A package for membrane segmentation in electron tomography

A. Martínez-Sánchez (1), I. García (2), J.J. Fernández (3)

(1) Associated unit CSIC+UAL. Univ. Almeria. 04120 Almeria. Spain.
(2) Dept. Computer Architecture. Univ. Málaga. 29080 Málaga. Spain.
(3) Centro Nacional de Biotecnologia - CSIC. 28049 Madrid. Spain.

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TomoSegMem is a software suite intended to assist users in segmenting membranes in tomograms. It is based on a local differential structure approach and on a Gaussian-like model of membrane profile. The approach is composed of a number of sequential stages. First, it isolates information through scale-space and finds potential membrane-like points at a local scale. Then, the structural information is integrated at a global scale to yield the definite segmentation. Code optimization and multithreading techniques have been used in the implementation in order to reduce the processing time and memory consumption. Additional programs are provided to convert the segmentation results to formats directly acceptable by well-known tools like Amira and IMOD. This allows the users to supervise and edit the segmentation results as necessary with their favourite visualization tools.

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

A differential structure approach to membrane segmentation in electron tomography.
A. Martinez-Sanchez, I. Garcia, J.J. Fernandez.
Journal of Structural Biology 175:372-383, 2011

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

Current version: December 2011

Available material:
  • Documentation in PDF:  tomosegmem.pdf

  • Dataset for training (see the manual)

  • Binaries for x86-based platforms under linux (64 and 32 bits)

  • Binaries for Intel-based Macs under OSX (10.6 and onwards)