Biophysical Reviews

, Volume 4, Issue 3, pp 223–229 | Cite as

Developing a denoising filter for electron microscopy and tomography data in the cloud

  • Zbigniew Starosolski
  • Marek Szczepanski
  • Manuel Wahle
  • Mirabela Rusu
  • Willy Wriggers
Review

Abstract

The low radiation conditions and the predominantly phase-object image formation of cryo-electron microscopy (cryo-EM) result in extremely high noise levels and low contrast in the recorded micrographs. The process of single particle or tomographic 3D reconstruction does not completely eliminate this noise and is even capable of introducing new sources of noise during alignment or when correcting for instrument parameters. The recently developed Digital Paths Supervised Variance (DPSV) denoising filter uses local variance information to control regional noise in a robust and adaptive manner. The performance of the DPSV filter was evaluated in this review qualitatively and quantitatively using simulated and experimental data from cryo-EM and tomography in two and three dimensions. We also assessed the benefit of filtering experimental reconstructions for visualization purposes and for enhancing the accuracy of feature detection. The DPSV filter eliminates high-frequency noise artifacts (density gaps), which would normally preclude the accurate segmentation of tomography reconstructions or the detection of alpha-helices in single-particle reconstructions. This collaborative software development project was carried out entirely by virtual interactions among the authors using publicly available development and file sharing tools.

Keywords

cryo-EM Digital paths Filtering Helix detection Supervised classification Remote collaboration 

Supplementary material

12551_2012_83_MOESM1_ESM.pdf (1.9 mb)
ESM 1(PDF 1920 kb)

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Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer 2012

Authors and Affiliations

  • Zbigniew Starosolski
    • 1
    • 2
    • 3
  • Marek Szczepanski
    • 1
  • Manuel Wahle
    • 2
  • Mirabela Rusu
    • 2
    • 4
  • Willy Wriggers
    • 5
    • 6
  1. 1.Faculty of Automatic Control, Electronics and Computer ScienceSilesian University of TechnologyGliwicePoland
  2. 2.School of Biomedical InformaticsUniversity of Texas Health Science CenterHoustonUSA
  3. 3.Department of Pediatric RadiologyTexas Children’s HospitalHoustonUSA
  4. 4.Department of Biomedical Engineering, RutgersThe State University of New JerseyPiscatawayUSA
  5. 5.Department of Physiology and Biophysics and Institute for Computational BiomedicineWeill Medical College of Cornell UniversityNew YorkUSA
  6. 6.D. E. Shaw ResearchNew YorkUSA

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