title: Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM.
abstract: Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the "missing wedge" and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging.
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.
authors.forename: Gregory P
authors.initials: GP
authors.lastname: Kishchenko
authors.affiliation: Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Radostin
authors.initials: R
authors.lastname: Danev
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Fisher
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.
authors.forename: Jie
authors.initials: J
authors.lastname: He
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.
authors.forename: Chyongere
authors.initials: C
authors.lastname: Hsieh
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Marko
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12201, United States. Electronic address: haixin.sui@health.ny.gov.
authors.forename: Haixin
authors.initials: H
authors.lastname: Sui
mesh_terms: D016477:Artifacts; D020285:Cryoelectron Microscopy / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods; D046911:Macromolecular Substances / Q000737:chemistry; D046529:Microscopy, Electron, Transmission / Q000379:methods*; D008858:Microscopy, Phase-Contrast / Q000379:methods
chemical_list: D046911:Macromolecular Substances
keywords: Electron tomography; Image processing; Sub-volume averaging; Zernike phase-plate