TrakEM2 pipeline

TrakEM2 specifications


Unique identifier OMICS_27137
Name TrakEM2
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Output data A neural circuit.
Output format NeuroML
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Requirements ImageJ, Java3D
Source code URL
Maintained Yes


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  • person_outline Albert Cardona <>
  • person_outline Albert Cardona <>

Additional information

Publication for TrakEM2

TrakEM2 citation

PMCID: 3916342

[…] px., three independent human annotators (trained by an expert neuroscientist, but themselves inexpert) then marked all synapses in the rectangle [[1000, 1120, 30], [6000, 6120, 36]], using the fiji trakem2 plugin [33]. the three annotation sets were compared automatically and an expert neuroscientist resolved all cases where the three annotators did not agree. the resulting test set contained […]

TrakEM2 institution(s)
Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Massachusetts Institute of Technology, Boston, MA, USA; Molecular Cell and Developmental Biology Department, University of California Los Angeles, Los Angeles, CA, USA
TrakEM2 funding source(s)
Supported by Kevan A. Martin, the Institute of Neuroinformatics, University of Zurich and ETH Zurich; and by grant NIH 1- R01 NS054814-05 and grant SNSF 31003A_132969.

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