TrakEM2 software for neural circuit reconstruction.

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PLoS One. 2012;7(6):e38011. doi: 10.1371/journal.pone.0038011

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TrakEM2 software for neural circuit reconstruction. Saalfeld LabCardona Lab

Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ

Note: Research in this publication was not performed at Janelia.

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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.

PMID: 22723842 [PubMed - indexed for MEDLINE]

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TrakEM2 software for neural circuit reconstruction.

Note: Research in this publication was not performed at Janelia.

Abstract

PMID: 22723842 [PubMed - indexed for MEDLINE]

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