The research software provided on this page is an Amira extension package that implements the methods described in:
Britta Weber, Garrett Greenan, Steffen Prohaska, Daniel Baum, Hans-Christian Hege,Thomas Müller-Reichert, Anthony A. Hyman, Jean-Marc Verbavatz (2012). Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos, Journal of Structural Biology, 178(2):129–138, doi:10.1016/j.jsb.2011.12.004.
The software was developed at Zuse Institute Berlin (ZIB) and Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). The microtubule tracing software is based on Amira 5.4. For users without Amira 5.4, a trial version of Amira 5.4 together with a time-limited license can be obtained from FEI Visualization Sciences Group
In order to obtain the software, you need to register. Registering requires that you read and accept the software license. After registration, we will send you an email containing all necessary information for downloading and installing the software.
A brief introduction how to get started is available at http://amira.zib.de/packages/microtubuleSeg/MicrotubuleSegAmiraTutorial.pdf
An online version of the software is available at http://amitube.mpi-cbg.de.
A commercial add-on to Amira with equivalent features, simplified usage, and greater stability is now also available. Contact FEI Visualization Sciences Group for details.
Some of the data sets used in the publication are available at http://publications.mpi-cbg.de/4629-data.
If you use any of the data sets, please cite the publication above.