Evaluation of denoising algorithms for biological electron tomography.

Journal Article (Journal Article)

Tomograms of biological specimens derived using transmission electron microscopy can be intrinsically noisy due to the use of low electron doses, the presence of a "missing wedge" in most data collection schemes, and inaccuracies arising during 3D volume reconstruction. Before tomograms can be interpreted reliably, for example, by 3D segmentation, it is essential that the data be suitably denoised using procedures that can be individually optimized for specific data sets. Here, we implement a systematic procedure to compare various nonlinear denoising techniques on tomograms recorded at room temperature and at cryogenic temperatures, and establish quantitative criteria to select a denoising approach that is most relevant for a given tomogram. We demonstrate that using an appropriate denoising algorithm facilitates robust segmentation of tomograms of HIV-infected macrophages and Bdellovibrio bacteria obtained from specimens at room and cryogenic temperatures, respectively. We validate this strategy of automated segmentation of optimally denoised tomograms by comparing its performance with manual extraction of key features from the same tomograms.

Full Text

Duke Authors

Cited Authors

  • Narasimha, R; Aganj, I; Bennett, AE; Borgnia, MJ; Zabransky, D; Sapiro, G; McLaughlin, SW; Milne, JLS; Subramaniam, S

Published Date

  • October 2008

Published In

Volume / Issue

  • 164 / 1

Start / End Page

  • 7 - 17

PubMed ID

  • 18585059

Pubmed Central ID

  • PMC2435207

Electronic International Standard Serial Number (EISSN)

  • 1095-8657

Digital Object Identifier (DOI)

  • 10.1016/j.jsb.2008.04.006


  • eng

Conference Location

  • United States