TrakEM2 Software for Neural Circuit Reconstruction

被引：696

作者：

Cardona, Albert ^{[1
,2
]}

Saalfeld, Stephan ^{[3
]}

Schindelin, Johannes ^{[3
]}

Arganda-Carreras, Ignacio ^{[4
]}

Preibisch, Stephan ^{[3
]}

Longair, Mark ^{[1
,2
]}

Tomancak, Pavel ^{[3
]}

Hartenstein, Volker ^{[5
]}

Douglas, Rodney J. ^{[1
,2
]}

机构：

[1] Univ Zurich, Inst Neuroinformat, Zurich, Switzerland

[2] ETH, Zurich, Switzerland

[3] Max Planck Inst Mol Cell Biol & Genet, Dresden, Germany

[4] MIT, Boston, MA USA

[5] Univ Calif Los Angeles, Mol Cell & Dev Biol Dept, Los Angeles, CA USA

来源：

PLOS ONE | 2012年 / 7卷 / 06期

关键词：

IMAGE DATA; TOMOGRAPHY; MICROSCOPY; VISUALIZATION; REGISTRATION; SYSTEM;

D O I：

10.1371/journal.pone.0038011

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：8

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