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KONRAD-ZUSE-ZENTRUM
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Actin Segmentation

The software provided on this page is an implementation of the actin segmentation methods described in [1]. The software was developed at Zuse Institute Berlin (ZIB) and Max Planck Institute of Biochemistry (MPI). The actin segmentation software is based on Amira 5.4.5. For users without Amira 5.4.5, a trial version of Amira 5.4.5 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. 



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.


Note: A new module enabling the detection of branching point candidates has been added to the package. The step by step instructions on how to use this module can be found in the tutorial.


Documentation

 A step by step tutorial shows you 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.

 Below you can find a series of tutorial videos covering the steps shown in the tutorial. 



Reference


 [1] 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 networksJournal of Structural Biology, 2011, doi:10.1016/j.jsb.2011.08.012