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dc.contributor.authorMihaljević, Bojan-
dc.contributor.authorLarrañaga, Pedro-
dc.contributor.authorBenavides-Piccione, Ruth-
dc.contributor.authorHill, Sean-
dc.contributor.authorDeFelipe, Javier-
dc.contributor.authorBielza, Concha-
dc.date.accessioned2018-12-23T04:16:39Z-
dc.date.available2018-12-23T04:16:39Z-
dc.date.issued2018-12-17-
dc.identifier.citationBMC Bioinformatics 19(1): 511 (2018)-
dc.identifier.urihttp://hdl.handle.net/10261/173607-
dc.description.abstract[Background] The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical values. [Results] We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single laboratory and pre-classified into eight types. We quantified 103 axonal and dendritic morphometrics, including novel ones that capture features such as arbor orientation, extent in layer one, and dendritic polarity. We trained a one-versus-rest classifier for each type, combining well-known supervised classification algorithms with feature selection and over- and under-sampling. We accurately classified the nest basket, Martinotti, and basket cell types with the Martinotti model outperforming 39 out of 42 leading neuroscientists. We had moderate accuracy for the double bouquet, small and large basket types, and limited accuracy for the chandelier and bitufted types. We characterized the types with interpretable models or with up to ten morphometrics. [Conclusion] Except for large basket, 50 high-quality reconstructions sufficed to learn an accurate model of a type. Improving these models may require quantifying complex arborization patterns and finding correlates of bouton-related features. Our study brings attention to practical aspects important for neuron classification and is readily reproducible, with all code and data available online.-
dc.description.sponsorshipThis project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreement No. 785907 (HBP SGA2), the Spanish Ministry of Economy and Competitiveness through the Cajal Blue Brain (C080020-09; the Spanish partner of the EPFL Blue Brain initiative) and TIN2016-79684-P projects, from the Regional Government of Madrid through theS2013/ICE-2845-CASI-CAM-CM project, and from Fundación BBVA grants to Scientific Research Teams in Big Data 2016.-
dc.publisherBioMed Central-
dc.relationinfo:eu-repo/grantAgreement/EC/H2020/785907-
dc.relationinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TIN2016-79684-P-
dc.relation2013/ICE-2845-CASI-CAM-CM-
dc.relationinfo:eu-repo/grantAgreement/EC/H2020/785907-
dc.relation.isversionofPublisher's version-
dc.rightsopenAccess-
dc.subjectFeature selection-
dc.subjectMartinotti-
dc.subjectMorphometrics-
dc.subjectFeature selection-
dc.subjectMartinott-
dc.subjectMorphometrics-
dc.titleTowards a supervised classification of neocortical interneuron morphologies-
dc.typeartículo-
dc.identifier.doi10.1186/s12859-018-2470-1-
dc.description.peerreviewedPeer reviewed-
dc.relation.publisherversionhttps://doi.org/10.1186/s12859-018-2470-1-
dc.identifier.e-issn1471-2105-
dc.date.updated2018-12-23T04:16:40Z-
dc.language.rfc3066en-
dc.rights.holderThe Author(s)-
dc.rights.licensehttp://creativecommons.org/licenses/by/4.0/-
dc.contributor.funderMinisterio de Economía, Industria y Competitividad (España)-
dc.contributor.funderEuropean Commission-
dc.contributor.funderComunidad de Madrid-
dc.contributor.funderFundación BBVA-
dc.relation.csic-
dc.identifier.funderhttp://dx.doi.org/10.13039/100007406es_ES
dc.identifier.funderhttp://dx.doi.org/10.13039/501100000780es_ES
dc.identifier.funderhttp://dx.doi.org/10.13039/100012818es_ES
dc.identifier.funderhttp://dx.doi.org/10.13039/501100010198es_ES
dc.identifier.pmid30558530-
dc.type.coarhttp://purl.org/coar/resource_type/c_6501es_ES
item.fulltextWith Fulltext-
item.openairetypeartículo-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
item.grantfulltextopen-
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