Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
Journal article, 2018
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. 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.
Melbournevirus
image reconstruction
coherent diffractive imaging
LCLS
XFELs
Author
Ida V. Lundholm
Uppsala University
Jonas A. Sellberg
Royal Institute of Technology (KTH)
Tomas Ekeberg
Uppsala University
Max F. Hantke
University of Oxford
Kenta Okamoto
Uppsala University
Gijs van der Schot
Uppsala University
Jakob Andreasson
Chalmers, Physics, Condensed Matter Physics
Anton Barty
Deutsches Elektronen-Synchrotron (DESY)
Johan Bielecki
Uppsala University
European XFEL
Petr Bruza
Chalmers, Physics, Condensed Matter Physics
Max Bucher
Argonne National Laboratory
Technische Universität Berlin
Stanford University
Sebastian Carron
Stanford University
Benedikt J. Daurer
Uppsala University
Ken Ferguson
Stanford University
PULSE Inst, 2575 Sand Hill Rd
Dirk Hasse
Uppsala University
Jacek Krzywinski
Stanford University
Daniel S. D. Larsson
Uppsala University
Andrew Morgan
Deutsches Elektronen-Synchrotron (DESY)
Kerstin Muhlig
Uppsala University
Maria Mueller
Technische Universität Berlin
Carl Nettelblad
Uppsala University
Alberto Pietrini
Uppsala University
Hemanth K. N. Reddy
Uppsala University
Daniela Rupp
Technische Universität Berlin
Mario Sauppe
Technische Universität Berlin
Marvin Seibert
Uppsala University
Martin Svenda
Uppsala University
Michelle Swiggers
Stanford University
Nicusor Timneanu
Uppsala University
Anatoli Ulmer
Technische Universität Berlin
Daniel Westphal
Uppsala University
Garth Williams
Brookhaven National Laboratory
Stanford University
Alessandro Zani
Uppsala University
Gyula Faigel
Hungarian Academy of Sciences
Henry N. Chapman
Deutsches Elektronen-Synchrotron (DESY)
Thomas Moeller
Technische Universität Berlin
Christoph Bostedt
Northwestern University
PULSE Inst, 2575 Sand Hill Rd
Stanford University
Argonne National Laboratory
Janos Hajdu
Uppsala University
Czech Academy of Sciences
Tais Gorkhover
PULSE Inst, 2575 Sand Hill Rd
Stanford University
Technische Universität Berlin
Filipe R. N. C. Maia
Lawrence Berkeley National Laboratory
Uppsala University
IUCrJ
2052-2525 (eISSN)
Vol. 5 531-541Subject Categories
Accelerator Physics and Instrumentation
Atom and Molecular Physics and Optics
Other Physics Topics
DOI
10.1107/S2052252518010047
PubMed
30224956