Q. Xia, and M. Zimmer, “AGIPD, a high dynamic range fast detector for the European XFEL,” J. Instrum. 10, C01023 (2015).
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Martin, A.

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Miessner, D.

L. Strüder, S. Epp, D. Rolles, R. Hartmann, P. Holl, G. Lutz, H. Soltau, R. Eckart, C. Reich, K. Heinzinger, C. Thamm, A. Rudenko, F. Krasniqi, K. Kuehnel, C. Bauer, C. Schroeter, R. Moshammer, S. Techert, D. Miessner, and J. Ullrich, “Large-format, high-speed, X-ray pnCCDs combined with electron and ion imaging spectrometers in a multipurpose chamber for experiments at 4th generation light sources,” Nucl. Instrum. Methods Phys. Res. A 614, 483–496 (2010).
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Figures (15)

Fig. 1.
Fig. 1. Proposed FXI data analysis pipeline. (a) The preliminary filtering selects a potential single-particle dataset from the raw FXI data. (b) From the initial dataset, the data selection procedure selects limited but sufficient number of high-quality single-particle diffraction patterns. (c) The 3D reconstruction procedure produces a maximum likelihood estimate of the 3D Fourier intensity. (d) In the post-analysis step, the 3D real-space structure is estimated together with the overall resolution uncertainty.
Fig. 2.
Fig. 2. Illustration of the typical FXI experimental setup. The front detector captures signals at higher diffraction angles, and the back detector captures signals at lower angles. The sample particles are injected into the X-ray beam at random, and hence we get diffraction patterns of various types and qualitites, i.e., from single particles, multiple particles, contaminants, and blank frames. The particle orientations are unknown, and so is the relative strengths (photon fluence $\phi$) of the diffraction signals.
Fig. 3.
Fig. 3. Statistical measures from the EigenImage classifier. (a) Pattern distances (the relative Euclidean distance between the testing pattern and the best matched template); (b) estimated fluence (the ratio of the total photon counts in the test pattern to the best-matched template); and (c) estimated particle sizes. In (a) and (b), we used 1000 equal sized bins, and the bin sizes were $2.062 \times {10^{- 4}}$ and 0.0381 for (a) and (b), respectively. In (c), we used 12 equal sized bins of size 1.159 nm. Consult [26] for the notation and definitions of pattern distance and estimated fluence.
Fig. 4.
Fig. 4. Most likely probability ${\bf M}$ at the final EMC iteration for datasets (a) ${N_{1k}}$ and (b) ${N_{3k}}$; cf. Eq. (4). The corresponding isosurface plots of Fourier intensities are (c) and (d), respectively, and the red dots show the corresponding rotations of the most likely probabilities.
Fig. 5.
Fig. 5. 3D electron density distributions of the PR772 virus. (a) and (c) are the isosurface plots at 10% values of the maximum electron density for ${N_{1k}}$ and ${N_{3k}}$, respectively. (b) and (d) are the corresponding interior structures as isosurface plots at 10%, 50%, 79%, and 89% values of the maximum electron density. In the second row, (e) and (g) are projection images from (a) and (c), and (f) and (h) are cross section slices through the particle center. The red scale bars denote 70 nm. The resolution was 10.7 nm according to a PRTF analysis, which was better than the detector edge resolution (11.6 nm). The particle size was determined to be 68.9 nm and 69.4 nm, respectively, for ${N_{1k}}$ and ${N_{3k}}$.
Fig. 6.
Fig. 6. 3D electron density distributions of the PR772 virus with background subtraction. See Fig. 5 for a detailed description. The resolution was 9.5 nm from a PRTF analysis for ${N_{1k}}$ and 8.4 nm for ${N_{3k}}$, and the particle size was determined to be 68.6 nm and 68.9 nm, respectively.
Fig. 7.
Fig. 7. Windowed 3D electron density distributions for ${N_{1k}}$ (left two columns) and ${N_{3k}}$ (right two columns), respectively. The top two rows are from reconstructions with background noises, and the bottom two are windowed electron densities from reconstructions with subtracted background noise. The Hann windows made the retrieved intensities much smother and effectively removed the concentric layers; cf. Figs. 5 and 6. Further, the intensity is heavily concentrated at the particle centers with background noise, and by removing the background noise, the intensity spreads out in the retrieved particles. The resolution was 10 nm from a PRTF analysis with threshold ${e^{- 1}}$. (j)–(q) The corresponding results with background removed. The resolution from ${N_{1k}}$ was here 11.2 nm and 8.7 nm for ${N_{3k}}$. The combination of Hann window and background subtraction made the retrieved particle smooth and of comparably high resolution. (i) and (r) are color bars showing the density of our retrieved viruses.
Fig. 8.
Fig. 8. Phasing results of COACS healed ${N_{3k}}$. (a) shows the interior structures as isosurface plots at 10%, 50%, 79%, and 89% values of the maximum electron density, and here the electron density was phased without applying any constraint. (b)–(d) are three orthogonal slices through the particle center of (a).
Fig. 9.
Fig. 9. Bootstrap analysis. (a) and (b) Isosurface at 10%, 50%, 77%, and 87% values of the maximum electron density of the average phased object of ${{\mathbb W}_r}$ and the phased object of ${{\mathbb W}_m}$ for ${N_{1k}}$ (see text). (c) and (d) Isosurface from the phased objects of ${{\mathbb W}_r}$ and ${{\mathbb W}_m}$ for ${N_{3k}}$. (e)–(h) Slice through the particle center of (a)–(d). (j) and (k) The estimated uncertainties in Fourier and real space, respectively.
Fig. 10.
Fig. 10. Top row, cross section images of the retrieved particles from the dataset ${N_{3k}}$ in Fig. 5. Middle row, cross section images from a smoothed regular icosahedron object at the same rotations. To create the smooth icosahedron, we first generated an ideal icosahedron, whose outer radius was 12 pixels, and then smoothed it using two Gaussian convolution kernels. (i)–(k) The surfaces of a ideal icosahedron object at the same rotations. The retrieved particle (the top row) matched well to the smoothed icosahedron (the middle row), but the vertices were much smoother than vertices of an ideal icosahedron (the bottom row).
Fig. 11.
Fig. 11. Masks used in the EMC algorithm. (a) The masks used for computing the rotational probability in each EMC iteration. (b) The mask used in the final EMC compression step. (c) is a random pattern from our selected dataset ${N_{1k}}$. (d) is the background scattering estimated via averaging of 100 diffraction patterns without particles. (e) is an estimated background with extra scattering; see more details in Appendix C. (f) is a synthetic pattern with the small mask in (b). (c)–(f) were plotted on a logarithmic scale.
Fig. 12.
Fig. 12. Sum absolute differences of two EMC models from two adjacent iterations.
Fig. 13.
Fig. 13. PRTF analysis for different reconstruction of datasets (a) ${N_{1k}}$ and (b) ${N_{3k}}$.
Fig. 14.
Fig. 14. (a)–(d) illustrate interior structures as isosurfacess plot at 10%, 50%, 79%, and 89% values of the maximum electron density for a synthetic Poissonian dataset $K$ ${K^f}$, ${K^b}$, and ${K^e}$. (e)–(h) are random cross section images from (a)–(d). As can be seen, aliasing effects existed in all retrieved electron intensities, even when we used a uniform-intensity icosahedron to generate the diffraction patterns. The background noise and the extra scattering contributed to the high-intensity central ring as shown in (g) and (h).
Fig. 15.
Fig. 15. (a) and (c) were the cross section plots of the original EMC intensities at the final EMC iteration for ${N_{1k}}$ and ${N_{3k}}$, respectively. (b) and (d) were the corresponding background corrected data. The intensities and the background values were illustrated in (f) and (g). It is obvious that the contrast between speckles is bigger in the background removed intensities [(b) and (d)] than the original ones [(a) and (c)].

Tables (1)

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Table 1. Shape and Error Analysis for the Phased Objects from the Datasets N 1 k and N 3 k a

Equations (12)

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Ψ ( x ) = Ψ ( 0 ) ( x ) + Ψ ( 1 ) ( x ) = Ψ 0 exp ( i k 0 x ) + Ψ 0 k 2 4 π [ 1 n 2 ( x ) ] exp ( i k 0 x ) exp ( i k | x x | ) | x x | d x ,
I I 0 | F ( q ) | 2 ,
P ( K ik = κ | W ij , R j , ϕ jk ) = j = 1 M rot ( W ij ϕ jk ) κ e W ij ϕ jk κ ! ,
M k = max j P jk ,
C = I max I min I max + I min ,
R total 2 = R bias 2 + R std 2 + R ^ S 2 = | W a W m | 2 + Var ( W r ) + R ^ S 2 ,
R total 2 = R bias 2 + R std 2 + R ^ S 2 = | A a A m | 2 + Var ( A r ) + R ^ S 2 ,
E f = i = 1 M pix ( | h ~ i | I i ) 2 i = 1 M pix I i ,
E r = i S ¯ ( | h i | ) 2 S ¯ S | h i | 2 ,
D r = 2 m ( 3 V 4 π ) 3 ,
B u = β min s S u ( W ) s ,
D u = | S u | 1 s S u ( W ) s ,