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:
-
- Stony Brook Univ., Stony Brook, NY (United States)
- 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. doi: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 = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}
Web of Science
Works referenced in this record:
Potential operating region for ultrasoft x-ray microscopy of biological materials
journal, June 1977
- Sayre, D.; Kirz, J.; Feder, R.
- Science, Vol. 196, Issue 4296
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
X-ray microscopy with synchrotron radiation
journal, January 1976
- Niemann, B.; Rudolph, D.; Schmahl, G.
- Applied Optics, Vol. 15, Issue 8
Zone-plate X-ray microscopy
journal, August 1980
- Schmahl, G.; Rudolph, D.; Niemann, B.
- Quarterly Reviews of Biophysics, Vol. 13, Issue 3
Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast
journal, November 1998
- Schneider, Gerd
- Ultramicroscopy, Vol. 75, Issue 2
Computed tomography of cryogenic biological specimens based on X-ray microscopic images
journal, August 2000
- Weiß, D.; Schneider, G.; Niemann, B.
- Ultramicroscopy, Vol. 84, Issue 3-4
Soft X-ray microscopy with a cryo scanning transmission X-ray microscope: I. Instrumentation, imaging and spectroscopy
journal, January 2000
- Maser,
- Journal of Microscopy, Vol. 197, Issue 1
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
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
Reconstruction of an object from the modulus of its Fourier transform
journal, January 1978
- Fienup, J. R.
- Optics Letters, Vol. 3, Issue 1, p. 27-29
Transmission microscopy of unmodified biological materials. Comparative radiation dosages with electrons and ultrasoft X-ray photons
journal, January 1976
- Sayre, D.; Kirz, J.; Feder, R.
- Ultramicroscopy, Vol. 2
On estimating signal-to-noise ratio using the sample correlation coefficient (Corresp.)
journal, January 1974
- Bershad, N.; Rockmore, A.
- IEEE Transactions on Information Theory, Vol. 20, Issue 1
Signal-to-noise ratio of electron micrographs obtained by cross correlation
journal, July 1975
- Frank, J.; Al-Ali, L.
- Nature, Vol. 256, Issue 5516
Spiegelsysteme streifenden Einfalls als abbildende Optiken für Röntgenstrahlen
journal, January 1952
- Wolter, Hans
- Annalen der Physik, Vol. 445, Issue 1-2
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
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
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
Computed Tomography of Cryogenic Cells
journal, February 2002
- Schneider, G.; Anderson, E.; Vogt, S.
- Surface Review and Letters, Vol. 09, Issue 01
Phase zone plates for x rays and the extreme uv
journal, January 1974
- Kirz, Janos
- Journal of the Optical Society of America, Vol. 64, Issue 3
Phase retrieval by iterated projections
journal, January 2003
- Elser, Veit
- Journal of the Optical Society of America A, Vol. 20, Issue 1
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
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
A Unified Approach to the Performance of Photographic Film, Television Pickup Tubes, and the Human Eye<!--<xref ref-type="other" rid="fn1-10.5594_J12772">*</xref>-->
journal, October 1946
- Rose, Albert
- Journal of the Society of Motion Picture Engineers, Vol. 47, Issue 4
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
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
High-Resolution Scanning X-ray Diffraction Microscopy
journal, July 2008
- Thibault, P.; Dierolf, M.; Menzel, A.
- Science, Vol. 321, Issue 5887
Signal-to-noise ratio of electron micrographs obtained by cross correlation
book, April 2018
- Frank, J.; Al-Ali, L.
- Series in Structural Biology
An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy
text, January 2005
- Howells, M. R.; Beetz, T.; Chapman, H. N.
- arXiv
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
Lensless imaging using broadband X-ray sources
journal, June 2011
- Abbey, Brian; Whitehead, Lachlan W.; Quiney, Harry M.
- Nature Photonics, Vol. 5, Issue 7
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
Identifying Defects with Guided Algorithms in Bragg Coherent Diffractive Imaging
journal, August 2017
- Ulvestad, A.; Nashed, Y.; Beutier, G.
- Scientific Reports, Vol. 7, Issue 1
Few-photon computed x-ray imaging
journal, December 2018
- Zhu, Zheyuan; Pang, Shuo
- Applied Physics Letters, Vol. 113, Issue 23
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
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
Dose requirements for resolving a given feature in an object by coherent x-ray diffraction imaging
journal, March 2010
- Schropp, Andreas; Schroer, Christian G.
- New Journal of Physics, Vol. 12, Issue 3
A comparison of absorption and phase contrast for X-ray imaging of biological cells
journal, August 2018
- Nave, Colin
- Journal of Synchrotron Radiation, Vol. 25, Issue 5
A comparison of absorption and phase contrast for X-ray imaging of biological cells. Erratum
journal, February 2019
- Nave, Colin
- Journal of Synchrotron Radiation, Vol. 26, Issue 2
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
Beyond crystallography: Diffractive imaging using coherent x-ray light sources
journal, April 2015
- Miao, J.; Ishikawa, T.; Robinson, I. K.
- Science, Vol. 348, Issue 6234
Quantitative ptychographic bio-imaging in the water window
text, January 2018
- Rose, Max; Senkbeil, Tobias; Von Gundlach, Andreas
- Deutsches Elektronen-Synchrotron, DESY, Hamburg
Ab initio nonrigid X-ray nanotomography
text, January 2019
- Odstrcil, Michal; Holler, Mirko; Raabe, Jörg
- Deutsches Elektronen-Synchrotron, DESY, Hamburg
Ab initio nonrigid X-ray nanotomography.
journalarticle, January 2019
- Odstrcil, Michal; Holler, Mirko; Raabe, Jörg
- Springer Science and Business Media LLC
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
X-ray microscopy
journal, July 1965
- Cosslett, V. E.
- Reports on Progress in Physics, Vol. 28, Issue 1