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Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data

The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomo...

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Autores principales: Pelt, Daniël M., Gürsoy, Doǧa, Palenstijn, Willem Jan, Sijbers, Jan, De Carlo, Francesco, Batenburg, Kees Joost
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315009/
https://www.ncbi.nlm.nih.gov/pubmed/27140167
http://dx.doi.org/10.1107/S1600577516005658
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author Pelt, Daniël M.
Gürsoy, Doǧa
Palenstijn, Willem Jan
Sijbers, Jan
De Carlo, Francesco
Batenburg, Kees Joost
author_facet Pelt, Daniël M.
Gürsoy, Doǧa
Palenstijn, Willem Jan
Sijbers, Jan
De Carlo, Francesco
Batenburg, Kees Joost
author_sort Pelt, Daniël M.
collection PubMed
description The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it is shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy’s standard reconstruction method.
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spelling pubmed-53150092017-03-01 Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data Pelt, Daniël M. Gürsoy, Doǧa Palenstijn, Willem Jan Sijbers, Jan De Carlo, Francesco Batenburg, Kees Joost J Synchrotron Radiat Computer Programs The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it is shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy’s standard reconstruction method. International Union of Crystallography 2016-04-28 /pmc/articles/PMC5315009/ /pubmed/27140167 http://dx.doi.org/10.1107/S1600577516005658 Text en © Daniël M. Pelt et al. 2016 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/2.0/uk/
spellingShingle Computer Programs
Pelt, Daniël M.
Gürsoy, Doǧa
Palenstijn, Willem Jan
Sijbers, Jan
De Carlo, Francesco
Batenburg, Kees Joost
Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
title Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
title_full Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
title_fullStr Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
title_full_unstemmed Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
title_short Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
title_sort integration of tomopy and the astra toolbox for advanced processing and reconstruction of tomographic synchrotron data
topic Computer Programs
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315009/
https://www.ncbi.nlm.nih.gov/pubmed/27140167
http://dx.doi.org/10.1107/S1600577516005658
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