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Analysis of institutional authors

Quintana, AAuthorMarabini, RAuthorCarazo, JmAuthor

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Article

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

Publicated to:JOURNAL OF STRUCTURAL BIOLOGY. 195 (1): 93-9-99 - 2016-07-01 195(1), DOI: 10.1016/j.jsb.2016.04.010

Authors: de la Rosa-Trevín JM, Quintana A, Del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM

Affiliations

Campus Univ Autonoma Madrid, CSIC, Natl Biotechnol Ctr, Biocomp Unit, Darwin 3, Madrid 28049, Spain.      Consejo Superior de Investigaciones Cientificas (CSIC) - Author
Campus Univ Autonoma Madrid, CSIC, Natl Biotechnol Ctr, Biocomp Unit, Darwin 3, Madrid 28049, Spain      Consejo Superior de Investigaciones Cientificas (CSIC) - Author
EyeSeeTea Ltd, Delta Pl,27 Bath Rd, Cheltenham GL53 7TH, Glos, England - Author
Inst Genet & Biol Mol & Cellulaire, 1 Rue Laurent Fries, F-67400 Illkirch Graffenstaden, France      Universites de Strasbourg Etablissements Associes    Institut National de la Sante et de la Recherche Medicale (Inserm)    Universite de Strasbourg - Author
UCL, Neurosci Physiol & Pharmacol Dept, Gower St, London WC1E 6BT, England      University of London    University College London       - Author
Univ Autonoma Madrid, Escuela Politecn Super, Campus Univ Autonoma, E-28049 Madrid, Spain      Autonomous University of Madrid - Author
Univ CEU San Pablo, Bioengn Lab, Campus Urb Monteprincipe S-N, Madrid 28668, Spain      San Pablo CEU University - Author
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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.Copyright © 2016 Elsevier Inc. All rights reserved.

Keywords

electron microscopyimage processingreproducibilitysingle particle analysissoftware packageElectron microscopyImage processingReproducibilitySingle particle analysisSoftware packageWorkflows

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal JOURNAL OF STRUCTURAL BIOLOGY due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2016, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Structural Biology.

This publication has been distinguished as a “Highly Cited Paper” by the agencies WoS (ESI, Clarivate) and ESI (Clarivate), meaning that it ranks within the top 1% of the most cited articles in its thematic field during the year of its publication. In terms of the observed impact of the contribution, this work is considered one of the most influential worldwide, as it is recognized as highly cited. (source consulted: ESI Nov 14, 2024)

And this is evidenced by the extremely high normalized impacts through some of the main indicators of this type, which, although dynamic over time and dependent on the set of average global citations at the time of calculation, already indicate that they are well above the average in different agencies:

  • Normalization of citations relative to the expected citation rate (ESI) by the Clarivate agency: 11.51 (source consulted: ESI Nov 14, 2024)
  • Weighted Average of Normalized Impact by the Scopus agency: 13.55 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 49.59 (source consulted: Dimensions Jun 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-06-27, the following number of citations:

  • WoS: 376
  • Scopus: 401
  • Europe PMC: 268

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-06-27:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 334.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 334 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 11.08.

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France; United Kingdom.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (de la Rosa-Trevin, JM) and Last Author (CARAZO GARCIA, JOSE MARIA S.).