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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...

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Detalles Bibliográficos
Autores principales: René de Cotret, Laurent P., Otto, Martin R., Stern, Mark J., Siwick, Bradley J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2018
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.
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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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