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

David Knoetel, Ronald Seidel, Steffen Prohaska, Mason N. Dean, Daniel Baum. Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage. PLOS ONE (in review)

The software was developed at the Zuse Institute Berlin (ZIB) and the Max Planck Institute of Colloids and Interfaces (MPI-CI) and is provided under an MIT-style license (see download archive). The commercial software Amira is required to run the extension package.

To use the software:

  1. Obtain Amira 6.3. Users without Amira 6.3 may request a trial version with a time-limited license from FEI Visualization Sciences Group.
  2. Download and install the ZIB extension package. The extension package is available for Windows 64-bit (Visual C++ 2013, VC12) and Linux 64-bit (GCC 4.4) at

Supplementary data is available from the digital repository Dryad (