Literature DB >> 21172911

Fast tomographic reconstruction on multicore computers.

J I Agulleiro1, J J Fernandez.   

Abstract

SUMMARY: Tomo3D implements a multithreaded vectorized approach to tomographic reconstruction that takes full advantage of the computer power in modern multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements. Tomo3D has the most common reconstruction methods implemented, namely weighted Back-projection (WBP) and simultaneous iterative reconstruction technique (SIRT). It proves to be competitive with current graphic processor unit solutions in terms of processing time, in the order of a few seconds with WBP or minutes with SIRT. The program is compatible with standard packages, which easily allows integration in the electron tomography workflow.

Mesh:

Year:  2010        PMID: 21172911     DOI: 10.1093/bioinformatics/btq692

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  99 in total

1.  Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins.

Authors:  Ariane Briegel; Xiaoxiao Li; Alexandrine M Bilwes; Kelly T Hughes; Grant J Jensen; Brian R Crane
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-21       Impact factor: 11.205

2.  Three-dimensional structure of the bovine sperm connecting piece revealed by electron cryotomography.

Authors:  Puey Ounjai; Keunhwan D Kim; Polina V Lishko; Kenneth H Downing
Journal:  Biol Reprod       Date:  2012-09-28       Impact factor: 4.285

3.  Removing Contamination-Induced Reconstruction Artifacts from Cryo-electron Tomograms.

Authors:  Jose-Jesus Fernandez; Ulrike Laugks; Miroslava Schaffer; Felix J B Bäuerlein; Maryam Khoshouei; Wolfgang Baumeister; Vladan Lucic
Journal:  Biophys J       Date:  2015-12-30       Impact factor: 4.033

4.  Three-dimensional imaging of localized surface plasmon resonances of metal nanoparticles.

Authors:  Olivia Nicoletti; Francisco de la Peña; Rowan K Leary; Daniel J Holland; Caterina Ducati; Paul A Midgley
Journal:  Nature       Date:  2013-10-03       Impact factor: 49.962

5.  Accurate membrane tracing in three-dimensional reconstructions from electron cryotomography data.

Authors:  Christopher Page; Dorit Hanein; Niels Volkmann
Journal:  Ultramicroscopy       Date:  2015-03-30       Impact factor: 2.689

6.  In situ imaging of the bacterial flagellar motor disassembly and assembly processes.

Authors:  Mohammed Kaplan; Poorna Subramanian; Debnath Ghosal; Catherine M Oikonomou; Sahand Pirbadian; Ruth Starwalt-Lee; Shrawan Kumar Mageswaran; Davi R Ortega; Jeffrey A Gralnick; Mohamed Y El-Naggar; Grant J Jensen
Journal:  EMBO J       Date:  2019-05-20       Impact factor: 11.598

7.  In vivo structures of an intact type VI secretion system revealed by electron cryotomography.

Authors:  Yi-Wei Chang; Lee A Rettberg; Davi R Ortega; Grant J Jensen
Journal:  EMBO Rep       Date:  2017-05-09       Impact factor: 8.807

8.  Routine single particle CryoEM sample and grid characterization by tomography.

Authors:  Venkata P Dandey; Hui Wei; Alex J Noble; Julia Brasch; Jillian Chase; Priyamvada Acharya; Yong Zi Tan; Zhening Zhang; Laura Y Kim; Giovanna Scapin; Micah Rapp; Edward T Eng; William J Rice; Anchi Cheng; Carl J Negro; Lawrence Shapiro; Peter D Kwong; David Jeruzalmi; Amedee des Georges; Clinton S Potter; Bridget Carragher
Journal:  Elife       Date:  2018-05-29       Impact factor: 8.140

9.  Local Tension on Talin in Focal Adhesions Correlates with F-Actin Alignment at the Nanometer Scale.

Authors:  Abhishek Kumar; Karen L Anderson; Mark F Swift; Dorit Hanein; Niels Volkmann; Martin A Schwartz
Journal:  Biophys J       Date:  2018-09-10       Impact factor: 4.033

10.  Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.

Authors:  Gongpu Zhao; Juan R Perilla; Ernest L Yufenyuy; Xin Meng; Bo Chen; Jiying Ning; Jinwoo Ahn; Angela M Gronenborn; Klaus Schulten; Christopher Aiken; Peijun Zhang
Journal:  Nature       Date:  2013-05-30       Impact factor: 49.962

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