Literature DB >> 25913484

CTF Challenge: Result summary.

Roberto Marabini1, Bridget Carragher2, Shaoxia Chen3, James Chen4, Anchi Cheng2, Kenneth H Downing5, Joachim Frank6, Robert A Grassucci6, J Bernard Heymann7, Wen Jiang8, Slavica Jonic9, Hstau Y Liao6, Steven J Ludtke10, Shail Patwari11, Angela L Piotrowski11, Adrian Quintana12, Carlos O S Sorzano12, Henning Stahlberg13, Javier Vargas12, Neil R Voss11, Wah Chiu10, Jose M Carazo12.   

Abstract

Image formation in bright field electron microscopy can be described with the help of the contrast transfer function (CTF). In this work the authors describe the "CTF Estimation Challenge", called by the Madrid Instruct Image Processing Center (I2PC) in collaboration with the National Center for Macromolecular Imaging (NCMI) at Houston. Correcting for the effects of the CTF requires accurate knowledge of the CTF parameters, but these have often been difficult to determine. In this challenge, researchers have had the opportunity to test their ability in estimating some of the key parameters of the electron microscope CTF on a large micrograph data set produced by well-known laboratories on a wide set of experimental conditions. This work presents the first analysis of the results of the CTF Estimation Challenge, including an assessment of the performance of the different software packages under different conditions, so as to identify those areas of research where further developments would be desirable in order to achieve high-resolution structural information.
Copyright © 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Benchmarking; Challenge; Contrast transfer function; Electron microscopy; High-resolution

Mesh:

Substances:

Year:  2015        PMID: 25913484      PMCID: PMC4672951          DOI: 10.1016/j.jsb.2015.04.003

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  4 in total

1.  Automatic particle selection: results of a comparative study.

Authors:  Yuanxin Zhu; Bridget Carragher; Robert M Glaeser; Denis Fellmann; Chandrajit Bajaj; Marshall Bern; Fabrice Mouche; Felix de Haas; Richard J Hall; David J Kriegman; Steven J Ludtke; Satya P Mallick; Pawel A Penczek; Alan M Roseman; Fred J Sigworth; Niels Volkmann; Clinton S Potter
Journal:  J Struct Biol       Date:  2004 Jan-Feb       Impact factor: 2.867

2.  Novel algorithms and the benefits of comparative validation.

Authors:  Robert Smith; Dan Ventura; John T Prince
Journal:  Bioinformatics       Date:  2013-04-14       Impact factor: 6.937

3.  The 2010 cryo-EM modeling challenge.

Authors:  Steven J Ludtke; Catherine L Lawson; Gerard J Kleywegt; Helen Berman; Wah Chiu
Journal:  Biopolymers       Date:  2012-09       Impact factor: 2.505

4.  Influence of electron dose rate on electron counting images recorded with the K2 camera.

Authors:  Xueming Li; Shawn Q Zheng; Kiyoshi Egami; David A Agard; Yifan Cheng
Journal:  J Struct Biol       Date:  2013-08-20       Impact factor: 2.867

  4 in total
  15 in total

Review 1.  Principles of cryo-EM single-particle image processing.

Authors:  Fred J Sigworth
Journal:  Microscopy (Oxf)       Date:  2015-12-24       Impact factor: 1.571

2.  Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Authors:  Carlos Oscar S Sorzano; Amaya Jiménez-Moreno; David Maluenda; Erney Ramírez-Aportela; Marta Martínez; Ana Cuervo; Robert Melero; Jose Javier Conesa; Ruben Sánchez-García; David Strelak; Jiri Filipovic; Estrella Fernández-Giménez; Federico de Isidro-Gómez; David Herreros; Pablo Conesa; Laura Del Caño; Yunior Fonseca; Jorge Jiménez de la Morena; Jose Ramon Macías; Patricia Losana; Roberto Marabini; Jose-Maria Carazo
Journal:  Methods Mol Biol       Date:  2021

3.  Real-time detection and single-pass minimization of TEM objective lens astigmatism.

Authors:  Rui Yan; Kunpeng Li; Wen Jiang
Journal:  J Struct Biol       Date:  2016-11-10       Impact factor: 2.867

Review 4.  Emerging Themes in CryoEM─Single Particle Analysis Image Processing.

Authors:  Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Chem Rev       Date:  2022-07-04       Impact factor: 72.087

5.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

Authors:  Alexis Rohou; Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2015-08-13       Impact factor: 2.867

6.  Defocus and magnification dependent variation of TEM image astigmatism.

Authors:  Rui Yan; Kunpeng Li; Wen Jiang
Journal:  Sci Rep       Date:  2018-01-10       Impact factor: 4.379

7.  The Electron Microscopy eXchange (EMX) initiative.

Authors:  Roberto Marabini; Steven J Ludtke; Stephen C Murray; Wah Chiu; Jose M de la Rosa-Trevín; Ardan Patwardhan; J Bernard Heymann; Jose M Carazo
Journal:  J Struct Biol       Date:  2016-02-09       Impact factor: 2.867

Review 8.  Databases and Archiving for CryoEM.

Authors:  A Patwardhan; C L Lawson
Journal:  Methods Enzymol       Date:  2016-06-16       Impact factor: 1.600

9.  Gctf: Real-time CTF determination and correction.

Authors:  Kai Zhang
Journal:  J Struct Biol       Date:  2015-11-19       Impact factor: 2.867

10.  EMDataBank unified data resource for 3DEM.

Authors:  Catherine L Lawson; Ardan Patwardhan; Matthew L Baker; Corey Hryc; Eduardo Sanz Garcia; Brian P Hudson; Ingvar Lagerstedt; Steven J Ludtke; Grigore Pintilie; Raul Sala; John D Westbrook; Helen M Berman; Gerard J Kleywegt; Wah Chiu
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971

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