Reprint of “Fiducial-less alignment of cryo-sections” [J. Struct. Biol. 159 (2007) 413–423]

Castaño-Díez, Daniel; Al‐Amoudi, Ashraf; Glynn, Anne-Marie; Seybert, Anja; Frangakis, Achilleas S.

doi:10.1016/s1047-8477(08)00060-9

Cited by 2 publications

(2 citation statements)

References 22 publications

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“…With sufficient contrast of image features, markerless alignment can be used. A method has been developed in which a large array of randomly chosen points is tracked by cross-correlation . Because of the continually changing images, tracking is done through many overlapping short trails.…”

Section: Image Alignmentmentioning

confidence: 99%

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

2011

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Introduction 7711 1.1. Light and Electron Microscopy and Their Impact in Biology 7711 1.2. EM of Macromolecular Assemblies, Isolated and in Situ 7711 2. EM Imaging 7711 2.1. Sample Preparation 7711 2.1.1. Negative Staining of Isolated Assemblies 7712 2.1.2. Cryo EM of Isolated and Subcellular Assemblies 7712 2.1.3. Stabilization of Dynamic Assemblies 7713 2.1.4. EM Preparation of Cells and Tissues 7713 2.2. Interaction of Electrons with the Specimen 7714 2.

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Section: Image Alignmentmentioning

confidence: 99%

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

2011

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“…A second approach is feature-based alignment. In this method, rather than relying on gold nanoparticles as fiducial markers, feature points (such as Harris corners (Harris and Stephens, 1988)) are extracted from the images themselves, and these are used as the fiducial markers that are tracked across the image stack (Castano-Diez et al, 2010; Castano-Diez et al, 2008b; Sorzano et al, 2009; Winkler and Taylor, 2006). A third approach is known as a 3D model-based method, in which an initial alignment is used to generate a tomographic reconstruction, and the projections are iteratively aligned to this volume and then used to generate a new refined volume (Amat et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Automatic alignment and reconstruction of images for soft X-ray tomography

Parkinson

Knoechel

Yang

et al. 2012

Journal of Structural Biology

106

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Soft x-ray tomography (SXT) is a powerful imaging technique that generates quantitative, 3D images of the structural organization of whole cells in a near-native state. SXT is also a high-throughput imaging technique. At the National Center for X-ray Tomography (NCXT), specimen preparation and image collection for tomographic reconstruction of a whole cell require only minutes. Aligning and reconstructing the data, however, take significantly longer. Here we describe a new component of the high throughput computational pipeline used for processing data at the NCXT. We have developed a new method for automatic alignment of projection images that does not require fiducial markers or manual interaction with the software. This method has been optimized for SXT data sets, which routinely involve full rotation of the specimen. This software gives users of the NCXT SXT instrument a new capability - virtually real-time initial 3D results during an imaging experiment, which can later be further refined. The new code, Automatic Reconstruction 3D (AREC3D), is also fast, reliable and robust. The fundamental architecture of the code is also adaptable to high performance GPU processing, which enables significant improvements in speed and fidelity.

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Reprint of “Fiducial-less alignment of cryo-sections” [J. Struct. Biol. 159 (2007) 413–423]

Cited by 2 publications

References 22 publications

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

Automatic alignment and reconstruction of images for soft X-ray tomography

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