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Title: Reconstruction of a yeast cell from x-ray diffraction data

Abstract

We provide details of the algorithm used for the reconstruction of yeast cell images in the recent demonstration of diffraction microscopy by Shapiro, Thibault, Beetz, Elser, Howells, Jacobsen, Kirz, Lima, Miao, Nieman & Sayre. Two refinements of the iterative constraint-based scheme are developed to address the current experimental realities of this imaging technique, which include missing central data and noise. A constrained power operator is defined whose eigenmodes allow the identification of a small number of degrees of freedom in the reconstruction that are negligibly constrained as a result of the missing data. To achieve reproducibility in the algorithm's output, a special intervention is required for these modes. Weak incompatibility of the constraints caused by noise in both direct and Fourier space leads to residual phase fluctuations. This problem is addressed by supplementing the algorithm with an averaging method. The effect of averaging may be interpreted in terms of an effective modulation transfer function, as used in optics, to quantify the resolution. The reconstruction details are prefaced with simulations of wave propagation through a model yeast cell. These show that the yeast cell is a strong-phase-contrast object for the conditions in the experiment.

Authors:
 [1];  [1];  [2];  [3];  [3]
  1. Cornell Univ., Ithaca, NY (United States)
  2. Stony Brook Univ., Stony Brook, NY (United States); Brookhaven National Lab., Upton, NY (United States)
  3. Stony Brook Univ., Stony Brook, NY (United States)
Publication Date:
Research Org.:
Stony Brook Univ., Stony Brook, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1164140
Grant/Contract Number:  
FG02-04ER46128
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section A, Foundations of Crystallography
Additional Journal Information:
Journal Volume: 62; Journal Issue: 4; Journal ID: ISSN 0108-7673
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; 77 NANOSCIENCE AND NANOTECHNOLOGY; cell reconstruction; imaging techniques; yeast cell image

Citation Formats

Thibault, Pierre, Elser, Veit, Jacobsen, Chris, Shapiro, David, and Sayre, David. Reconstruction of a yeast cell from x-ray diffraction data. United States: N. p., 2006. Web. doi:10.1107/S0108767306016515.
Thibault, Pierre, Elser, Veit, Jacobsen, Chris, Shapiro, David, & Sayre, David. Reconstruction of a yeast cell from x-ray diffraction data. United States. doi:10.1107/S0108767306016515.
Thibault, Pierre, Elser, Veit, Jacobsen, Chris, Shapiro, David, and Sayre, David. Wed . "Reconstruction of a yeast cell from x-ray diffraction data". United States. doi:10.1107/S0108767306016515. https://www.osti.gov/servlets/purl/1164140.
@article{osti_1164140,
title = {Reconstruction of a yeast cell from x-ray diffraction data},
author = {Thibault, Pierre and Elser, Veit and Jacobsen, Chris and Shapiro, David and Sayre, David},
abstractNote = {We provide details of the algorithm used for the reconstruction of yeast cell images in the recent demonstration of diffraction microscopy by Shapiro, Thibault, Beetz, Elser, Howells, Jacobsen, Kirz, Lima, Miao, Nieman & Sayre. Two refinements of the iterative constraint-based scheme are developed to address the current experimental realities of this imaging technique, which include missing central data and noise. A constrained power operator is defined whose eigenmodes allow the identification of a small number of degrees of freedom in the reconstruction that are negligibly constrained as a result of the missing data. To achieve reproducibility in the algorithm's output, a special intervention is required for these modes. Weak incompatibility of the constraints caused by noise in both direct and Fourier space leads to residual phase fluctuations. This problem is addressed by supplementing the algorithm with an averaging method. The effect of averaging may be interpreted in terms of an effective modulation transfer function, as used in optics, to quantify the resolution. The reconstruction details are prefaced with simulations of wave propagation through a model yeast cell. These show that the yeast cell is a strong-phase-contrast object for the conditions in the experiment.},
doi = {10.1107/S0108767306016515},
journal = {Acta Crystallographica. Section A, Foundations of Crystallography},
number = 4,
volume = 62,
place = {United States},
year = {2006},
month = {6}
}

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