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

Journal Article · · IUCrJ
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  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)
+ Show Author Affiliations

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.

Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Organization:
USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
K115504; AC02-76SF00515; AC02-05CH11231; SC0012704
OSTI ID:
1468673
Alternate ID(s):
OSTI ID: 1475539; OSTI ID: 1477402; OSTI ID: 1480964
Report Number(s):
BNL-209371-2018-JAAM; IUCRAJ; PII: S2052252518010047
Journal Information:
IUCrJ, Vol. 5, Issue 5; ISSN 2052-2525
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 34 works
Citation information provided by
Web of Science

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Cited By (9)

The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation journal April 2019
Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
  • Lundholm, Ida
  • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Uppsala University, CFEL DESY, University of Hamburg, SLAC National Accelerator Laboratory, Arizona State University, Lawrence Berkeley National Laboratory https://doi.org/10.11577/1638360
dataset January 2020
Coherent diffractive imaging of microtubules using an X-ray laser text January 2019
Megahertz single-particle imaging at the European XFEL text January 2020
Megahertz single-particle imaging at the European XFEL journal May 2020
The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation text January 2019
Experimental 3D coherent diffractive imaging from photon-sparse random projections text January 2019
Coherent diffractive imaging of microtubules using an X-ray laser journal June 2019
Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
  • Lundholm, Ida
  • Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Uppsala University, CFEL DESY, University of Hamburg, SLAC National Accelerator Laboratory, Arizona State University, Lawrence Berkeley National Laboratory https://doi.org/10.11577/1638360
dataset January 2020

Figures / Tables (10)

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Fig. 7(p. 23)figure Fig. 7
Fig. 8(p. 25)figure Fig. 8
Fig. 9(p. 27)figure Fig. 9
Fig. 10(p. 29)figure Fig. 10

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