{rfName}
Mu

Indexed in

License and use

Icono OpenAccess

Citations

22

Altmetrics

Grant support

This work has been partially supported by the Spanish Ministry of Economy and Competitiveness through the Cajal Blue Brain (C080020-09; the Spanish partner of the Blue Brain initiative from EPFL) and TIN2016-79684-P projects, by the Regional Government of Madrid through the S2013/ICE-2845-CASI-CAM-CM project, and by Fundacion BBVA grants to Scientific Research Teams in Big Data 2016. This project has received funding from the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No. 785907 (HBP SGA2).

Analysis of institutional authors

Varando, GherardoCorresponding AuthorMunoz, AlbertoAuthorKastanauskaite, AstaAuthorBielza, ConchaAuthorLarranaga, PedroAuthor

Share

Publications
>
Article

MultiMap: A Tool to Automatically Extract and Analyse Spatial Microscopic Data From Large Stacks of Confocal Microscopy Images

Publicated to:Frontiers In Neuroanatomy. 12 (37): 37- - 2018-05-23 12(37), DOI: 10.3389/fnana.2018.00037

Authors: Varando, G; Benavides-Piccione, R; Muñoz, A; Kastanauskaite, A; Bielza, C; Larrañaga, P; DeFelipe, J

Affiliations

Abstract

The development of 3D visualization and reconstruction methods to analyse microscopic structures at different levels of resolutions is of great importance to define brain microorganization and connectivity. MultiMap is a new tool that allows the visualization, 3D segmentation and quantification of fluorescent structures selectively in the neuropil from large stacks of confocal microscopy images. The major contribution of this tool is the posibility to easily navigate and create regions of interest of any shape and size within a large brain area that will be automatically 3D segmented and quantified to determine the density of puncta in the neuropil. As a proof of concept, we focused on the analysis of glutamatergic and GABAergic presynaptic axon terminals in the mouse hippocampal region to demonstrate its use as a tool to provide putative excitatory and inhibitory synaptic maps. The segmentation and quantification method has been validated over expert labeled images of the mouse hippocampus and over two benchmark datasets, obtaining comparable results to the expert detections.

Keywords

brain atlasfluorescent imageimagejobject detectionpuncta segmentationsegmentationvgatBrain atlasFluorescent imageImagejNeuroanatomyObject detectionPuncta segmentationReconstructionSegmentationSetsVesicular gaba transporterVgatVglut1

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, 2018, it was in position 2/21, 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 2025-06-09:

  • Google Scholar: 9
  • WoS: 5
  • Scopus: 5
  • Europe PMC: 3
  • OpenCitations: 5

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 2025-06-09:

  • 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: 36.
  • 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: 36 (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: 1.25.
  • The number of mentions on the social network X (formerly Twitter): 3 (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 (VARANDO, GHERARDO) and Last Author (Defelipe, Javier).

the author responsible for correspondence tasks has been VARANDO, GHERARDO.