IUCrJ (Sep 2018)
Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
- Ida V. Lundholm,
- Jonas A. Sellberg,
- Tomas Ekeberg,
- Max F. Hantke,
- Kenta Okamoto,
- Gijs van der Schot,
- Jakob Andreasson,
- Anton Barty,
- Johan Bielecki,
- Petr Bruza,
- Max Bucher,
- Sebastian Carron,
- Benedikt J. Daurer,
- Ken Ferguson,
- Dirk Hasse,
- Jacek Krzywinski,
- Daniel S. D. Larsson,
- Andrew Morgan,
- Kerstin Mühlig,
- Maria Müller,
- Carl Nettelblad,
- Alberto Pietrini,
- Hemanth K. N. Reddy,
- Daniela Rupp,
- Mario Sauppe,
- Marvin Seibert,
- Martin Svenda,
- Michelle Swiggers,
- Nicusor Timneanu,
- Anatoli Ulmer,
- Daniel Westphal,
- Garth Williams,
- Alessandro Zani,
- Gyula Faigel,
- Henry N. Chapman,
- Thomas Möller,
- Christoph Bostedt,
- Janos Hajdu,
- Tais Gorkhover,
- Filipe R. N. C. Maia
Affiliations
- Ida V. Lundholm
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Jonas A. Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Max F. Hantke
- University of Oxford, UK
- Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Petr Bruza
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
- Max Bucher
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Sebastian Carron
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Benedikt J. Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Ken Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Jacek Krzywinski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Daniel S. D. Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Andrew Morgan
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Kerstin Mühlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Maria Müller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Hemanth K. N. Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Daniela Rupp
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Mario Sauppe
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Michelle Swiggers
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Anatoli Ulmer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Garth Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Alessandro Zani
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Gyula Faigel
- Research Institute for Solid State Physics and Optics, 1525 Budapest, Hungary
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Thomas Möller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
- Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Tais Gorkhover
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA
- Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- DOI
- https://doi.org/10.1107/S2052252518010047
- Journal volume & issue
-
Vol. 5,
no. 5
pp. 531 – 541
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 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.
Keywords
