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Impact on the Sustainable Development Goals (SDGs)

Analysis of institutional authors

Toharia P.AuthorFernaud-Espinosa, IsabelAuthorBrito, Juan PAuthorMata, SusanaAuthorPastor, LuisAuthorBayona, SofiaAuthor

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November 23, 2020
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Article

Neuronize v2: Bridging the Gap Between Existing Proprietary Tools to Optimize Neuroscientific Workflows

Publicated to: Frontiers in Neuroanatomy. 14 (585793): 585793- - 2020-10-06 14(585793), DOI: 10.3389/fnana.2020.585793

Authors:

Velasco, I; Toharia, P; Benavides-Piccione, R; Fernaud-Espinosa, I; Brito, JP; Mata, S; DeFelipe, J; Pastor, L; Bayona, S
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Affiliations

CSIC, Inst Cajal - Author
Ctr Invest Biomed Red Enfermedades Neurodegenerat - Author
Univ Politecn Madrid, Ctr Computat Simulat - Author
Univ Rey Juan Carlos, Dept Comp Sci - Author
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Abstract

Knowledge about neuron morphology is key to understanding brain structure and function. There are a variety of software tools that are used to segment and trace the neuron morphology. However, these tools usually utilize proprietary formats. This causes interoperability problems since the information extracted with one tool cannot be used in other tools. This article aims to improve neuronal reconstruction workflows by facilitating the interoperability between two of the most commonly used software tools-Neurolucida (NL) and Imaris (Filament Tracer). The new functionality has been included in an existing tool-Neuronize-giving rise to its second version. Neuronize v2 makes it possible to automatically use the data extracted with Imaris Filament Tracer to generate a tracing with dendritic spine information that can be read directly by NL. It also includes some other new features, such as the ability to unify and/or correct inaccurately-formed meshes (i.e., dendritic spines) and to calculate new metrics. This tool greatly facilitates the process of neuronal reconstruction, bridging the gap between existing proprietary tools to optimize neuroscientific workflows.
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Keywords

3d morphological reconstructionAlgorithmArticleBrainCellsCerebrospinal fluidCorpus callosumData sharingDendriteDendritic spineGenetic recombinationGray matterHumanHuman prefrontal cortexImage processingImage reconstructionInsightsInteroperabilityMorphologyNeurologyNeuron morphologyNeuronal tracingPyramidal neuronsPyramidal structureQuality educationSignal noise ratioSkeletonSpine meshesSpinesStructure activity relationWorkflow

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Frontiers in Neuroanatomy 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, 2020, it was in position 1/21, thus managing to position itself as a Q1 (Primer Cuartil), in the category Anatomy & Morphology. Notably, the journal is positioned above the 90th percentile.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-25:

  • Google Scholar: 5
  • WoS: 4
  • Scopus: 4
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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: 19.
  • 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: 19 (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: 10.
  • The number of mentions on the social network X (formerly Twitter): 2 (Altmetric).
  • The number of mentions in news outlets: 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/86627/

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: 177
  • Downloads: 34
Continuing with the social impact of the work, it is important to emphasize that, due to its content, it can be assigned to the area of interest of ODS 4 - Quality Education, with a probability of 64% according to the mBERT algorithm developed by Aurora University.
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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: Last Author (BAYONA BERISO, SOFIA).

the author responsible for correspondence tasks has been Benavides-Piccione, Ruth.

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Project objectives

El presente trabajo persigue los siguientes objetivos: mejorar los flujos de trabajo de reconstrucción neuronal facilitando la interoperabilidad entre los softwares Neurolucida e Imaris Filament Tracer; incorporar nuevas funcionalidades en la herramienta Neuronize para permitir el uso automático de datos extraídos con Imaris y generar trazados compatibles con Neurolucida; unificar y corregir mallas formadas incorrectamente, especialmente en espinas dendríticas; calcular nuevas métricas relacionadas con la morfología neuronal; y optimizar los procesos de reconstrucción neuronal mediante la integración de herramientas propietarias, contribuyendo así a superar las limitaciones de formatos propietarios y mejorar la eficiencia en estudios neurocientíficos.
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Most relevant results

Los resultados más relevantes de esta aportación se centran en la mejora de los flujos de trabajo en la reconstrucción neuronal mediante la interoperabilidad entre herramientas propietarias. En primer lugar, Neuronize v2 permite utilizar automáticamente los datos extraídos con Imaris Filament Tracer para generar un trazado que incluye información de espinas dendríticas y que es compatible con Neurolucida. En segundo lugar, incorpora funcionalidades para unificar y corregir mallas formadas incorrectamente, mejorando la precisión de las reconstrucciones. Finalmente, la herramienta añade la capacidad de calcular nuevas métricas relevantes para el análisis morfológico neuronal, optimizando así los procesos de segmentación y trazado en neurociencia.
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Awards linked to the item

This work was supported by grants from the following entities: the Spanish ``Ministerio de Ciencia, Innovacion y Universidades'' regarding grant TIN2017-83132-C2 (corresponding to the project Analytical Applied Visualization,'' VIANA), grant PGC2018-094307-B-I00, the Cajal Blue Brain Project [the Spanish partner of the Blue Brain Project initiative from L'Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland]; and the European Union's Horizon 2020 Framework Programme for Research and Innovation under the specific grant agreement No. 785907 (Human Brain Project SGA2) and the specific grant agreement No. 945539 (Human Brain Project SGA3).
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