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Title: High-resolution ab initio three-dimensional x-ray diffraction microscopy

Abstract

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [2];  [3];  [3];  [3];  [4];  [4];  [4]
+ Show Author Affiliations
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Arizona State Univ., Tempe, AZ (United States) Dept. Physics and Astronomy
  4. Stony Brook Univ., NY (United States) Dept. Physics and Astronomy
Publication Date:
Research Org.:
Stony Brook Univ., NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1164141
Grant/Contract Number:  
FG02-04ER46128
Resource Type:
Accepted Manuscript
Journal Name:
Journal of the Optical Society of America. A, Optics, Image Science, and Vision
Additional Journal Information:
Journal Volume: 23; Journal Issue: 5; Journal ID: ISSN 1084-7529
Publisher:
Optical Society of America (OSA)
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; 77 NANOSCIENCE AND NANOTECHNOLOGY

Citation Formats

Chapman, Henry N., Barty, Anton, Marchesini, Stefano, Noy, Aleksandr, Hau-Riege, Stefan P., Cui, Congwu, Howells, Malcolm R., Rosen, Rachel, He, Haifeng, Spence, John C. H., Weierstall, Uwe, Beetz, Tobias, Jacobsen, Chris, and Shapiro, David. High-resolution ab initio three-dimensional x-ray diffraction microscopy. United States: N. p., 2006. Web. doi:10.1364/JOSAA.23.001179.
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Chapman, Henry N., Barty, Anton, Marchesini, Stefano, Noy, Aleksandr, Hau-Riege, Stefan P., Cui, Congwu, Howells, Malcolm R., Rosen, Rachel, He, Haifeng, Spence, John C. H., Weierstall, Uwe, Beetz, Tobias, Jacobsen, Chris, & Shapiro, David. High-resolution ab initio three-dimensional x-ray diffraction microscopy. United States. https://doi.org/10.1364/JOSAA.23.001179
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Chapman, Henry N., Barty, Anton, Marchesini, Stefano, Noy, Aleksandr, Hau-Riege, Stefan P., Cui, Congwu, Howells, Malcolm R., Rosen, Rachel, He, Haifeng, Spence, John C. H., Weierstall, Uwe, Beetz, Tobias, Jacobsen, Chris, and Shapiro, David. Sun . "High-resolution ab initio three-dimensional x-ray diffraction microscopy". United States. https://doi.org/10.1364/JOSAA.23.001179. https://www.osti.gov/servlets/purl/1164141.
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@article{osti_1164141,
title = {High-resolution ab initio three-dimensional x-ray diffraction microscopy},
author = {Chapman, Henry N. and Barty, Anton and Marchesini, Stefano and Noy, Aleksandr and Hau-Riege, Stefan P. and Cui, Congwu and Howells, Malcolm R. and Rosen, Rachel and He, Haifeng and Spence, John C. H. and Weierstall, Uwe and Beetz, Tobias and Jacobsen, Chris and Shapiro, David},
abstractNote = {Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.},
doi = {10.1364/JOSAA.23.001179},
journal = {Journal of the Optical Society of America. A, Optics, Image Science, and Vision},
number = 5,
volume = 23,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
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    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
    text, January 2016

    • Ekeberg, Tomas; Svenda, Martin; Seibert, M. Marvin
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2016-05742

    Computed stereo lensless X-ray imaging
    text, January 2019

    Imaging outside the box: Resolution enhancement in X-ray coherent diffraction imaging by extrapolation of diffraction patterns
    text, January 2015

    • Latychevskaia, Tatiana; Chushkin, Yuriy; Zontone, Federico
    • American Institute of Physics
    • DOI: 10.5167/uzh-119709

    Imaging Catalysts at Work: A Hierarchical Approach from the Macro- to the Meso- and Nano-scale
    journal, November 2012

    • Grunwaldt, Jan-Dierk; Wagner, Jakob B.; Dunin-Borkowski, Rafal E.
    • ChemCatChem, Vol. 5, Issue 1
    • DOI: 10.1002/cctc.201200356

    Electron Nanodiffraction
    book, January 2019

    Three-dimensional structure determination from a single view
    journal, December 2009

    • Raines, Kevin S.; Salha, Sara; Sandberg, Richard L.
    • Nature, Vol. 463, Issue 7278
    • DOI: 10.1038/nature08705

    Ultrafast single-shot diffraction imaging of nanoscale dynamics
    journal, June 2008

    Room temperature giant magnetostriction in single-crystal nickel nanowires
    journal, October 2019

    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
    journal, August 2016

    • Ekeberg, Tomas; Svenda, Martin; Seibert, M. Marvin
    • Scientific Data, Vol. 3, Issue 1
    • DOI: 10.1038/sdata.2016.60

    Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae
    journal, February 2015

    • Deng, Junjing; Vine, David J.; Chen, Si
    • Proceedings of the National Academy of Sciences, Vol. 112, Issue 8
    • DOI: 10.1073/pnas.1413003112

    Aerosol Imaging with a Soft X-Ray Free Electron Laser
    journal, February 2010

    • Bogan, Michael J.; Boutet, Sébastien; Chapman, Henry N.
    • Aerosol Science and Technology, Vol. 44, Issue 3
    • DOI: 10.1080/02786820903485800

    The history and future of X-ray microscopy
    journal, September 2009

    Bragg projection ptychography on niobium phase domains
    text, January 2017

    • Burdet, Nicolas; Shi, Xiaowen; Clark, Jesse N.
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2018-00378

    Single-particle imaging without symmetry constraints at an X-ray free-electron laser
    text, January 2018

    • Rose, Max; Bobkov, Sergey; Ayyer, Kartik
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2018-03083

    X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution
    text, January 2014

    Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
    text, January 2018

    Practical algorithms for simulation and reconstruction of digital in-line holograms
    text, January 2015

    • Latychevskaia, Tatiana; Fink, Hans-Werner
    • Optical Society of America
    • DOI: 10.5167/uzh-109953

    Time-domain ptychography
    text, January 2015

    • Rohwer, Erich; Neethling, Pieter; Feurer, Thomas
    • American Physical Society
    • DOI: 10.7892/boris.74987

    Nanotomography in the Chemical, Biological and Materials Sciences
    journal, December 2007

    • Midgley, Paul A.; Ward, Edmund P. W.; Hungria, Ana B.
    • ChemInform, Vol. 38, Issue 49
    • DOI: 10.1002/chin.200749279

    Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution
    journal, May 2018

    • Nakano, Miki; Miyashita, Osamu; Jonic, Slavica
    • Journal of Synchrotron Radiation, Vol. 25, Issue 4
    • DOI: 10.1107/s1600577518005568

    Beyond crystallography: Diffractive imaging using coherent x-ray light sources
    journal, April 2015

    Versatility of a hard X-ray Kirkpatrick-Baez focus characterized by ptychography
    text, January 2013

    • Giewekemeyer, K.; Wilke, R. N.; Osterhoff, M.
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/phppubdb-26500

    A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser
    text, January 2016

    • Yoon, Chun Hong; Yurkov, Mikhail; Schneidmiller, Evgeny Alexanrdovich
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2016-01805

    Real-time coherent diffraction inversion using deep generative networks
    journal, November 2018

    • Cherukara, Mathew J.; Nashed, Youssef S. G.; Harder, Ross J.
    • Scientific Reports, Vol. 8, Issue 1
    • DOI: 10.1038/s41598-018-34525-1

    Design of a liquid cell toward three-dimensional imaging of unidirectionally-aligned particles in solution using X-ray free-electron lasers
    journal, January 2020

    • Suzuki, Akihiro; Kimura, Takashi; Yang, Ying
    • Physical Chemistry Chemical Physics, Vol. 22, Issue 5
    • DOI: 10.1039/c9cp03658j

    Towards a quantitative determination of strain in Bragg Coherent X-ray Diffraction Imaging: artefacts and sign convention in reconstructions
    text, January 2019

    • Carnis, Jerome; Gao, Lu; Labat, Stéphane
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-00283

    Open data set of live cyanobacterial cells imaged using an X-ray laser
    journal, August 2016

    • van der Schot, Gijs; Svenda, Martin; Maia, Filipe R. N. C.
    • Scientific Data, Vol. 3, Issue 1
    • DOI: 10.1038/sdata.2016.58

    Structure Determination by Continuous Diffraction from Imperfect Crystals
    text, January 2018

    • Ayyer, Kartik; Yefanov, Oleksandr; Chapman, Henry N.
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2019-00073

    High Speed and High Resolution Table-Top Nanoscale Imaging
    text, January 2016

    Sparse recovery of undersampled intensity patterns for coherent diffraction imaging at high X-ray energies
    text, January 2017

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