July 17, 2020
Publications
>
Article

Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study

Publicated to: CEREBRAL CORTEX. 24 (6): 1579-1588 - 2014-06-01 24(6), DOI: 10.1093/cercor/bht018

Authors:

Merchán-Pérez, A; Rodríguez, JR; González, S; Robles, V; DeFelipe, J; Larrañaga, P; Bielza, C
[+]

Affiliations

CSIC, Inst Cajal, E-28002 Madrid, Spain - Author
Univ Politecn Madrid, Ctr Tecnol Biomed, Lab Cajal Circuitos Corticales, Madrid 28223, Spain - Author
Univ Politecn Madrid, Ctr Tecnol Biomed, Lab Mineria Datos & Simulac, Madrid 28223, Spain - Author
Univ Politecn Madrid, Dept Arquitectura & Tecnol Sistemas Informat, Madrid 28223, Spain - Author
Univ Politecn Madrid, Dept Inteligencia Artificial, E-28660 Madrid, Spain - Author
See more

Abstract

In the cerebral cortex, most synapses are found in the neuropil, but relatively little is known about their 3-dimensional organization. Using an automated dual-beam electron microscope that combines focused ion beam milling and scanning electron microscopy, we have been able to obtain 10 three-dimensional samples with an average volume of 180 A mu m(3) from the neuropil of layer III of the young rat somatosensory cortex (hindlimb representation). We have used specific software tools to fully reconstruct 1695 synaptic junctions present in these samples and to accurately quantify the number of synapses per unit volume. These tools also allowed us to determine synapse position and to analyze their spatial distribution using spatial statistical methods. Our results indicate that the distribution of synaptic junctions in the neuropil is nearly random, only constrained by the fact that synapses cannot overlap in space. A theoretical model based on random sequential absorption, which closely reproduces the actual distribution of synapses, is also presented.
[+]

Keywords

dual-beam electron microscopyfocused ion beam milling/scanning electron microscopyneocortexspatial distribution of synapsesspatial statisticsCerebral-cortexCircuitDual-beam electron microscopyFocused ion beam millingFocused ion beam milling/scanning electron microscopyModesNeocortexPoint patternsRandom sequential adsorptionReceptorsReconstructionScanning electron microscopySpatial distribution of synapsesSpatial statisticsSynapsesTransmissionUltrastructural analysisVisual-cortex

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal CEREBRAL CORTEX due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2014, it was in position 16/252, thus managing to position itself as a Q1 (Primer Cuartil), in the category Neurosciences.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 1.18. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 13, 2025)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 1.19 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-04-25, the following number of citations:

  • WoS: 51
  • Scopus: 56
  • Europe PMC: 37
  • Google Scholar: 83
[+]

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 2026-04-25:

  • 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: 62.
  • 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: 62 (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: 1.
  • The number of mentions on the social network X (formerly Twitter): 1 (Altmetric).

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.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/35609/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 459
  • Downloads: 278
[+]

Leadership analysis of institutional authors

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 (MERCHAN PEREZ, ANGEL) and Last Author (BIELZA LOZOYA, MARIA CONCEPCION).

the author responsible for correspondence tasks has been MERCHAN PEREZ, ANGEL.

[+]

Awards linked to the item

The study was supported by Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED, CB06/05/0066) and Spanish Ministry of Economy and Competitiveness (grants SAF2009-09394, SAF 2010-18218, TIN2010-21289-C02-02, TIN2010-20900-C04-04, and the Cajal Blue Brain Project, Spanish partner of the Blue Brain Project initiative from EPFL). Funding to pay the Open Access publication charges for this article was provided by the Cajal Blue Brain Project.
[+]