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J Struct Biol. 2016 Jul;195(1):93-9. doi: 10.1016/j.jsb.2016.04.010. Epub 2016 Apr 20.

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

Author information

1
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain; Escuela Politécnica Superior, Universidad Autónoma de Madrid, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain. Electronic address: jmdelarosa@cnb.csic.es.
2
Neuroscience, Physiology and Pharmacology Dept., Univ. College London, Gower Street, London WC1E 6BT, United Kingdom.
3
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
4
EyeSeeTea Ltd., Delta Place, 27 Bath Road, Cheltenham, Gloucestershire GL53 7TH, United Kingdom.
5
L'Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, 67400 Illkirch-Graffenstaden, France.
6
Escuela Politécnica Superior, Universidad Autónoma de Madrid, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.
7
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain; Bioengineering Lab., Universidad CEU San Pablo, Campus Urb. Montepríncipe s/n, 28668 Boadilla del Monte, Madrid, Spain.

Abstract

In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.

KEYWORDS:

Electron microscopy; Image processing; Reproducibility; Single particle analysis; Software package; Workflows

PMID:
27108186
DOI:
10.1016/j.jsb.2016.04.010
[Indexed for MEDLINE]

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