From gigabytes to bytes: Automated denoising and feature identification in electron tomograms of intact bacterial cells

Rajesh Narasimha, Iman Aganj, Mario Borgnia, Guillermo Sapiro, Steven McLaughlin, Jacqueline Milne, Sriram Subramaniam

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Advances in automated data acquisition in electron tomography have led to an explosion in the amount of data that can be obtained about the spatial architecture of a variety of biologically and medically relevant objects with resolutions in the "nano" range of 10-1000 nm. The development of methods to automatically analyze the vast amounts of information contained in these tomograms is a major challenge since the electron tomograms are intrinsically very noisy. A fundamental step in the automatic analysis of large amounts of data for statistical inference is to segment relevant 3D features in cellular tomograms. Procedures for segmentation must work robustly and rapidly in spite of the low signal to noise ratios inherent to biological electron microscopy. This work first evaluates various non-linear denoising techniques on tomograms recorded at cryogenic temperatures. Using datasets of bacterial tomograms as an example, we demonstrate that non-linear diffusion techniques significantly improve the fidelity of automated feature extraction. Our approach represents an important step in automating the efficient extraction of useful information from large datasets in biological tomography, and facilitates the overall goal of speeding up the process of reducing gigabyte-sized tomograms to relevant byte-sized data.

Original languageEnglish (US)
Title of host publication2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings
Pages304-307
Number of pages4
DOIs
StatePublished - 2007
Externally publishedYes
Event2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro; ISBI'07 - Arlington, VA, United States
Duration: Apr 12 2007Apr 15 2007

Other

Other2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro; ISBI'07
CountryUnited States
CityArlington, VA
Period4/12/074/15/07

Keywords

  • Automated techniques
  • Denoising
  • Diffusion
  • Electron tomography
  • Feature extraction
  • Template matching

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Medicine(all)

Fingerprint Dive into the research topics of 'From gigabytes to bytes: Automated denoising and feature identification in electron tomograms of intact bacterial cells'. Together they form a unique fingerprint.

Cite this