Literature DB >> 20221416

Deblurring of Class-Averaged Images in Single-Particle Electron Microscopy.

Wooram Park1, Dean R Madden, Daniel N Rockmore, Gregory S Chirikjian.   

Abstract

This paper proposes a method for deblurring of class-averaged images in single-particle electron microscopy (EM). Since EM images of biological samples are very noisy, the images which are nominally identical projection images are often grouped, aligned and averaged in order to cancel or reduce the background noise. However, the noise in the individual EM images generates errors in the alignment process, which creates an inherent limit on the accuracy of the resulting class averages. This inaccurate class average due to the alignment errors can be viewed as the result of a convolution of an underlying clear image with a blurring function. In this work, we develop a deconvolution method that gives an estimate for the underlying clear image from a blurred class-averaged image using precomputed statistics of misalignment. Since this convolution is over the group of rigid body motions of the plane, SE(2), we use the Fourier transform for SE(2) in order to convert the convolution into a matrix multiplication in the corresponding Fourier space. For practical implementation we use a Hermite-function-based image modeling technique, because Hermite expansions enable lossless Cartesian-polar coordinate conversion using the Laguerre-Fourier expansions, and Hermite expansion and Laguerre-Fourier expansion retain their structures under the Fourier transform. Based on these mathematical properties, we can obtain the deconvolution of the blurred class average using simple matrix multiplication. Tests of the proposed deconvolution method using synthetic and experimental EM images confirm the performance of our method.

Entities:  

Year:  2010        PMID: 20221416      PMCID: PMC2835172          DOI: 10.1088/0266-5611/26/3/035002

Source DB:  PubMed          Journal:  Inverse Probl        ISSN: 0266-5611            Impact factor:   2.407


  23 in total

1.  EMAN: semiautomated software for high-resolution single-particle reconstructions.

Authors:  S J Ludtke; P R Baldwin; W Chiu
Journal:  J Struct Biol       Date:  1999-12-01       Impact factor: 2.867

2.  Widefield deconvolution epifluorescence microscopy combined with fluorescence in situ hybridization reveals the spatial arrangement of bacteria in sponge tissue.

Authors:  W Manz; G Arp; G Schumann-Kindel; U Szewzyk; J Reitner
Journal:  J Microbiol Methods       Date:  2000-04       Impact factor: 2.363

3.  Three-dimensional organization of microtubules in tumor cells studied by confocal laser scanning microscopy and computer-assisted deconvolution and image reconstruction.

Authors:  A R Strohmaier; T Porwol; H Acker; E Spiess
Journal:  Cells Tissues Organs       Date:  2000       Impact factor: 2.481

4.  Efficiency of 2D alignment methods.

Authors:  Laurent Joyeux; Pawel A Penczek
Journal:  Ultramicroscopy       Date:  2002-07       Impact factor: 2.689

5.  The pore structure of the closed RyR1 channel.

Authors:  Steven J Ludtke; Irina I Serysheva; Susan L Hamilton; Wah Chiu
Journal:  Structure       Date:  2005-08       Impact factor: 5.006

Review 6.  Cryo-EM and single particles.

Authors:  Liguo Wang; Fred J Sigworth
Journal:  Physiology (Bethesda)       Date:  2006-02

7.  SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.

Authors:  Tanvir R Shaikh; Haixiao Gao; William T Baxter; Francisco J Asturias; Nicolas Boisset; Ardean Leith; Joachim Frank
Journal:  Nat Protoc       Date:  2008       Impact factor: 13.491

8.  Cryo-EM image alignment based on nonuniform fast Fourier transform.

Authors:  Zhengfan Yang; Pawel A Penczek
Journal:  Ultramicroscopy       Date:  2008-04-08       Impact factor: 2.689

9.  A Stochastic Kinematic Model of Class Averaging in Single-Particle Electron Microscopy.

Authors:  Wooram Park; Charles R Midgett; Dean R Madden; Gregory S Chirikjian
Journal:  Int J Rob Res       Date:  2011-05-01       Impact factor: 4.703

10.  The correlation averaging of a regularly arranged bacterial cell envelope protein.

Authors:  W O Saxton; W Baumeister
Journal:  J Microsc       Date:  1982-08       Impact factor: 1.758

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  4 in total

1.  Rotationally invariant image representation for viewing direction classification in cryo-EM.

Authors:  Zhizhen Zhao; Amit Singer
Journal:  J Struct Biol       Date:  2014-03-12       Impact factor: 2.867

2.  Spherical deconvolution improves quality of single particle reconstruction.

Authors:  Gregory P Kishchenko; Ardean Leith
Journal:  J Struct Biol       Date:  2014-05-16       Impact factor: 2.867

3.  A Stochastic Kinematic Model of Class Averaging in Single-Particle Electron Microscopy.

Authors:  Wooram Park; Charles R Midgett; Dean R Madden; Gregory S Chirikjian
Journal:  Int J Rob Res       Date:  2011-05-01       Impact factor: 4.703

4.  A Fast Image Alignment Approach for 2D Classification of Cryo-EM Images Using Spectral Clustering.

Authors:  Xiangwen Wang; Yonggang Lu; Jiaxuan Liu
Journal:  Curr Issues Mol Biol       Date:  2021-10-18       Impact factor: 2.976

  4 in total

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