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Title: Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy

Abstract

Using a signal-to-noise ratio estimation based on correlations between multiple simulated images, we compare the dose efficiency of two soft x-ray imaging systems: incoherent brightfield imaging using zone plate optics in a transmission x-ray microscope (TXM), and x-ray diffraction microscopy (XDM) where an image is reconstructed from the far-field coherent diffraction pattern. In XDM one must computationally phase weak diffraction signals; in TXM one suffers signal losses due to the finite numerical aperture and efficiency of the optics. In simulations with objects representing isolated cells such as yeast, we find that XDM has the potential for delivering equivalent resolution images using fewer photons. As a result, this can be an important advantage for studying radiation-sensitive biological and soft matter specimens.

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [1];  [1]
  1. Stony Brook Univ., Stony Brook, NY (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Stony Brook Univ., NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1164146
Grant/Contract Number:  
FG02-04ER46128
Resource Type:
Accepted Manuscript
Journal Name:
Optics Express
Additional Journal Information:
Journal Volume: 17; Journal Issue: 16; Journal ID: ISSN 1094-4087
Publisher:
Optical Society of America (OSA)
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; X-ray imaging; diffraction; image reconstruction techniques; noise in imaging systems

Citation Formats

Huang, Xiaojing, Miao, Huijie, Steinbrener, Jan, Nelson, Johanna, Shapiro, David, Stewart, Andrew, Turner, Joshua, and Jacobsen, Chris. Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy. United States: N. p., 2009. Web. https://doi.org/10.1364/OE.17.013541.
Huang, Xiaojing, Miao, Huijie, Steinbrener, Jan, Nelson, Johanna, Shapiro, David, Stewart, Andrew, Turner, Joshua, & Jacobsen, Chris. Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy. United States. https://doi.org/10.1364/OE.17.013541
Huang, Xiaojing, Miao, Huijie, Steinbrener, Jan, Nelson, Johanna, Shapiro, David, Stewart, Andrew, Turner, Joshua, and Jacobsen, Chris. Thu . "Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy". United States. https://doi.org/10.1364/OE.17.013541. https://www.osti.gov/servlets/purl/1164146.
@article{osti_1164146,
title = {Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy},
author = {Huang, Xiaojing and Miao, Huijie and Steinbrener, Jan and Nelson, Johanna and Shapiro, David and Stewart, Andrew and Turner, Joshua and Jacobsen, Chris},
abstractNote = {Using a signal-to-noise ratio estimation based on correlations between multiple simulated images, we compare the dose efficiency of two soft x-ray imaging systems: incoherent brightfield imaging using zone plate optics in a transmission x-ray microscope (TXM), and x-ray diffraction microscopy (XDM) where an image is reconstructed from the far-field coherent diffraction pattern. In XDM one must computationally phase weak diffraction signals; in TXM one suffers signal losses due to the finite numerical aperture and efficiency of the optics. In simulations with objects representing isolated cells such as yeast, we find that XDM has the potential for delivering equivalent resolution images using fewer photons. As a result, this can be an important advantage for studying radiation-sensitive biological and soft matter specimens.},
doi = {10.1364/OE.17.013541},
journal = {Optics Express},
number = 16,
volume = 17,
place = {United States},
year = {2009},
month = {1}
}

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Cited by: 33 works
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Works referenced in this record:

Potential operating region for ultrasoft x-ray microscopy of biological materials
journal, June 1977


Soft X-ray microscopes and their biological applications
journal, February 1995

  • Kirz, Janos; Jacobsen, Chris; Howells, Malcolm
  • Quarterly Reviews of Biophysics, Vol. 28, Issue 1
  • DOI: 10.1017/S0033583500003139

X-ray microscopy with synchrotron radiation
journal, January 1976


Zone-plate X-ray microscopy
journal, August 1980


Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast
journal, November 1998


Computed tomography of cryogenic biological specimens based on X-ray microscopic images
journal, August 2000


X-ray Tomography Generates 3-D Reconstructions of the Yeast, Saccharomyces cerevisiae , at 60-nm Resolution
journal, March 2004

  • Larabell, Carolyn A.; Le Gros, Mark A.
  • Molecular Biology of the Cell, Vol. 15, Issue 3
  • DOI: 10.1091/mbc.e03-07-0522

Interferometer-controlled scanning transmission X-ray microscopes at the Advanced Light Source
journal, February 2003

  • Kilcoyne, A. L. D.; Tyliszczak, T.; Steele, W. F.
  • Journal of Synchrotron Radiation, Vol. 10, Issue 2
  • DOI: 10.1107/S0909049502017739

Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens
journal, July 1999

  • Miao, Jianwei; Charalambous, Pambos; Kirz, Janos
  • Nature, Vol. 400, Issue 6742
  • DOI: 10.1038/22498

Reconstruction of an object from the modulus of its Fourier transform
journal, January 1978


On estimating signal-to-noise ratio using the sample correlation coefficient (Corresp.)
journal, January 1974


Signal-to-noise ratio of electron micrographs obtained by cross correlation
journal, July 1975


Spiegelsysteme streifenden Einfalls als abbildende Optiken für Röntgenstrahlen
journal, January 1952


X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92
journal, July 1993

  • Henke, B. L.; Gullikson, E. M.; Davis, J. C.
  • Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342
  • DOI: 10.1006/adnd.1993.1013

Wavelength choice for soft x-ray laser holography of biological samples
journal, January 1989

  • London, Richard A.; Rosen, Mordecai D.; Trebes, James E.
  • Applied Optics, Vol. 28, Issue 16
  • DOI: 10.1364/AO.28.003397

Reconstruction of a yeast cell from X-ray diffraction data
journal, June 2006

  • Thibault, Pierre; Elser, Veit; Jacobsen, Chris
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 62, Issue 4
  • DOI: 10.1107/S0108767306016515

Computed Tomography of Cryogenic Cells
journal, February 2002


Phase zone plates for x rays and the extreme uv
journal, January 1974


Phase retrieval by iterated projections
journal, January 2003


An assessment of the resolution limitation due to radiation-damage in X-ray diffraction microscopy
journal, March 2009

  • Howells, M. R.; Beetz, T.; Chapman, H. N.
  • Journal of Electron Spectroscopy and Related Phenomena, Vol. 170, Issue 1-3
  • DOI: 10.1016/j.elspec.2008.10.008

Diffractive imaging of nonperiodic materials with future coherent X-ray sources
journal, August 2004

  • Shen, Qun; Bazarov, Ivan; Thibault, Pierre
  • Journal of Synchrotron Radiation, Vol. 11, Issue 5
  • DOI: 10.1107/S0909049504016772

Biological imaging by soft x-ray diffraction microscopy
journal, October 2005

  • Shapiro, D.; Thibault, P.; Beetz, T.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 43
  • DOI: 10.1073/pnas.0503305102

High-resolution ab initio three-dimensional x-ray diffraction microscopy
journal, January 2006

  • Chapman, Henry N.; Barty, Anton; Marchesini, Stefano
  • Journal of the Optical Society of America A, Vol. 23, Issue 5
  • DOI: 10.1364/JOSAA.23.001179

High-Resolution Scanning X-ray Diffraction Microscopy
journal, July 2008


    Works referencing / citing this record:

    Imaging single cells in a beam of live cyanobacteria with an X-ray laser
    journal, February 2015

    • van der Schot, Gijs; Svenda, Martin; Maia, Filipe R. N. C.
    • Nature Communications, Vol. 6, Issue 1
    • DOI: 10.1038/ncomms6704

    Lensless imaging using broadband X-ray sources
    journal, June 2011


    Subwavelength coherent imaging of periodic samples using a 13.5 nm tabletop high-harmonic light source
    journal, March 2017

    • Gardner, Dennis F.; Tanksalvala, Michael; Shanblatt, Elisabeth R.
    • Nature Photonics, Vol. 11, Issue 4
    • DOI: 10.1038/nphoton.2017.33

    Identifying Defects with Guided Algorithms in Bragg Coherent Diffractive Imaging
    journal, August 2017


    Few-photon computed x-ray imaging
    journal, December 2018

    • Zhu, Zheyuan; Pang, Shuo
    • Applied Physics Letters, Vol. 113, Issue 23
    • DOI: 10.1063/1.5050890

    High-resolution x-ray diffraction microscopy of specifically labeled yeast cells
    journal, April 2010

    • Nelson, J.; Huang, X.; Steinbrener, J.
    • Proceedings of the National Academy of Sciences, Vol. 107, Issue 16
    • DOI: 10.1073/pnas.0910874107

    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

    Dose requirements for resolving a given feature in an object by coherent x-ray diffraction imaging
    journal, March 2010


    Soft X-Ray Diffraction Microscopy of a Frozen Hydrated Yeast Cell
    journal, November 2009


    Hollow Electron Ptychographic Diffractive Imaging
    journal, October 2018


    The fluence–resolution relationship in holographic and coherent diffractive imaging
    journal, March 2017


    A comparison of absorption and phase contrast for X-ray imaging of biological cells
    journal, August 2018


    A comparison of absorption and phase contrast for X-ray imaging of biological cells. Erratum
    journal, February 2019


    A Monte Carlo ray-tracing simulation of coherent X-ray diffractive imaging
    journal, January 2020

    • Fevola, Giovanni; Bergbäck Knudsen, Erik; Ramos, Tiago
    • Journal of Synchrotron Radiation, Vol. 27, Issue 1
    • DOI: 10.1107/s1600577519014425

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


    Incorrect support and missing center tolerances of phasing algorithms
    journal, January 2010

    • Huang, Xiaojing; Nelson, Johanna; Steinbrener, Jan
    • Optics Express, Vol. 18, Issue 25
    • DOI: 10.1364/oe.18.026441

    Ultrahigh 22 nm resolution coherent diffractive imaging using a desktop 13 nm high harmonic source
    journal, January 2011

    • Seaberg, Matthew D.; Adams, Daniel E.; Townsend, Ethan L.
    • Optics Express, Vol. 19, Issue 23
    • DOI: 10.1364/oe.19.022470

    Three-dimensional structure of a single colloidal crystal grain studied by coherent x-ray diffraction
    journal, January 2012

    • Gulden, J.; Yefanov, O. M.; Mancuso, A. P.
    • Optics Express, Vol. 20, Issue 4
    • DOI: 10.1364/oe.20.004039

    Optimization of overlap uniformness for ptychography
    journal, January 2014

    • Huang, Xiaojing; Yan, Hanfei; Harder, Ross
    • Optics Express, Vol. 22, Issue 10
    • DOI: 10.1364/oe.22.012634

    Multislice does it all—calculating the performance of nanofocusing X-ray optics
    journal, January 2017

    • Li, Kenan; Wojcik, Michael; Jacobsen, Chris
    • Optics Express, Vol. 25, Issue 3
    • DOI: 10.1364/oe.25.001831

    3D x-ray imaging of continuous objects beyond the depth of focus limit
    journal, January 2018


    Quantitative ptychographic bio-imaging in the water window
    text, January 2018

    • Rose, Max; Senkbeil, Tobias; Von Gundlach, Andreas
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2018-00468

    Ab initio nonrigid X-ray nanotomography
    text, January 2019

    • Odstrcil, Michal; Holler, Mirko; Raabe, Jörg
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-00848

    Quantitative ptychographic bio-imaging in the water window
    journal, January 2018

    • Rose, Max; Senkbeil, Tobias; von Gundlach, Andreas R.
    • Optics Express, Vol. 26, Issue 2
    • DOI: 10.1364/oe.26.001237

    X-ray microscopy
    journal, February 2017