Noise Reduction in Electron Tomographic Reconstructions Using Nonlinear Anisotropic Diffusion

Frangakis, Achilleas S.; Hegerl, R.

doi:10.1006/jsbi.2001.4406

Cited by 409 publications

(287 citation statements)

References 15 publications

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“…Tomographic volumes were reconstructed with IMOD software (57). Contrast was enhanced by nonlinear anisotropic diffusion (58) and segmentation was performed using Amira software (Mercury Systems).…”

Section: Methodsmentioning

confidence: 99%

Chloroplast Omp85 proteins change orientation during evolution

Sommer

Daum

Groß

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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The majority of outer membrane proteins (OMPs) from Gramnegative bacteria and many of mitochondria and chloroplasts are β-barrels. Insertion and assembly of these proteins are catalyzed by the Omp85 protein family in a seemingly conserved process. All members of this family exhibit a characteristic N-terminal polypeptide-transport-associated (POTRA) and a C-terminal 16-stranded β-barrel domain. In plants, two phylogenetically distinct and essential Omp85's exist in the chloroplast outer membrane, namely Toc75-III and Toc75-V. Whereas Toc75-V, similar to the mitochondrial Sam50, is thought to possess the original bacterial function, its homolog, Toc75-III, evolved to the pore-forming unit of the TOC translocon for preprotein import. In all current models of OMP biogenesis and preprotein translocation, a topology of Omp85 with the POTRA domain in the periplasm or intermembrane space is assumed. Using selfassembly GFP-based in vivo experiments and in situ topology studies by electron cryotomography, we show that the POTRA domains of both Toc75-III and Toc75-V are exposed to the cytoplasm. This unexpected finding explains many experimental observations and requires a reevaluation of current models of OMP biogenesis and TOC complex function.

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Section: Methodsmentioning

confidence: 99%

Chloroplast Omp85 proteins change orientation during evolution

Sommer

Daum

Groß

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…Denoising was then necessary to discern and interpret structural features. A combination of Gaussian filtering (31) and anisotropic nonlinear diffusion (AND) (32,33) was used in this work. (For details, see the supporting information, which is published on the PNAS web site.)…”

Section: Methodsmentioning

confidence: 99%

Cryo-electron tomography of vaccinia virus

Cyrklaff

Risco²,

Fernández³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

186

150

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The combination of cryo-microscopy and electron tomographic reconstruction has allowed us to determine the structure of one of the more complex viruses, intracellular mature vaccinia virus, at a resolution of 4 -6 nm. The tomographic reconstruction allows us to dissect the different structural components of the viral particle, avoiding projection artifacts derived from previous microscopic observations. A surface-rendering representation revealed brickshaped viral particles with slightly rounded edges and dimensions of Ϸ360 ؋ 270 ؋ 250 nm. The outer layer was consistent with a lipid membrane (5-6 nm thick), below which usually two lateral bodies were found, built up by a heterogeneous material without apparent ordering or repetitive features. The internal core presented an inner cavity with electron dense coils of presumptive DNA-protein complexes, together with areas of very low density. The core was surrounded by two layers comprising an overall thickness of Ϸ18 -19 nm; the inner layer was consistent with a lipid membrane. The outer layer was discontinuous, formed by a periodic palisade built by the side interaction of T-shaped protein spikes that were anchored in the lower membrane and were arranged into small hexagonal crystallites. It was possible to detect a few pore-like structures that communicated the inner side of the core with the region outside the layer built by the T-shaped spike palisade.cryo-EM ͉ virus structure ͉ 3D reconstruction

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“…Also, the performance of the anisotropic diffusion filter was studied in order to facilitate the best choice among the various options of the governing parameters and to provide a complete image-adapted denoising tool.AD filter is devoted to medical images processing [16][17][18]. It permits di usion along edges and inhibits smoothing across them.…”

Section: Discussionmentioning

confidence: 99%

Structural similarity analysis for brain MR image quality assessment

Punga¹,

Moldovanu²,

Moraru³

2014

AIP Conference Proceedings

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Abstract. Brain MR images are affected and distorted by various artifacts as noise, blur, blotching, down sampling or compression and as well by inhomogeneity. Usually, the performance of pre-processing operation is quantified by using the quality metrics as mean squared error and its related metrics such as peak signal to noise ratio, root mean squared error and signal to noise ratio. The main drawback of these metrics is that they fail to take the structural fidelity of the image into account. For this reason, we addressed to investigate the structural changes related to the luminance and contrast variation (as non-structural distortions) and to denoising process (as structural distortion)through an alternative metric based on structural changes in order to obtain the best image quality.

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Noise Reduction in Electron Tomographic Reconstructions Using Nonlinear Anisotropic Diffusion

Cited by 409 publications

References 15 publications

Chloroplast Omp85 proteins change orientation during evolution

Chloroplast Omp85 proteins change orientation during evolution

Cryo-electron tomography of vaccinia virus

Structural similarity analysis for brain MR image quality assessment

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