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TrakEM2 software for neural circuit reconstruction

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Item Type:Article
Title:TrakEM2 software for neural circuit reconstruction
Creators Name:Cardona, A. and Saalfeld, S. and Schindelin, J. and Arganda-Carreras, I. and Preibisch, S. and Longair, M. and Tomancak, P. and Hartenstein, V. and Douglas, R.J.
Abstract: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.
Keywords:Nerve Net, Neurological Models, Neuroimaging, Neurons, Software, Synapses, Synaptic Transmission, Animals
Source:PLoS ONE
Publisher:Public Library of Science
Page Range:e38011
Date:19 June 2012
Official Publication:https://doi.org/10.1371/journal.pone.0038011
PubMed:View item in PubMed

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