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

doi:10.1016/j.jsb.2016.04.010

. 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

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

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

J M de la Rosa-Trevín et al. J Struct Biol. 2016 Jul.

. 2016 Jul;195(1):93-9.

doi: 10.1016/j.jsb.2016.04.010. Epub 2016 Apr 20.

Authors

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.

PubMed Disclaimer

Cited by

Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus.
Ortega-Esteban Á, Mata CP, Rodríguez-Espinosa MJ, Luque D, Irigoyen N, Rodríguez JM, de Pablo PJ, Castón JR. Ortega-Esteban Á, et al. J Virol. 2020 Nov 23;94(24):e01542-20. doi: 10.1128/JVI.01542-20. Print 2020 Nov 23. J Virol. 2020. PMID: 32938763 Free PMC article.
Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution.
Kejzar N, Laanto E, Rissanen I, Abrishami V, Selvaraj M, Moineau S, Ravantti J, Sundberg LR, Huiskonen JT. Kejzar N, et al. Nat Commun. 2022 Dec 3;13(1):7478. doi: 10.1038/s41467-022-35123-6. Nat Commun. 2022. PMID: 36463224 Free PMC article.
Antiviral action of a functionalized plastic surface against human coronaviruses.
Shroff S, Haapakoski M, Tapio K, Laajala M, Leppänen M, Plavec Z, Haapala A, Butcher SJ, Ihalainen JA, Toppari JJ, Marjomäki V. Shroff S, et al. Microbiol Spectr. 2024 Feb 6;12(2):e0300823. doi: 10.1128/spectrum.03008-23. Epub 2024 Jan 16. Microbiol Spectr. 2024. PMID: 38226803 Free PMC article.
Cryo-EM structure of the yeast respiratory supercomplex.
Rathore S, Berndtsson J, Marin-Buera L, Conrad J, Carroni M, Brzezinski P, Ott M. Rathore S, et al. Nat Struct Mol Biol. 2019 Jan;26(1):50-57. doi: 10.1038/s41594-018-0169-7. Epub 2018 Dec 31. Nat Struct Mol Biol. 2019. PMID: 30598556
Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion.
Maluenda D, Majtner T, Horvath P, Vilas JL, Jiménez-Moreno A, Mota J, Ramírez-Aportela E, Sánchez-García R, Conesa P, Del Caño L, Rancel Y, Fonseca Y, Martínez M, Sharov G, García CA, Strelak D, Melero R, Marabini R, Carazo JM, Sorzano COS. Maluenda D, et al. Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):882-894. doi: 10.1107/S2059798319011860. Epub 2019 Oct 1. Acta Crystallogr D Struct Biol. 2019. PMID: 31588920 Free PMC article.

See all "Cited by" articles

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

LinkOut - more resources

Full Text Sources
- Elsevier Science
Other Literature Sources
- The Lens - Patent Citations Database
- scite Smart Citations
Molecular Biology Databases
- NIAID Data Ecosystem - Find datasets on Infectious and Immune-mediated Diseases
Miscellaneous
- NCI CPTAC Assay Portal

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

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

Affiliations

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

Authors

Affiliations

Abstract

Similar articles

Cited by

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases

Miscellaneous