TrakEM2 software for neural circuit reconstruction.

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application,...

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Autores principales:	Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney J Douglas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cb094fa841bf4fa09b6925752f8100fd
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spelling	oai:doaj.org-article:cb094fa841bf4fa09b6925752f8100fd2021-11-18T07:15:04ZTrakEM2 software for neural circuit reconstruction.1932-620310.1371/journal.pone.0038011https://doaj.org/article/cb094fa841bf4fa09b6925752f8100fd2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22723842/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.Albert CardonaStephan SaalfeldJohannes SchindelinIgnacio Arganda-CarrerasStephan PreibischMark LongairPavel TomancakVolker HartensteinRodney J DouglasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e38011 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Albert Cardona Stephan Saalfeld Johannes Schindelin Ignacio Arganda-Carreras Stephan Preibisch Mark Longair Pavel Tomancak Volker Hartenstein Rodney J Douglas TrakEM2 software for neural circuit reconstruction.
description	A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.
format	article
author	Albert Cardona Stephan Saalfeld Johannes Schindelin Ignacio Arganda-Carreras Stephan Preibisch Mark Longair Pavel Tomancak Volker Hartenstein Rodney J Douglas
author_facet	Albert Cardona Stephan Saalfeld Johannes Schindelin Ignacio Arganda-Carreras Stephan Preibisch Mark Longair Pavel Tomancak Volker Hartenstein Rodney J Douglas
author_sort	Albert Cardona
title	TrakEM2 software for neural circuit reconstruction.
title_short	TrakEM2 software for neural circuit reconstruction.
title_full	TrakEM2 software for neural circuit reconstruction.
title_fullStr	TrakEM2 software for neural circuit reconstruction.
title_full_unstemmed	TrakEM2 software for neural circuit reconstruction.
title_sort	trakem2 software for neural circuit reconstruction.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/cb094fa841bf4fa09b6925752f8100fd
work_keys_str_mv	AT albertcardona trakem2softwareforneuralcircuitreconstruction AT stephansaalfeld trakem2softwareforneuralcircuitreconstruction AT johannesschindelin trakem2softwareforneuralcircuitreconstruction AT ignacioargandacarreras trakem2softwareforneuralcircuitreconstruction AT stephanpreibisch trakem2softwareforneuralcircuitreconstruction AT marklongair trakem2softwareforneuralcircuitreconstruction AT paveltomancak trakem2softwareforneuralcircuitreconstruction AT volkerhartenstein trakem2softwareforneuralcircuitreconstruction AT rodneyjdouglas trakem2softwareforneuralcircuitreconstruction
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TrakEM2 software for neural circuit reconstruction.

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