TomoSegMemTV

A package for robust membrane segmentation based on Tensor Voting for electron tomography

A. Martínez-Sánchez (1,3), I. García (2), S. Asano (3), V. Lucic (3), J.J. Fernández (4)

(1) Associated unit CSIC+UAL. Univ. Almeria. 04120 Almeria. Spain.
(2) Dept. Computer Architecture. Univ. Málaga. 29080 Málaga. Spain.
(3) Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
(4) Centro Nacional de Biotecnologia - CSIC. 28049 Madrid. Spain.

Contact: an.martinez.s.sw@gmail.com






Description

TomoSegMemTV is a software package for segmenting membranes in tomograms. It is based on (1) a Gaussian-like model of membrane profile, (2) a local differential structure approach and (3) anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures.The method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The software is provided as a set of Matlab functions. The kernels of the most computationaly intensive operations were coded in C++ using code optimization and multithreading and are provided as binaries to be used within Matlab. A complementary package, SynapSegTools, with Graphical User Interface for intuitive and friendly segmentation of synapsis is also available.

 A detailed description of the procedure implemented in the package can be found in the following article:

Robust membrane detection based on tensor voting for electron tomography.
A. Martinez-Sanchez, I. Garcia, S. Asano, V. Lucic, J.J. Fernandez.
Journal of Structural Biology  186:49-61, 2014.

Please, cite this article if you use TomoSegMemTV in your works.



Request the package
Current version: April 2014


Available material:
  • Package for x86-based platforms under linux (64 bits)

  • Package for Intel-based Macs under OSX (10.7 and onwards)
  • Package for Windows 64 bits.