Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.
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.
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.
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de la Rosa-Trevín
Neuroscience, Physiology and Pharmacology Dept., Univ. College London, Gower Street, London WC1E 6BT, United Kingdom.
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Quintana
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Del Cano
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Zaldívar
EyeSeeTea Ltd., Delta Place, 27 Bath Road, Cheltenham, Gloucestershire GL53 7TH, United Kingdom.
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Foche
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Gutiérrez
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Gómez-Blanco
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Burguet-Castell
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Cuenca-Alba
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Abrishami
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Vargas
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Otón
L'Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, 67400 Illkirch-Graffenstaden, France.
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Sharov
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Vilas
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Navas
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Conesa
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Kazemi
Escuela Politécnica Superior, Universidad Autónoma de Madrid, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.
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Marabini
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.
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Sorzano
Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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Carazo
D000465:Algorithms; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000295:instrumentation* / Q000379:methods; D008854:Microscopy, Electron / Q000379:methods*; D015203:Reproducibility of Results; D057188:Workflow
Electron microscopy; Image processing; Reproducibility; Single particle analysis; Software package; Workflows