Literature DB >> 25194826

The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections.

Delei Chen1, Bart Goris2, Folkert Bleichrodt3, Hamed Heidari Mezerji2, Sara Bals2, Kees Joost Batenburg3, Gijsbertus de With4, Heiner Friedrich5.   

Abstract

In electron tomography, the fidelity of the 3D reconstruction strongly depends on the employed reconstruction algorithm. In this paper, the properties of SIRT, TVM and DART reconstructions are studied with respect to having only a limited number of electrons available for imaging and applying different angular sampling schemes. A well-defined realistic model is generated, which consists of tubular domains within a matrix having slab-geometry. Subsequently, the electron tomography workflow is simulated from calculated tilt-series over experimental effects to reconstruction. In comparison with the model, the fidelity of each reconstruction method is evaluated qualitatively and quantitatively based on global and local edge profiles and resolvable distance between particles. Results show that the performance of all reconstruction methods declines with the total electron dose. Overall, SIRT algorithm is the most stable method and insensitive to changes in angular sampling. TVM algorithm yields significantly sharper edges in the reconstruction, but the edge positions are strongly influenced by the tilt scheme and the tubular objects become thinned. The DART algorithm markedly suppresses the elongation artifacts along the beam direction and moreover segments the reconstruction which can be considered a significant advantage for quantification. Finally, no advantage of TVM and DART to deal better with fewer projections was observed.
Copyright © 2014 Elsevier B.V. All rights reserved.

Keywords:  Beam-sensitive material; Discrete algebraic reconstruction (DART); Electron tomography; Reconstruction algorithm; Simultaneous iterative reconstruction technique (SIRT); Total variation minimization (TVM)

Year:  2014        PMID: 25194826     DOI: 10.1016/j.ultramic.2014.08.005

Source DB:  PubMed          Journal:  Ultramicroscopy        ISSN: 0304-3991            Impact factor:   2.689


  9 in total

1.  High resolution 3D visualization of the spinal cord in a post-mortem murine model.

Authors:  Inna Bukreeva; Victor Asadchikov; Alexey Buzmakov; Marina Chukalina; Anastasya Ingacheva; Nikolay A Korolev; Alberto Bravin; Alberto Mittone; Gabriele E M Biella; Alejandra Sierra; Francesco Brun; Lorenzo Massimi; Michela Fratini; Alessia Cedola
Journal:  Biomed Opt Express       Date:  2020-03-27       Impact factor: 3.732

Review 2.  A Review of Experimentally Informed Micromechanical Modeling of Nanoporous Metals: From Structural Descriptors to Predictive Structure-Property Relationships.

Authors:  Claudia Richert; Norbert Huber
Journal:  Materials (Basel)       Date:  2020-07-24       Impact factor: 3.623

3.  Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.

Authors:  Xiaohua Wan; Tsvi Katchalski; Christopher Churas; Sreya Ghosh; Sebastien Phan; Albert Lawrence; Yu Hao; Ziying Zhou; Ruijuan Chen; Yu Chen; Fa Zhang; Mark H Ellisman
Journal:  J Struct Biol       Date:  2017-04-06       Impact factor: 2.867

4.  Multiscale characterization of pathological bone tissue.

Authors:  E Deniz Eren; Wouter H Nijhuis; Freek van der Weel; Aysegul Dede Eren; Sana Ansari; Paul H H Bomans; Heiner Friedrich; Ralph J Sakkers; Harrie Weinans; Gijsbertus de With
Journal:  Microsc Res Tech       Date:  2021-09-07       Impact factor: 2.893

5.  Nanoscale Morphology of PTB7 Based Organic Photovoltaics as a Function of Fullerene Size.

Authors:  John D Roehling; Derya Baran; Joseph Sit; Thaer Kassar; Tayebeh Ameri; Tobias Unruh; Christoph J Brabec; Adam J Moulé
Journal:  Sci Rep       Date:  2016-08-08       Impact factor: 4.379

6.  The advent of structural biology in situ by single particle cryo-electron tomography.

Authors:  Jesús G Galaz-Montoya; Steven J Ludtke
Journal:  Biophys Rep       Date:  2017-05-29

7.  In-line three-dimensional holography of nanocrystalline objects at atomic resolution.

Authors:  F-R Chen; D Van Dyck; C Kisielowski
Journal:  Nat Commun       Date:  2016-02-18       Impact factor: 14.919

8.  Doping porous silicon with erbium: pores filling as a method to limit the Er-clustering effects and increasing its light emission.

Authors:  Guido Mula; Tony Printemps; Christophe Licitra; Elisa Sogne; Francesco D'Acapito; Narciso Gambacorti; Nicola Sestu; Michele Saba; Elisa Pinna; Daniele Chiriu; Pier Carlo Ricci; Alberto Casu; Francesco Quochi; Andrea Mura; Giovanni Bongiovanni; Andrea Falqui
Journal:  Sci Rep       Date:  2017-07-20       Impact factor: 4.379

9.  Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography.

Authors:  James M Parkhurst; Maud Dumoux; Mark Basham; Daniel Clare; C Alistair Siebert; Trond Varslot; Angus Kirkland; James H Naismith; Gwyndaf Evans
Journal:  Open Biol       Date:  2021-10-27       Impact factor: 6.411

  9 in total

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