Fast nonlocal filtering applied to electron cryomicroscopy

Jérôme Darbon*, Alexandre Cunha, Tony Chan, Stanley Osher, Grant J. Jensen

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

190 Scopus citations

Abstract

We present an efficient algorithm for nonlocal image filtering with applications in electron cryomicroscopy. Our denoising algorithm is a rewriting of the recently proposed nonlocal mean filter. It builds on the separable property of neighborhood filtering to offer a fast parallel and vectorized implementation in contemporary shared memory computer architectures while reducing the theoretical computational complexity of the original filter. In practice, our approach is much faster than a serial, non-vectorized implementation and it scales linearly with image size. We demonstrate its efficiency in data sets fromCaulobacter crescentus tomograms and a cryoimage containing viruses and provide visual evidences attesting the remarkable quality of the nonlocal means scheme in the context of cryoimaging. With such development we provide biologists with an attractive filtering tool to facilitate their scientific discoveries.

Original languageEnglish (US)
Title of host publication2008 5th IEEE International Symposium on Biomedical Imaging
Subtitle of host publicationFrom Nano to Macro, Proceedings, ISBI
Pages1331-1334
Number of pages4
DOIs
StatePublished - Sep 10 2008
Event2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI - Paris, France
Duration: May 14 2008May 17 2008

Publication series

Name2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Proceedings, ISBI

Conference

Conference2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI
CountryFrance
CityParis
Period05/14/0805/17/08

Keywords

  • Electron cryomicroscopy
  • Image denoising
  • Image vectorization
  • Nonlocal mean filtering
  • Parallel image processing
  • SIMD

ASJC Scopus subject areas

  • Biomedical Engineering

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