Electron Tomography: A 3D View of the Subcellular World

Downing, Kenneth H.; Sui, Haixin; Auer, Manfred

doi:10.1021/ac071982u

Cited by 17 publications

(10 citation statements)

References 29 publications

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“…Electron tomography is a powerful technique that can reveal the 3D structure of a sample at the nanometer scale. In electron tomography, a sample is placed on a platform and tomographic measurements are obtained as this platform is tilted relative to a fixed X-ray source [41]. Because of the physical constraints of the system, the tilting can only cover a limited angular range, resulting in a limited-angle tomographic inversion problem.…”

Section: B Discrete Tomographymentioning

confidence: 99%

Graph-Cut Based Discrete-Valued Image Reconstruction

Tüysüzoğlu

Karl

Stojanović

et al. 2015

IEEE Trans. on Image Process.

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Efficient graph-cut methods have been used with great success for labeling and denoising problems occurring in computer vision. Unfortunately, the presence of linear image mappings has prevented the use of these techniques in most discrete-amplitude image reconstruction problems. In this paper, we develop a graph-cut based framework for the direct solution of discrete amplitude linear image reconstruction problems cast as regularized energy function minimizations. We first analyze the structure of discrete linear inverse problem cost functions to show that the obstacle to the application of graph-cut methods to their solution is the variable mixing caused by the presence of the linear sensing operator. We then propose to use a surrogate energy functional that overcomes the challenges imposed by the sensing operator yet can be utilized efficiently in existing graph-cut frameworks. We use this surrogate energy functional to devise a monotonic iterative algorithm for the solution of discrete valued inverse problems. We first provide experiments using local convolutional operators and show the robustness of the proposed technique to noise and stability to changes in regularization parameter. Then we focus on nonlocal, tomographic examples where we consider limited-angle data problems. We compare our technique with state-of-the-art discrete and continuous image reconstruction techniques. Experiments show that the proposed method outperforms state-of-the-art techniques in challenging scenarios involving discrete valued unknowns.

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Section: B Discrete Tomographymentioning

confidence: 99%

Graph-Cut Based Discrete-Valued Image Reconstruction

Tüysüzoğlu

Karl

Stojanović

et al. 2015

IEEE Trans. on Image Process.

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“…By means of sub-tomogram averaging of molecular motifs, cryo-electron tomography can facilitate identification of macromolecules by their shape, and reveal their relationship to component proteins of the local cellular architecture. For example, cryo-electron tomography with sub-volume averaging has been used to successfully determine the molecular architectures of a number of ciliar/flagellar protein complexes of eukaryotic or bacterial cells in native state and in situ (Bui et al, 2008; Downing et al, 2007; Liu et al, 2008; Nicastro et al, 2006; Sui and Downing, 2006). For such work, the voxel intensity of the molecular motif must reliably represent the actual shape of the molecule.…”

Section: Introductionmentioning

confidence: 99%

Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM

Kishchenko

Danev

Fisher

et al. 2015

Journal of Structural Biology

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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.

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“…In this technique, a tilt series of tomographic projections is obtained and then reconstructed to obtain volumetric information. 1 Because of the physical limitations of the electron microscope, only a limited angular range of tilts can be obtained, producing data equivalent to that seen in limited angle tomography.…”

Section: Introductionmentioning

confidence: 99%

Joint reconstruction and segmentation of electron tomography data

Tüysüzoğlu

Karl

Castañón

et al. 2013

Computational Imaging XI

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Scanning transmission electron tomography is often used to reveal the internal structure of material samples. In this technique, a tilt series of tomographic projections is reconstructed to obtain volumetric information. The reconstructed scene is then segmented into regions with homogeneous properties to localize and quantify various material elements. Unfortunately, physical constraints limit the extent of the projection tilt series, leading to artifacts in the reconstructed volume, which can make subsequent segmentation difficult. In this work we use a different, discrete tomography, approach wherein we directly reconstruct only a limited and discrete set of pixel amplitudes, effectively performing the reconstruction and segmentation in a joint fashion. Unlike existing methods, the approach is based on direct formulation of the problem in the discrete domain. Solution of the subsequent challenging optimization problem is achieved through the iterative use of graph-cut methods applied to a physically motivated surrogate cost function. We show reconstruction results using synthetic phantom images for limited angle scenarios and compare them to conventional reconstruction techniques.

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Electron Tomography: A 3D View of the Subcellular World

Cited by 17 publications

References 29 publications

Graph-Cut Based Discrete-Valued Image Reconstruction

Graph-Cut Based Discrete-Valued Image Reconstruction

Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM

Joint reconstruction and segmentation of electron tomography data

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