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TrakEM2 Software for Neural Circuit Reconstruction

Author

Listed:
  • Albert Cardona
  • Stephan Saalfeld
  • Johannes Schindelin
  • Ignacio Arganda-Carreras
  • Stephan Preibisch
  • Mark Longair
  • Pavel Tomancak
  • Volker Hartenstein
  • Rodney J Douglas

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.

Suggested Citation

  • Albert Cardona & Stephan Saalfeld & Johannes Schindelin & Ignacio Arganda-Carreras & Stephan Preibisch & Mark Longair & Pavel Tomancak & Volker Hartenstein & Rodney J Douglas, 2012. "TrakEM2 Software for Neural Circuit Reconstruction," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-8, June.
    • Handle: RePEc:plo:pone00:0038011
    DOI: 10.1371/journal.pone.0038011
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    References listed on IDEAS

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    1. Davi D. Bock & Wei-Chung Allen Lee & Aaron M. Kerlin & Mark L. Andermann & Greg Hood & Arthur W. Wetzel & Sergey Yurgenson & Edward R. Soucy & Hyon Suk Kim & R. Clay Reid, 2011. "Network anatomy and in vivo physiology of visual cortical neurons," Nature, Nature, vol. 471(7337), pages 177-182, March.
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    Cited by:

    1. Chenlong Zhang & Nicholas C Anzalone & Rodrigo P Faria & Joshua M Pearce, 2013. "Open-Source 3D-Printable Optics Equipment," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-13, March.

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