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Simulation of transmission electron microscope images of biological specimens
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2011 (English)In: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818, Vol. 243, no 3, 234-256 p.Article in journal (Refereed) Published
Abstract [en]

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrodinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated.

Place, publisher, year, edition, pages
2011. Vol. 243, no 3, 234-256 p.
Keyword [en]
Absorption potential, coherent imaging, computer modelling, contrast transfer function, electrostatic potential, image simulation, inelastic scattering, modulation transfer function, phantom generator, software package, transmission electron microscopy
National Category
Computational Mathematics
URN: urn:nbn:se:kth:diva-39055DOI: 10.1111/j.1365-2818.2011.03497.xISI: 000293699000003ScopusID: 2-s2.0-80051471655OAI: diva2:439347
Swedish Research CouncilKnut and Alice Wallenberg Foundation
QC 20110907Available from: 2011-09-07 Created: 2011-09-07 Last updated: 2012-01-31Bibliographically approved

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Öktem, Ozan
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Mathematics (Dept.)Center for Industrial and Applied Mathematics, CIAM
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