Neuronize v2: Bridging the Gap Between Existing Proprietary Tools to Optimize Neuroscientific Workflows.
3D morphological reconstruction
data sharing
interoperability
neuron morphology
neuronal tracing
pyramidal structure
spine meshes
Journal
Frontiers in neuroanatomy
ISSN: 1662-5129
Titre abrégé: Front Neuroanat
Pays: Switzerland
ID NLM: 101477943
Informations de publication
Date de publication:
2020
2020
Historique:
received:
21
07
2020
accepted:
07
09
2020
entrez:
16
11
2020
pubmed:
17
11
2020
medline:
17
11
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33192345
doi: 10.3389/fnana.2020.585793
pmc: PMC7646287
doi:
Types de publication
Journal Article
Langues
eng
Pagination
585793Informations de copyright
Copyright © 2020 Velasco, Toharia, Benavides-Piccione, Fernaud-Espinosa, Brito, Mata, DeFelipe, Pastor and Bayona.
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