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Grant support

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).

Analysis of institutional authors

Velasco, ICorresponding AuthorMata, SAuthorPastor, LAuthorBayona, SAuthor

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September 27, 2022
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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, Ivan; Toharia, Pablo; Benavides-Piccione, Ruth; Fernaud-Espinosa, Isabel; Brito, Juan P; Mata, Susana; DeFelipe, Javier; Pastor, Luis; Bayona, Sofia

Affiliations

CSIC, Inst Cajal, Madrid, Spain - Author
Ctr Invest Biomed Red Enfermedades Neurodegenerat, Madrid, Spain - Author
Univ Politecn Madrid, Ctr Computat Simulat, Madrid, Spain - Author
Univ Politecn Madrid, Ctr Tecnol Biomed, Lab Cajal Circuitos Cort, Madrid, Spain - Author
Univ Politecn Madrid, ETSIINF, DATSI, Madrid, Spain - Author
Univ Politecn Madrid, ETSIINF, DLSIIS, Madrid, Spain - Author
Univ Rey Juan Carlos, Dept Comp Sci, Madrid, Spain - 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.

Keywords

3d morphological reconstructionAlgorithmArticleBrainCellsCerebrospinal fluidCorpus callosumData sharingDendriteDendritic spineGenetic recombinationGray matterHumanHuman prefrontal cortexImage processingImage reconstructionInsightsInteroperabilityMorphologyNeurologyNeuron morphologyNeuronal tracingPyramidal neuronsPyramidal structureSignal 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.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 1.4, which 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: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-22, the following number of citations:

  • WoS: 3
  • Scopus: 4
  • Europe PMC: 3

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 2025-07-22:

  • 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: 9.5.
  • 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.

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 (Velasco González, Iván) and Last Author (Bayona Beriso, Sofía).

the author responsible for correspondence tasks has been Velasco González, Iván.