TrakEM2 Software for Neural Circuit Reconstruction
Name
Cardona-2012-TrakEM2 Software for.pdf
Size
667.63 KB
Format
Adobe PDF
Checksum (MD5)
41bd988c2912a2414628ead303ec1575
Author(s)
Cardona, Albert
Saalfeld, Stephan
Schindelin, Johannes
Arganda-Carreras, Ignacio
Preibisch, Stephan
Longair, Mark
Tomancak, Pavel
Hartenstein, Volker
Douglas, Rodney J.
Date Issued
June 2012
Journal
PLoS ONE
Publisher
Public Library of Science
Citation
Cardona, Albert et al. “TrakEM2 Software for Neural Circuit Reconstruction.” Ed. Aravinthan Samuel. PLoS ONE 7.6 (2012): e38011.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences
Terms of Use
Creative Commons Attribution
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1371/journal.pone.0038011
