The research software provided on this page is an Amira extension package that implements the methods described in:

Alexander Rigort, David Günther, Reiner Hegerl, Daniel Baum, Britta Weber, Steffen Prohaska, Ohad Medalia, Wolfgang Baumeister, and Hans-Christian Hege, Automated segmentation of electron tomograms for a quantitative description of actin filament networks, Journal of Structural Biology, 2011, doi:10.1016/j.jsb.2011.08.012.

The software was developed at Zuse Institute Berlin (ZIB) and Max Planck Institute of Biochemistry (MPI). The actin segmentation software is based on Amira. It is available for Amira 5.4.5, 5.6.0, 6.0.0, and 6.3.0. For users without Amira, a trial version of Amira 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 new module enabling the detection of branching point candidates has been added to the package after publication. Instructions how to use this module are found in the tutorial.

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.

System Requirements

In order to use the software, you need an NVIDIA graphics card supporting CUDA 1.2. To find out whether your graphics card supports CUDA 1.2, click here. We recommend using a graphics card with at least 256MB of memory. Concerning the CPU, a standard CPU should be sufficient. The software should work properly with 4GB of main memory, but we recommend 8GB or more. Furthermore, a 64-bit system is recommended and in fact is needed for Linux and Windows. On MacX, unfortunately, there is only a 32-bit version available.

Documentation

A step-by-step tutorial explains how to use the software for automated segmentation of actin filaments. The results of the step by step tutorial can be seen in a demo network.

A series of tutorial videos covering the steps shown in the tutorial are available at the links below: 

Teaser image