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Jose-maria Carazo - One of the best experts on this subject based on the ideXlab platform.

  • A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the Contrast Transfer Function.
    Ultramicroscopy, 2015
    Co-Authors: Vahid Abrishami, Jose-maria Carazo, J.r. Bilbao-castro, Javier Vargas, Roberto Marabini, Carlos Oscar S. Sorzano
    Abstract:

    We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the Contrast Transfer Function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.

  • corrigendum to fast robust and accurate determination of transmission electron microscopy Contrast Transfer Function j struct biol 160 2007 249 262
    Journal of Structural Biology, 2012
    Co-Authors: Carlos Oscar S. Sorzano, Slavica Jonic, Nicolas Boisset, Rafael Nunezramirez, Jose-maria Carazo
    Abstract:

    Unidad de Biocomputacion, Centro Nacional de Biotecnologia (CSIC), Campus Universidad Autonoma s/n, 28049 Cantoblanco, Madrid, Spain Department of Ingenieria de Sistemas Electronicos y de Telecomunicacion, University of San Pablo-CEU, Campus Urb. Monteprincipe s/n, 28668 Boadilla del Monte, Madrid, Spain Universite Pierre et Marie Curie, CNRS, IMPMC-UMR7590, Universite Paris 7, Paris F-75005, France

  • Corrigendum to “Fast, robust and accurate determination of transmission electron microscopy Contrast Transfer Function” [J. Struct. Biol. 160 (2007) 249–262]
    Journal of Structural Biology, 2012
    Co-Authors: Carlos Oscar S. Sorzano, Slavica Jonic, Rafael Núñez-ramírez, Nicolas Boisset, Jose-maria Carazo
    Abstract:

    Unidad de Biocomputacion, Centro Nacional de Biotecnologia (CSIC), Campus Universidad Autonoma s/n, 28049 Cantoblanco, Madrid, Spain Department of Ingenieria de Sistemas Electronicos y de Telecomunicacion, University of San Pablo-CEU, Campus Urb. Monteprincipe s/n, 28668 Boadilla del Monte, Madrid, Spain Universite Pierre et Marie Curie, CNRS, IMPMC-UMR7590, Universite Paris 7, Paris F-75005, France

  • Error analysis in the determination of the electron microscopical Contrast Transfer Function parameters from experimental power Spectra
    BMC structural biology, 2009
    Co-Authors: Carlos Oscar S. Sorzano, Abraham Otero, Estefanía M. Olmos, Jose-maria Carazo
    Abstract:

    Background The transmission electron microscope is used to acquire structural information of macromolecular complexes. However, as any other imaging device, it introduces optical aberrations that must be corrected if high-resolution structural information is to be obtained. The set of all aberrations are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Before correcting for the CTF, we must first estimate it from the electron micrographs. This is usually done by estimating a number of parameters specifying a theoretical model of the CTF. This estimation is performed by minimizing some error measure between the theoretical Power Spectrum Density (PSD) and the experimentally observed PSD. The high noise present in the micrographs, the possible local minima of the error Function for estimating the CTF parameters, and the cross-talking between CTF parameters may cause errors in the estimated CTF parameters.

  • Fast, robust, and accurate determination of transmission electron microscopy Contrast Transfer Function.
    Journal of structural biology, 2007
    Co-Authors: Carlos Oscar S. Sorzano, Slavica Jonic, Rafael Núñez-ramírez, Nicolas Boisset, Jose-maria Carazo
    Abstract:

    Transmission electron microscopy, as most imaging devices, introduces optical aberrations that in the case of thin specimens are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Accurate determination of the CTF is crucial for its posterior correction. Furthermore, the CTF estimation must be fast and robust if high-throughput three-dimensional electron microscopy (3DEM) studies are to be carried out. In this paper we present a robust algorithm that fits a theoretical CTF model to the power spectrum density (PSD) measured on a specific micrograph or micrograph area. Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes.

Carlos Oscar S. Sorzano - One of the best experts on this subject based on the ideXlab platform.

  • A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the Contrast Transfer Function.
    Ultramicroscopy, 2015
    Co-Authors: Vahid Abrishami, Jose-maria Carazo, J.r. Bilbao-castro, Javier Vargas, Roberto Marabini, Carlos Oscar S. Sorzano
    Abstract:

    We describe a fast and accurate method for the reconstruction of macromolecular complexes from a set of projections. Direct Fourier inversion (in which the Fourier Slice Theorem plays a central role) is a solution for dealing with this inverse problem. Unfortunately, the set of projections provides a non-equidistantly sampled version of the macromolecule Fourier transform in the single particle field (and, therefore, a direct Fourier inversion) may not be an optimal solution. In this paper, we introduce a gridding-based direct Fourier method for the three-dimensional reconstruction approach that uses a weighting technique to compute a uniform sampled Fourier transform. Moreover, the Contrast Transfer Function of the microscope, which is a limiting factor in pursuing a high resolution reconstruction, is corrected by the algorithm. Parallelization of this algorithm, both on threads and on multiple CPU's, makes the process of three-dimensional reconstruction even faster. The experimental results show that our proposed gridding-based direct Fourier reconstruction is slightly more accurate than similar existing methods and presents a lower computational complexity both in terms of time and memory, thereby allowing its use on larger volumes. The algorithm is fully implemented in the open-source Xmipp package and is downloadable from http://xmipp.cnb.csic.es.

  • corrigendum to fast robust and accurate determination of transmission electron microscopy Contrast Transfer Function j struct biol 160 2007 249 262
    Journal of Structural Biology, 2012
    Co-Authors: Carlos Oscar S. Sorzano, Slavica Jonic, Nicolas Boisset, Rafael Nunezramirez, Jose-maria Carazo
    Abstract:

    Unidad de Biocomputacion, Centro Nacional de Biotecnologia (CSIC), Campus Universidad Autonoma s/n, 28049 Cantoblanco, Madrid, Spain Department of Ingenieria de Sistemas Electronicos y de Telecomunicacion, University of San Pablo-CEU, Campus Urb. Monteprincipe s/n, 28668 Boadilla del Monte, Madrid, Spain Universite Pierre et Marie Curie, CNRS, IMPMC-UMR7590, Universite Paris 7, Paris F-75005, France

  • Corrigendum to “Fast, robust and accurate determination of transmission electron microscopy Contrast Transfer Function” [J. Struct. Biol. 160 (2007) 249–262]
    Journal of Structural Biology, 2012
    Co-Authors: Carlos Oscar S. Sorzano, Slavica Jonic, Rafael Núñez-ramírez, Nicolas Boisset, Jose-maria Carazo
    Abstract:

    Unidad de Biocomputacion, Centro Nacional de Biotecnologia (CSIC), Campus Universidad Autonoma s/n, 28049 Cantoblanco, Madrid, Spain Department of Ingenieria de Sistemas Electronicos y de Telecomunicacion, University of San Pablo-CEU, Campus Urb. Monteprincipe s/n, 28668 Boadilla del Monte, Madrid, Spain Universite Pierre et Marie Curie, CNRS, IMPMC-UMR7590, Universite Paris 7, Paris F-75005, France

  • Error analysis in the determination of the electron microscopical Contrast Transfer Function parameters from experimental power Spectra
    BMC structural biology, 2009
    Co-Authors: Carlos Oscar S. Sorzano, Abraham Otero, Estefanía M. Olmos, Jose-maria Carazo
    Abstract:

    Background The transmission electron microscope is used to acquire structural information of macromolecular complexes. However, as any other imaging device, it introduces optical aberrations that must be corrected if high-resolution structural information is to be obtained. The set of all aberrations are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Before correcting for the CTF, we must first estimate it from the electron micrographs. This is usually done by estimating a number of parameters specifying a theoretical model of the CTF. This estimation is performed by minimizing some error measure between the theoretical Power Spectrum Density (PSD) and the experimentally observed PSD. The high noise present in the micrographs, the possible local minima of the error Function for estimating the CTF parameters, and the cross-talking between CTF parameters may cause errors in the estimated CTF parameters.

  • Fast, robust, and accurate determination of transmission electron microscopy Contrast Transfer Function.
    Journal of structural biology, 2007
    Co-Authors: Carlos Oscar S. Sorzano, Slavica Jonic, Rafael Núñez-ramírez, Nicolas Boisset, Jose-maria Carazo
    Abstract:

    Transmission electron microscopy, as most imaging devices, introduces optical aberrations that in the case of thin specimens are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Accurate determination of the CTF is crucial for its posterior correction. Furthermore, the CTF estimation must be fast and robust if high-throughput three-dimensional electron microscopy (3DEM) studies are to be carried out. In this paper we present a robust algorithm that fits a theoretical CTF model to the power spectrum density (PSD) measured on a specific micrograph or micrograph area. Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes.

Wah Chiu - One of the best experts on this subject based on the ideXlab platform.

  • Estimating Contrast Transfer Function and associated parameters by constrained non-linear optimization
    Journal of microscopy, 2009
    Co-Authors: Chao Yang, Wen Jiang, Dong-hua Chen, Umesh Adiga, Wah Chiu
    Abstract:

    The three-dimensional reconstruction of macromolecules from two-dimensional single-particle electron images requires determination and correction of the Contrast Transfer Function (CTF) and envelope Function. A computational algorithm based on constrained non-linear optimization is developed to estimate the essential parameters in the CTF and envelope Function model simultaneously and automatically. The application of this estimation method is demonstrated with focal series images of amorphous carbon film as well as images of ice-embedded icosahedral virus particles suspended across holes.

  • Focal pair merging for Contrast enhancement of single particles
    Journal of Structural Biology, 2003
    Co-Authors: Steven J. Ludtke, Wah Chiu
    Abstract:

    A common technique in transmission electron microscopy is the collection of a focal pair, in which the first, close to focus image contains higher resolution information at lower Contrast, and the second, far from focus image has high Contrast but less reliable high-resolution information. Typically these second micrographs are used for purposes of particle selection, orientation estimate or micrograph evaluation. We introduce a technique for merging the information from both images, including signal to noise ratio weighting, Contrast Transfer Function correction, and optional Weiner filtration. This produces a composite image with reduced Contrast Transfer Function artifacts and optimized Contrast. This technique is useful in numerous cases where low-Contrast images are produced, such as small particles, proteins solubilized in detergent or projects with high-resolution goals when the first image is taken very close to focus.

  • Web-based Simulation for Contrast Transfer Function and Envelope Functions.
    Microscopy and microanalysis : the official journal of Microscopy Society of America Microbeam Analysis Society Microscopical Society of Canada, 2001
    Co-Authors: Wen Jiang, Wah Chiu
    Abstract:

    We have implemented a Web-based simulation program for the Contrast Transfer Function and envelope Functions in Java and JavaScript. The simulation provides interactive controls of all the parameters in those Functions. In addition to the predefined Functions, users can easily define new Functions that use any of the parameters in the preset Functions. The most useful feature of this new simulation program is the convenient, universal accessibility through Web browsers on any computer platform that supports Java, such as Netscape and Internet Explorer.

  • Scaling Structure Factor Amplitudes in Electron Cryomicroscopy Using X-Ray Solution Scattering
    Journal of structural biology, 1999
    Co-Authors: Michael F. Schmid, Michael B. Sherman, Paul Matsudaira, Hiro Tsuruta, Wah Chiu
    Abstract:

    The structure factors derived from electron cryomicroscopic images are modified by the Contrast Transfer Function of the microscope's objective lens and other influences. The phases of the structure factors can be corrected in a straightforward way when the positions of the Contrast Transfer Function rings are determined. However, corrected amplitudes are also essential to yield an accurate distribution of mass in the reconstruction. The correct scale factors for the amplitudes are difficult to evaluate for data that are merged from many different micrographs. We opt to use X-ray solution scattering intensity from a concentrated suspension of the specimen to correct the amplitudes of the spherically averaged structure factors. When this approach is applied to the three-dimensional image data of ice-embedded acrosomal bundles, the core of a filament in a three-dimensional reconstruction of the acrosomal bundle becomes denser and matches more closely the outer density ascribed to scruin.

  • CTF Determination of Images of Ice-Embedded Single Particles Using a Graphics Interface
    Journal of structural biology, 1996
    Co-Authors: Z. Hong Zhou, Steve Hardt, Bin Wang, Michael B. Sherman, Joanita Jakana, Wah Chiu
    Abstract:

    We implement a graphical user interface in an X-window/UNIX environment to compute and display the incoherently averaged Fourier transforms of electron images of single particles embedded in ice and the simulated Contrast Transfer Function with or without envelope Functions. This interface provides an easy and efficient operation for the determination of defocus value and the evaluation of the extent of Fourier amplitude falloff. This computational procedure is crucial for prescreening image data and performing image correction of Contrast Transfer Function in high-resolution three-dimensional reconstruction of single particles.

Baoli Yao - One of the best experts on this subject based on the ideXlab platform.

Slavica Jonic - One of the best experts on this subject based on the ideXlab platform.