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Title: Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging

Abstract

Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recentmore » inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. In conclusion, the anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.« less

Authors:
 [1]; ORCiD logo [2]; ORCiD logo [1];  [3];  [1];  [1];  [4];  [5];  [6];  [7];  [8];  [9]; ORCiD logo [1];  [10];  [1];  [9]; ORCiD logo [1]; ORCiD logo [5];  [1];  [11] more »;  [1];  [1];  [1];  [11];  [11];  [1];  [1];  [9]; ORCiD logo [1]; ORCiD logo [11];  [1];  [12];  [1];  [13]; ORCiD logo [5];  [11];  [14];  [15];  [16];  [1] « less
  1. Uppsala Univ., Uppsala (Sweden)
  2. KTH Royal Institute of Technology, Stockholm (Sweden)
  3. Univ. of Oxford (United Kingdom)
  4. Uppsala Univ., Uppsala (Sweden); Czech Academy of Sciences, Prague (Czech Republic); Chalmers Univ. of Technology, Gothenburg (Sweden)
  5. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  6. Uppsala Univ., Uppsala (Sweden); European XFEL GmbH, Schenefeld (Germany)
  7. Chalmers Univ. of Technology, Gothenburg (Sweden)
  8. SLAC National Accelerator Lab., Stanford, CA (United States); Technische Univ. Berlin, Berlin (Germany); Argonne National Lab. (ANL), Lemont, IL (United States)
  9. SLAC National Accelerator Lab., Stanford, CA (United States)
  10. SLAC National Accelerator Lab., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  11. Technische Univ. Berlin, Berlin (Germany)
  12. SLAC National Accelerator Lab., Stanford, CA (United States); Brookhaven National Lab. (BNL), Upton, NY (United States)
  13. Research Institute for Solid State Physics and Optics, Budapest (Hungary)
  14. SLAC National Accelerator Lab., Stanford, CA (United States); Argonne National Lab. (ANL), Lemont, IL (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States); Northwestern Univ., Evanston, IL (United States)
  15. Uppsala Univ., Uppsala (Sweden); Czech Academy of Science, Prague (Czech Republic)
  16. SLAC National Accelerator Lab., Stanford, CA (United States); Technische Univ. Berline, Berlin (Germany); SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1468673
Alternate Identifier(s):
OSTI ID: 1475539; OSTI ID: 1477402; OSTI ID: 1480964
Report Number(s):
BNL-209371-2018-JAAM
Journal ID: ISSN 2052-2525; IUCRAJ; PII: S2052252518010047
Grant/Contract Number:  
K115504; AC02-76SF00515; AC02-05CH11231; SC0012704
Resource Type:
Published Article
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 5; Journal Issue: 5; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
47 OTHER INSTRUMENTATION; XFELs; Melbournevirus; coherent diffractive imaging; LCLS; image reconstruction; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Lundholm, Ida V., Sellberg, Jonas A., Ekeberg, Tomas, Hantke, Max F., Okamoto, Kenta, van der Schot, Gijs, Andreasson, Jakob, Barty, Anton, Bielecki, Johan, Bruza, Petr, Bucher, Max, Carron, Sebastian, Daurer, Benedikt J., Ferguson, Ken, Hasse, Dirk, Krzywinski, Jacek, Larsson, Daniel S. D., Morgan, Andrew, Mühlig, Kerstin, Müller, Maria, Nettelblad, Carl, Pietrini, Alberto, Reddy, Hemanth K. N., Rupp, Daniela, Sauppe, Mario, Seibert, Marvin, Svenda, Martin, Swiggers, Michelle, Timneanu, Nicusor, Ulmer, Anatoli, Westphal, Daniel, Williams, Garth, Zani, Alessandro, Faigel, Gyula, Chapman, Henry N., Möller, Thomas, Bostedt, Christoph, Hajdu, Janos, Gorkhover, Tais, and Maia, Filipe R. N. C. Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. United States: N. p., 2018. Web. doi:10.1107/s2052252518010047.
Lundholm, Ida V., Sellberg, Jonas A., Ekeberg, Tomas, Hantke, Max F., Okamoto, Kenta, van der Schot, Gijs, Andreasson, Jakob, Barty, Anton, Bielecki, Johan, Bruza, Petr, Bucher, Max, Carron, Sebastian, Daurer, Benedikt J., Ferguson, Ken, Hasse, Dirk, Krzywinski, Jacek, Larsson, Daniel S. D., Morgan, Andrew, Mühlig, Kerstin, Müller, Maria, Nettelblad, Carl, Pietrini, Alberto, Reddy, Hemanth K. N., Rupp, Daniela, Sauppe, Mario, Seibert, Marvin, Svenda, Martin, Swiggers, Michelle, Timneanu, Nicusor, Ulmer, Anatoli, Westphal, Daniel, Williams, Garth, Zani, Alessandro, Faigel, Gyula, Chapman, Henry N., Möller, Thomas, Bostedt, Christoph, Hajdu, Janos, Gorkhover, Tais, & Maia, Filipe R. N. C. Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. United States. doi:10.1107/s2052252518010047.
Lundholm, Ida V., Sellberg, Jonas A., Ekeberg, Tomas, Hantke, Max F., Okamoto, Kenta, van der Schot, Gijs, Andreasson, Jakob, Barty, Anton, Bielecki, Johan, Bruza, Petr, Bucher, Max, Carron, Sebastian, Daurer, Benedikt J., Ferguson, Ken, Hasse, Dirk, Krzywinski, Jacek, Larsson, Daniel S. D., Morgan, Andrew, Mühlig, Kerstin, Müller, Maria, Nettelblad, Carl, Pietrini, Alberto, Reddy, Hemanth K. N., Rupp, Daniela, Sauppe, Mario, Seibert, Marvin, Svenda, Martin, Swiggers, Michelle, Timneanu, Nicusor, Ulmer, Anatoli, Westphal, Daniel, Williams, Garth, Zani, Alessandro, Faigel, Gyula, Chapman, Henry N., Möller, Thomas, Bostedt, Christoph, Hajdu, Janos, Gorkhover, Tais, and Maia, Filipe R. N. C. Sat . "Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging". United States. doi:10.1107/s2052252518010047.
@article{osti_1468673,
title = {Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging},
author = {Lundholm, Ida V. and Sellberg, Jonas A. and Ekeberg, Tomas and Hantke, Max F. and Okamoto, Kenta and van der Schot, Gijs and Andreasson, Jakob and Barty, Anton and Bielecki, Johan and Bruza, Petr and Bucher, Max and Carron, Sebastian and Daurer, Benedikt J. and Ferguson, Ken and Hasse, Dirk and Krzywinski, Jacek and Larsson, Daniel S. D. and Morgan, Andrew and Mühlig, Kerstin and Müller, Maria and Nettelblad, Carl and Pietrini, Alberto and Reddy, Hemanth K. N. and Rupp, Daniela and Sauppe, Mario and Seibert, Marvin and Svenda, Martin and Swiggers, Michelle and Timneanu, Nicusor and Ulmer, Anatoli and Westphal, Daniel and Williams, Garth and Zani, Alessandro and Faigel, Gyula and Chapman, Henry N. and Möller, Thomas and Bostedt, Christoph and Hajdu, Janos and Gorkhover, Tais and Maia, Filipe R. N. C.},
abstractNote = {Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. In conclusion, the anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.},
doi = {10.1107/s2052252518010047},
journal = {IUCrJ},
number = 5,
volume = 5,
place = {United States},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1107/s2052252518010047

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Cited by: 5 works
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Figures / Tables:

Fig. 1 Fig. 1: Nine high-quality diffraction patterns of MelV from the experiment. Gray areas represent masked out regions.

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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.