Three-Dimensional<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>GaN</mml:mi><mml:mtext mathvariant="normal">−</mml:mtext><mml:msub><mml:mi>Ga</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:math>Core Shell Structure Revealed by X-Ray Diffraction Microscopy

Miao, Jianwei; Chen, Chien-Chun; Song, Changyong; Nishino, Yoshinori; Kohmura, Yoshiki; Ishikawa, Tetsuya; Ramunno-Johnson, Damien; Lee, Ting-Kuo; Risbud, Subhash H.

doi:10.1103/physrevlett.97.215503

Cited by 129 publications

(79 citation statements)

References 24 publications

(16 reference statements)

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“…In our reconstructions, we terminated the algorithm after ∼150 iterations when the error function became stabilized. Both numerical simulations and experimental results from cryoelectron microscopy have indicated that EST produces superior results relative to FBP and the algebraic reconstruction technique when there is a limited number of projections as well as the missing wedge problem (12,39,40). After the 3D image was obtained by EST, we verified the fidelity of the reconstruction by calculating 25 diffraction patterns from the reconstructed 3D image.…”

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confidence: 86%

“…To address this problem, the EST method, an iterative reconstruction method that aims to solve for a portion of the missing projection data, was employed for the tomographic reconstruction. The EST method is coupled with an acquisition scheme for which the projections are acquired at equal slope intervals, instead of equal angle intervals, which results in the elimination of interpolative inaccuracies in conventional tomographic methods (12,39,40). EST iterates back and forth between real and reciprocal space.…”

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confidence: 99%

“…Because the projectional images can have an arbitrary shift along the x and y axes, they must be aligned before the 3D reconstruction. Although there exists a variety of image alignment approaches, we chose the method based on the moment of charge density distribution (38), which has been experimentally tested (12). Using this method, we aligned the 25 images to a common tilt axis (Materials and Methods).…”

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confidence: 99%

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Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy

Jiang

Song

Chen

et al. 2010

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

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Microscopy has greatly advanced our understanding of biology. Although significant progress has recently been made in optical microscopy to break the diffraction-limit barrier, reliance of such techniques on fluorescent labeling technologies prohibits quantitative 3D imaging of the entire contents of cells. Cryoelectron microscopy can image pleomorphic structures at a resolution of 3-5 nm, but is only applicable to thin or sectioned specimens. Here, we report quantitative 3D imaging of a whole, unstained cell at a resolution of 50-60 nm by X-ray diffraction microscopy. We identified the 3D morphology and structure of cellular organelles including cell wall, vacuole, endoplasmic reticulum, mitochondria, granules, nucleus, and nucleolus inside a yeast spore cell. Furthermore, we observed a 3D structure protruding from the reconstructed yeast spore, suggesting the spore germination process. Using cryogenic technologies, a 3D resolution of 5-10 nm should be achievable by X-ray diffraction microscopy. This work hence paves a way for quantitative 3D imaging of a wide range of biological specimens at nanometer-scale resolutions that are too thick for electron microscopy.coherent diffractive imaging | equally sloped tomography | lensless imaging | iterative phase-retrieval algorithms | oversampling A pplication of the long penetration depth of X-rays to the imaging of large, unstained biological specimens has long been recognized as a possible solution to the thickness restrictions of electron microscopy. Indeed, using sizable protein crystals, X-ray crystallography is currently the primary methodology used for determining the 3D structure of protein molecules at near-atomic or atomic resolution. However, many biological specimens such as whole cells, cellular organelles, some viruses, and many important protein molecules are difficult or impossible to crystallize and hence their structures are not accessible by crystallography. Overcoming these limitations requires the employment of different techniques. One promising approach currently under rapid development is coherent diffraction microscopy (also termed coherent diffractive imaging or lensless imaging) in which the coherent diffraction pattern of a noncrystalline specimen or a nanocrystal is measured and then directly phased to obtain an image (1-28). The well-known phase problem is solved by using the oversampling method (29) in combination with the iterative algorithms (30-33). Since its first experimental demonstration in 1999 (1), coherent diffraction microscopy has been applied to imaging a wide range of materials science and biological specimens such as nanoparticles, nanocrystals, biomaterials, cells, cellular organelles, viruses by using synchrotron radiation (2-21), high harmonic generation (22-24), soft X-ray laser sources (23, 25), and free electron lasers (26-28). Until now, however, the radiation damage problem and the difficulty of acquiring high-quality 3D diffraction patterns from individual whole cells have prevented the successful high-resolution ...

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Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy

Jiang

Song

Chen

et al. 2010

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

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262

153

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“…'. Indeed, since Sayre's first proposal of the method (Sayre, 1980) and its first demonstration by Miao (1999), it has been used to image three-dimensional micro-fabricated structures (Chapman, Barty, Beetz et al, 2006), small biological cells (Miao et al, 2003;Shapiro et al, 2005;Thibault et al, 2006), metallic microcrystals (Robinson et al, 2001;Pfeifer et al, 2006), ultralow-density foams (Barty et al, 2007) and quantum dots, among others (Miao et al, 2006). The maturity of the field can be most clearly seen in two recent contributions from Chapman and Barty.…”

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confidence: 99%

Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction. Addendum

Shapiro

2007

Acta Cryst Sect A

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In the paper by Sayre [Acta Cryst.(2008), A64, 33–35], a proposal is made to use stereoscopy as a short-term means of overcoming the primarily technological hurdles involved in three-dimensional imaging of the biological cell by soft X-ray diffraction microscopy. This addendum provides a broader perspective on the techniques used by this rapidly maturing community to investigate structural problems in the biological and material sciences.

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“…The program suite contains many useful tools for image analysis that could be used for analyzing XFEL data. We tested our reconstruction program using experimental diffraction data of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy (CXDM) (Miao et al, 2006;Barty et al, 2008;Jiang et al, 2010) instead of data from XFEL. These data are very similar to those from XFEL experiments, the main difference being that XFEL is 'single-shot' while X-ray diffraction microscopy allows (weaker but) repeating exposure.…”

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confidence: 99%

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

Nakano

Miyashita

Jonić

et al. 2017

J Synchrotron Radiat

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The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

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Three-DimensionalGaN−Ga2O3Core Shell Structure Revealed by X-Ray Diffraction Microscopy

Cited by 129 publications

References 24 publications

Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy

Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy

Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction. Addendum

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

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