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  TrakEM2 Software for Neural Circuit Reconstruction.

Cardona, A., Saalfeld, S., Schindelin, J., Arganda-Carreras, I., Preibisch, S. W., Longair, M., et al. (2012). TrakEM2 Software for Neural Circuit Reconstruction. PLoS ONE, 7(6): e38011.

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 Creators:
Cardona, Albert1, Author
Saalfeld, Stephan2, Author           
Schindelin, Johannes2, Author           
Arganda-Carreras, Ignacio, Author
Preibisch, Stephan W.2, Author           
Longair, Mark, Author
Tomancak, Pavel2, Author           
Hartenstein, Volker2, Author           
Douglas, Rodney J, Author
Affiliations:
1Max Planck Society, ou_persistent13              
2Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society, ou_2340692              

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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.

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 Dates: 2012
 Publication Status: Issued
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 Identifiers: eDoc: 645213
Other: 4851
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Title: PLoS ONE
Source Genre: Journal
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Pages: - Volume / Issue: 7 (6) Sequence Number: e38011 Start / End Page: - Identifier: -