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TrakEM2 software for neural circuit reconstruction.

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.

Pubmed ID: 22723842


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


PloS one

Publication Data

June 22, 2012

Associated Grants

  • Agency: NINDS NIH HHS, Id: 1-R01 NS054814-05
  • Agency: NINDS NIH HHS, Id: R01 NS054814

Mesh Terms

  • Animals
  • Models, Neurological
  • Nerve Net
  • Neuroimaging
  • Neurons
  • Software
  • Synapses
  • Synaptic Transmission