PMID- 22723842
OWN - NLM
STAT- MEDLINE
DCOM- 20121212
LR  - 20231105
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 7
IP  - 6
DP  - 2012
TI  - TrakEM2 software for neural circuit reconstruction.
PG  - e38011
LID - 10.1371/journal.pone.0038011 [doi]
LID - e38011
AB  - 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.
FAU - Cardona, Albert
AU  - Cardona A
AD  - Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, 
      Switzerland. sapristi@gmail.com
FAU - Saalfeld, Stephan
AU  - Saalfeld S
FAU - Schindelin, Johannes
AU  - Schindelin J
FAU - Arganda-Carreras, Ignacio
AU  - Arganda-Carreras I
FAU - Preibisch, Stephan
AU  - Preibisch S
FAU - Longair, Mark
AU  - Longair M
FAU - Tomancak, Pavel
AU  - Tomancak P
FAU - Hartenstein, Volker
AU  - Hartenstein V
FAU - Douglas, Rodney J
AU  - Douglas RJ
LA  - eng
GR  - R01 NS054814/NS/NINDS NIH HHS/United States
GR  - 1-R01 NS054814-05/NS/NINDS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20120619
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - Animals
MH  - *Models, Neurological
MH  - *Nerve Net
MH  - Neuroimaging
MH  - Neurons
MH  - *Software
MH  - Synapses
MH  - Synaptic Transmission/*physiology
PMC - PMC3378562
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2012/06/23 06:00
MHDA- 2012/12/13 06:00
PMCR- 2012/06/19
CRDT- 2012/06/23 06:00
PHST- 2012/03/22 00:00 [received]
PHST- 2012/04/28 00:00 [accepted]
PHST- 2012/06/23 06:00 [entrez]
PHST- 2012/06/23 06:00 [pubmed]
PHST- 2012/12/13 06:00 [medline]
PHST- 2012/06/19 00:00 [pmc-release]
AID - PONE-D-12-08402 [pii]
AID - 10.1371/journal.pone.0038011 [doi]
PST - ppublish
SO  - PLoS One. 2012;7(6):e38011. doi: 10.1371/journal.pone.0038011. Epub 2012 Jun 19.