Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function.

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.

[1]  Jun Zhu.  Three-Dimensional Reconstruction with Contrast Transfer Function Correction from Energy-Filtered Cryoelectron Micrographs : Procedure and Application to the 70 S Escherichia coli Ribosome , 1997 .

[2]  Joachim Frank,et al.  An assay for local quality in cryo-electron micrographs of single particles. , 2002, Ultramicroscopy.

[3]  N. Grigorieff,et al.  Accurate determination of local defocus and specimen tilt in electron microscopy. , 2003, Journal of structural biology.

[4]  J M Carazo,et al.  A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment. , 2003, Ultramicroscopy.

[5]  J. Frank.  Single-particle imaging of macromolecules by cryo-electron microscopy. , 2002, Annual review of biophysics and biomolecular structure.

[6]  D. DeRosier.  Correction of high-resolution data for curvature of the Ewald sphere. , 2000, Ultramicroscopy.

[7]  Koji Yonekura,et al.  Contrast transfer for frozen-hydrated specimens II. Amplitude contrast at very low frequencies , 1993 .

[8]  J M Carazo,et al.  Transfer function restoration in 3D electron microscopy via iterative data refinement , 2004, Physics in medicine and biology.

[9]  C O S Sorzano,et al.  A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas. , 2007, Journal of structural biology.

[10]  R. Henderson.  Realizing the potential of electron cryo-microscopy , 2004, Quarterly Reviews of Biophysics.

[11]  W Chiu,et al.  CTF determination of images of ice-embedded single particles using a graphics interface. , 1996, Journal of structural biology.

[12]  N. Unwin,et al.  Contrast transfer for frozen-hydrated specimens: determination from pairs of defocused images. , 1988, Ultramicroscopy.

[13]  Joachim Frank,et al.  On the correction of the contrast transfer function in biological electron microscopy , 1995 .

[14]  Clinton S Potter,et al.  ACE: automated CTF estimation. , 2005, Ultramicroscopy.

[15]  J. Frank.  Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State , 1996 .

[16]  Joachim Frank,et al.  THREE DIMENSIONAL RECONSTRUCTION WITH CONTRAST TRANSFER COMPENSATION FROM DEFOCUS SERIES , 1997 .

[17]  H. Stark,et al.  Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. , 2003, Journal of structural biology.

[18]  G Bricogne,et al.  Maximum-entropy three-dimensional reconstruction with deconvolution of the contrast transfer function: a test application with adenovirus. , 1996, Journal of structural biology.

[19]  William H. Press,et al.  Numerical recipes in C , 2002 .

[20]  X. Zou.  Electron crystallography of inorganic structures : theory and practice , 1995 .

[21]  José María Carazo,et al.  Structural basis for the cooperative assembly of large T antigen on the origin of replication. , 2006, Journal of molecular biology.

[22]  P. Unwin,et al.  Phase contrast electron microscopy of biological materials , 1973, Journal of microscopy.

[23]  Ansgar Philippsen,et al.  The contrast-imaging function for tilted specimens. , 2007, Ultramicroscopy.

[24]  José-Jesús Fernández,et al.  A spectral estimation approach to contrast transfer function detection in electron microscopy , 1997 .

[25]  J M Carazo,et al.  XMIPP: a new generation of an open-source image processing package for electron microscopy. , 2004, Journal of structural biology.

[26]  R. H. Wade.  A brief look at imaging and contrast transfer , 1992 .

[27]  T. Earnest,et al.  From words to literature in structural proteomics , 2003, Nature.

[28]  Joachim Frank,et al.  Large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication , 2003, The EMBO journal.

[29]  Rasmus R. Schröder,et al.  Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide , 2003, Nature.

[30]  P. Broersen,et al.  Facts and fiction in spectral analysis , 1998, IMTC/98 Conference Proceedings. IEEE Instrumentation and Measurement Technology Conference. Where Instrumentation is Going (Cat. No.98CH36222).

[31]  Gabor T. Herman,et al.  Three-dimensional reconstruction by Chahine’s method from electron microscopic projections corrupted by instrumental aberrations , 2003 .

[32]  Charles L. Lawson,et al.  Solving least squares problems , 1976, Classics in applied mathematics.

[33]  W Chiu,et al.  Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. , 2001, Journal of structural biology.

[34]  R. Brimacombe,et al.  Arrangement of tRNAs in Pre- and Posttranslocational Ribosomes Revealed by Electron Cryomicroscopy , 1997, Cell.

[35]  M. Heel,et al.  Single-particle electron cryo-microscopy: towards atomic resolution , 2000, Quarterly Reviews of Biophysics.

[36]  N Grigorieff,et al.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. , 1998, Journal of molecular biology.

[37]  J. Frank,et al.  Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. , 1997, Journal of structural biology.

[38]  P. Welch.  The use of fast Fourier transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms , 1967 .

[39]  Pawel A Penczek,et al.  Automated determination of parameters describing power spectra of micrograph images in electron microscopy. , 2003, Journal of structural biology.

[40]  M F Schmid,et al.  Electron cryomicroscopy of Bacillus stearothermophilus 50 S ribosomal subunits crystallized on phospholipid monolayers. , 1994, Journal of molecular biology.