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Reconstruction of a yeast cell from X-ray diffraction data

Reconstruction of a yeast cell from X-ray diffraction data
Reconstruction of a yeast cell from X-ray diffraction data
Details are provided 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 [Proc. Natl Acad. Sci. USA (2005), 102, 15343-15346]. 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.
2053-2733
248-261
Thibault, Pierre
975a4c7b-6ca9-4958-b362-9eba10ab926b
Elser, Veit
08e4cad6-438b-4250-ad2e-3511715e1860
Jacobsen, Chris
9e1f9d65-febd-4854-8c5e-d2b26bea9871
Shapiro, David
602dea41-c144-472c-a037-a324d3dac90d
Sayre, David
2fdd1490-060b-4ba2-afc1-a16b5c8564dd
Thibault, Pierre
975a4c7b-6ca9-4958-b362-9eba10ab926b
Elser, Veit
08e4cad6-438b-4250-ad2e-3511715e1860
Jacobsen, Chris
9e1f9d65-febd-4854-8c5e-d2b26bea9871
Shapiro, David
602dea41-c144-472c-a037-a324d3dac90d
Sayre, David
2fdd1490-060b-4ba2-afc1-a16b5c8564dd

Thibault, Pierre, Elser, Veit, Jacobsen, Chris, Shapiro, David and Sayre, David (2006) Reconstruction of a yeast cell from X-ray diffraction data. Acta Crystallographica Section A: Foundations and Advances, 62 (4), 248-261. (doi:10.1107/S0108767306016515).

Record type: Article

Abstract

Details are provided 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 [Proc. Natl Acad. Sci. USA (2005), 102, 15343-15346]. 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.

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More information

Accepted/In Press date: 4 May 2006
Published date: July 2006

Identifiers

Local EPrints ID: 419326
URI: http://eprints.soton.ac.uk/id/eprint/419326
ISSN: 2053-2733
PURE UUID: 5915ff9c-d006-4416-9ace-68d0174e87f6
ORCID for Pierre Thibault: ORCID iD orcid.org/0000-0003-1278-8846

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Date deposited: 10 Apr 2018 16:30
Last modified: 17 Dec 2019 01:33

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