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

J M de la Rosa-Trevín; A Quintana; L Del Cano; A Zaldívar; I Foche; J Gutiérrez; J Gómez-Blanco; J Burguet-Castell; J Cuenca-Alba; V Abrishami; J Vargas; J Otón; G Sharov; J L Vilas; J Navas; P Conesa; M Kazemi; R Marabini; C O S Sorzano; J M Carazo

doi:10.1016/j.jsb.2016.04.010

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

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

Authors

J M de la Rosa-Trevín¹, A Quintana², L Del Cano³, A Zaldívar³, I Foche⁴, J Gutiérrez³, J Gómez-Blanco³, J Burguet-Castell³, J Cuenca-Alba³, V Abrishami³, J Vargas³, J Otón³, G Sharov⁵, J L Vilas³, J Navas³, P Conesa³, M Kazemi³, R Marabini⁶, C O S Sorzano⁷, J M Carazo³

Affiliations

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.

PMID: 27108186
DOI: 10.1016/j.jsb.2016.04.010

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Image Processing, Computer-Assisted / methods*
Imaging, Three-Dimensional / instrumentation*
Imaging, Three-Dimensional / methods
Microscopy, Electron / methods*
Reproducibility of Results
Workflow