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An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, iris, is graphical user-interface program and library for interactive explorati...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153488/ https://www.ncbi.nlm.nih.gov/pubmed/30310764 http://dx.doi.org/10.1186/s40679-018-0060-y |
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author | René de Cotret, Laurent P. Otto, Martin R. Stern, Mark J. Siwick, Bradley J. |
author_facet | René de Cotret, Laurent P. Otto, Martin R. Stern, Mark J. Siwick, Bradley J. |
author_sort | René de Cotret, Laurent P. |
collection | PubMed |
description | This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, iris, is graphical user-interface program and library for interactive exploration of UES data. Under the hood, iris makes use of npstreams, an extensions of numpy to streaming array-processing, for high-throughput parallel data reduction. Finally, we present scikit-ued, a library of reusable routines and data structures for analysis of UES data, including specialized image processing algorithms, simulation routines, and crystal structure manipulation operations. In this paper, some of the features or all three packages are highlighted, such as parallel data reduction, image registration, interactive exploration. The packages are fully tested and documented and are released under permissive licenses. |
format | Online Article Text |
id | pubmed-6153488 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-61534882018-10-09 An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data René de Cotret, Laurent P. Otto, Martin R. Stern, Mark J. Siwick, Bradley J. Adv Struct Chem Imaging Methodology This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, iris, is graphical user-interface program and library for interactive exploration of UES data. Under the hood, iris makes use of npstreams, an extensions of numpy to streaming array-processing, for high-throughput parallel data reduction. Finally, we present scikit-ued, a library of reusable routines and data structures for analysis of UES data, including specialized image processing algorithms, simulation routines, and crystal structure manipulation operations. In this paper, some of the features or all three packages are highlighted, such as parallel data reduction, image registration, interactive exploration. The packages are fully tested and documented and are released under permissive licenses. Springer International Publishing 2018-09-22 2018 /pmc/articles/PMC6153488/ /pubmed/30310764 http://dx.doi.org/10.1186/s40679-018-0060-y Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Methodology René de Cotret, Laurent P. Otto, Martin R. Stern, Mark J. Siwick, Bradley J. An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
title | An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
title_full | An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
title_fullStr | An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
title_full_unstemmed | An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
title_short | An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
title_sort | open-source software ecosystem for the interactive exploration of ultrafast electron scattering data |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153488/ https://www.ncbi.nlm.nih.gov/pubmed/30310764 http://dx.doi.org/10.1186/s40679-018-0060-y |
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