Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion

J Struct Biol. 2001 Sep;135(3):239-50. doi: 10.1006/jsbi.2001.4406.


Electron tomography is a powerful technique capable of giving unique insights into the three-dimensional structural organization of pleomorphic biological objects. However, visualization and interpretation of the resulting volumetric data are hampered by an extremely low signal-to-noise ratio, especially when ice-embedded biological specimens are investigated. Usually, isosurface representation or volume rendering of such data is hindered without any further signal enhancement. We propose a novel technique for noise reduction based on nonlinear anisotropic diffusion. The approach combines efficient noise reduction with excellent signal preservation and is clearly superior to conventional methods (e.g., low-pass and median filtering) and invariant wavelet transform filtering. The gain in the signal-to-noise ratio is verified and demonstrated by means of Fourier shell correlation. Improved visualization performance after processing the 3D images is demonstrated with two examples, tomographic reconstructions of chromatin and of a mitochondrion. Parameter settings and discretization stencils are presented in detail.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anisotropy
  • Chromatin / chemistry
  • Chromatin / ultrastructure
  • Diffusion
  • Image Processing, Computer-Assisted / methods*
  • Image Processing, Computer-Assisted / statistics & numerical data
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Structure
  • Nonlinear Dynamics
  • Tomography / methods*
  • Tomography / statistics & numerical data


  • Chromatin
  • Macromolecular Substances