TrakEM2: Powerful Image Analysis Tool

TrakEM2 has been written using the Java programming language and uses numerous image processing libraries including ImageJ (Wayne Rasband), mpicbg (Stephan Saalfeld), LOCI bio-formats [37] (link), ImgLib (Stephan Preibisch, Stephan Saalfeld, Tobias Pietzsch and others), ImageJ 3D Viewer [38] (link), Stitching [39] (link), bUnwarpJ [40] , JaMa (Mathworks and NIST), postgresql-jdbc, JFreeChart (jfree.org), edu_mines_jtk (Dave Hale), Level Sets (Erwin Frise) and Simple Neurite Tracer [41] , among others. The source code is released under the General Public License and is under version control with git at http://repo.or.cz/w/TrakEM2.git. Binaries are distributed with Fiji (Schindelin et al, submitted to Nature Methods) via the automatic plugin updater.

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Cardona A., Saalfeld S., Schindelin J., Arganda-Carreras I., Preibisch S., Longair M., Tomancak P., Hartenstein V, & Douglas R.J. (2012). TrakEM2 Software for Neural Circuit Reconstruction. PLoS ONE, 7(6), e38011.

Publication 2012

Neurite

Corresponding Organization : ETH Zurich

Other organizations : Max Planck Institute of Molecular Cell Biology and Genetics, Massachusetts Institute of Technology, University of California, Los Angeles

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