2012-07-20 - TrakEM2 published in PLoS ONE

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The TrakEM2 software has been published in PLoS ONE [1], establishing a primary reference for this program. TrakEM2 started in 2005 when Albert Cardona worked for the whole Summer with Rodney J. Douglas at the Institute of Neuroinformatics in Zurich, Switzerland, to establish an ImageJ-based program to aid in the reconstruction of neural circuits from large image volumes.

In its path, TrakEM2 fostered the development of software libraries for image registration, leading to the extraordinary work of Stephan Saalfeld and Stephan Preibisch at the lab of Pavel Tomancak at MPI-CBG, Dresden. Albert Cardona's work on TraKEM2 contributed to the VIB libraries by Johannes Schindelin, Bene Schmid and Mark Longair, and in particular to the development of the 3D Viewer[2] for the rendering of meshes and skeletons in 3D. The scripting utilities now present in Fiji, and Fiji itself, spinned off from work in or related to TrakEM2.

TrakEM2 has now reached version 1.0 and is feature complete.


  1. Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein and Rodney J. Douglas (2012), "TrakEM2 software for neural circuit reconstruction", PLoS ONE, doi:10.1371/journal.pone.0038011, <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038011>
  2. Benjamin Schmid , Johannes Schindelin , Albert Cardona , Mark Longair and Martin Heisenberg (2010), "A high-level 3D visualization API for Java and ImageJ", BMC Bioinformatics 11: 274, <http://www.biomedcentral.com/1471-2105/11/274/abstract>