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Journal Article

TrakEM2 Software for Neural Circuit Reconstruction.

MPS-Authors

Cardona,  Albert
Max Planck Society;

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Saalfeld,  Stephan
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Schindelin,  Johannes
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Preibisch,  Stephan W.
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Tomancak,  Pavel
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219225

Hartenstein,  Volker
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

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.


Cite as: https://hdl.handle.net/21.11116/0000-0001-097B-C
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.