A package for feature-preserving noise filtering in electron tomography

J.J. Fernández (1,2)

(1) Centro Nacional de Biotecnologia - CSIC. 28049 Madrid. Spain.
(2) Associated unit CSIC+UAL. Univ. Almeria. 04120 Almeria. Spain.

Contact: @


The program TOMOBFLOW (pronounced as tomo-be-flow) is intended for noise filtering with preservation of biologically relevant information. It is an efficient implementation of the Beltrami flow, a nonlinear filtering method that locally tunes the strength of the smoothing according to an edge indicator based on geometry properties. TOMOBFLOW is equipped with the power of diffusion-based filtering methods, with the important advantage that it does not require complicated parameter tuning for successful denoising of datasets. Furthermore, the program has been optimized to reduce the computational demands, specially in terms of memory requirements. In addition, code optimization and multithread programming has been used to exploit modern multicore computers. TOMOBFLOW reads and writes 3D datasets in MRC format. It is compatible with standard packages, which easily allows integration in the electron tomography workflow.

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

TOMOBFLOW: Feature-preserving noise filtering for electron tomography.
J.J. Fernandez.
BMC Bioinformatics 2009, 10:178.

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

Current version: July 2011

Available material:
  • Documentation in PDF:  tomobflow.pdf

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

  • Binaries for Intel-based Macs under OSX (10.5 and onwards; 64 and 32 bits)

The development of tomobflow has been supported by the Spanish MEC and MCI, J.Andalucia and the European Network of Excellence 3DEM.

Copyright by the author.