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Reconstruction Of A Yeast Cell From X Ray Diffraction Data
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Book Synopsis Reconstruction of a Yeast Cell from X-ray Diffraction Data by :
Download or read book Reconstruction of a Yeast Cell from X-ray Diffraction Data written by and published by . This book was released on 2006 with total page 14 pages. Available in PDF, EPUB and Kindle. Book excerpt: Details are provided of the algorithm used for the reconstruction of yeast cell images in the recent demonstration of diffraction microscopy by Shapiro, Thibault, Beetz, Elser, Howells, Jacobsen, Kirz, Lima, Miao, Nieman & Sayre. Two refinements of the iterative constraint-based scheme are developed to address the current experimental realities of this imaging technique, which include missing central data and noise. A constrained power operator is defined whose eigenmodes allow the identification of a small number of degrees of freedom in the reconstruction that are negligibly constrained as a result of the missing data. To achieve reproducibility in the algorithm's output, a special intervention is required for these modes. Weak incompatibility of the constraints caused by noise in both direct and Fourier space leads to residual phase fluctuations. This problem is addressed by supplementing the algorithm with an averaging method. The effect of averaging may be interpreted in terms of an effective modulation transfer function, as used in optics, to quantify the resolution. The reconstruction details are prefaced with simulations of wave propagation through a model yeast cell. These show that the yeast cell is a strong-phase-contrast object for the conditions in the experiment.
Book Synopsis X-Ray Diffraction by : Oliver H. Seeck
Download or read book X-Ray Diffraction written by Oliver H. Seeck and published by CRC Press. This book was released on 2015-02-10 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-resolution x-ray diffraction and scattering is a key tool for structure analysis not only in bulk materials but also at surfaces and buried interfaces from the sub-nanometer range to micrometers. This book offers an overview of diffraction and scattering methods currently available at modern synchrotron sources and illustrates bulk and interface investigations of solid and liquid matter with up-to-date research examples. It presents important characteristics of the sources, experimental set-up, and new detector developments. The book also considers future exploitation of x-ray free electron lasers for diffraction applications.
Book Synopsis X-Rays in Nanoscience by : Jinghua Guo
Download or read book X-Rays in Nanoscience written by Jinghua Guo and published by John Wiley & Sons. This book was released on 2011-09-22 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: An up-to-date overview of the different x-ray based methods in the hot fields of nanoscience and nanotechnology, including methods for imaging nanomaterials, as well as for probing the electronic structure of nanostructured materials in order to investigate their different properties. Written by authors at one of the world's top facilities working with these methods, this monograph presents and discusses techniques and applications in the fields of x-ray scattering, spectroscopy and microscope imaging. The resulting systematic collection of these advanced tools will benefit graduate students, postdocs as well as professional researchers.
Book Synopsis X-Ray Microscopy by : Chris Jacobsen
Download or read book X-Ray Microscopy written by Chris Jacobsen and published by Cambridge University Press. This book was released on 2019-12-19 with total page 594 pages. Available in PDF, EPUB and Kindle. Book excerpt: A complete introduction to x-ray microscopy, covering optics, 3D and chemical imaging, lensless imaging, radiation damage, and applications.
Book Synopsis Lensless Holography Methods for Soft X-ray Resonant Coherent Imaging by : Diling Zhu
Download or read book Lensless Holography Methods for Soft X-ray Resonant Coherent Imaging written by Diling Zhu and published by Stanford University. This book was released on 2010 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to interpret and inverse x-ray diffraction patterns from crystals has largely shaped our understanding of the structure of matter. However, structure determination of noncrystalline objects from their diffraction patterns is a much more difficult task. The dramatic increase in available coherent x-ray photon flux over the past decade has made possible a technique known as lensless coherent diffractive imaging (CDI), that addresses exactly this problem. The central question around CDI is the so-called phase problem: upon detection of the diffraction intensity, the phase information of the diffracted wave is inevitably lost. Generally, the phase problem is approached using iterative phase retrieval algorithms. Holographic methods, through interference with reference diffractions, encode the phase information directly inside the measured x-ray holograms, and are therefore able to avoid the stagnation and uniqueness problems commonly encountered by the iterative algorithms. This dissertation discusses two novel holographic methods for coherent lensless imaging using resonant soft x-rays. The first part focuses on generalizing the multiple-wavelength anomalous diffraction technique, a highly successful method for solving the crystal structures of biomacromolecules, into a multiple-wavelength holography technique for nanoscale resonant x-ray imaging. Using this method I show element specific reconstructions of nanoparticles and magnetization distribution in magnetic thin films with sub 50 nm resolution. The second part discusses progress in X-ray Fourier holography, an ultrafast lensless imaging platform that can be used with the upcoming x-ray free electron lasers. In particular, I will present experiments using two novel types of extended reference structures that bring the resolution beyond the precision of reference fabrication, previously regarded as the resolution limit for x-ray Fourier transform holography. Finally, future applications of holographic methods, especially experimental considerations for time-resolved studies of nanostructures using X-FELs, will be discussed.
Book Synopsis A Study on New Approaches in Coherent X-ray Microscopy of Biological Specimens by : Klaus Giewekemeyer
Download or read book A Study on New Approaches in Coherent X-ray Microscopy of Biological Specimens written by Klaus Giewekemeyer and published by Universitätsverlag Göttingen. This book was released on 2011 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of coherent x rays for microscopic imaging has seen a rapid and ongoing development within the past decade, driven by an increasing availability of highly brilliant and coherent sources worldwide. Accordingly, novel methods have been developed, which replace the microscope‘s objective lens by a numerical reconstruction scheme. The aim of the present work is to study how very recent experimental and algorithmic developments in the field can be implemented towards a highly sensitive and fully quantitative microscopy method for imaging of biological cells. To this end, different experimental approaches are studied, based on coherent far-field as well as near-field diffraction. At first, an application of the novel ptychographic imaging method to single biological cells is presented. In particular, it is demonstrated how weakly scattering biological specimens can be imaged with fully quantitative density contrast. Alongside, a sueccessful extension of the method towards soft x-ray energies is described.In the second part of the work it is shown how x-ray waveguides can be used as a point source for propagation-based microscopy of single cells in the hard x-ray regime. The specifically devised iterative reconstruction scheme allows for full quantitativity and high sensitivity and thus enables an application to single biological cells. The work contains a thorough introduction into the x-ray optical methods applied and aims at a useful and self-contained overview on aspects of signal and Fourier theory relevant for the used numerical propagation schemes.
Book Synopsis X-Ray Near-Field Holography: Beyond Idealized Assumptions of the Probe by : Johannes Hagemann
Download or read book X-Ray Near-Field Holography: Beyond Idealized Assumptions of the Probe written by Johannes Hagemann and published by Göttingen University Press. This book was released on 2017 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: All images are flawed, no matter how good your lenses, mirrors etc. are. Especially in the hard X-ray regime it is challenging to manufacture high quality optics due to the weak interaction of multi-keV photons with matter. This is a tremendous challenge for obtaining high resolution quantitative X-ray microscopy images. In recent years lensless phase contrast imaging has become an alternative to classical absorptionbased imaging methods. Without any optics, the image is formed only by the free space propagation of the wave field. The actual image has to be formed posteriori by numerical reconstruction methods. Advanced phasing methods enable the experimentalist to recover a complex valued specimen from a single or a set of intensity measurement. This would be the ideal case - reality teaches us that there are no ideal imaging conditions. Describing, understanding and circumventing these non ideal imaging conditions and their effects on X-ray near-field holographic (NFH) imaging are the leitmotifs for this thesis. In NFH the non ideal conditions manifest themselves in the illuminating wave field or probe. The probe generally does not satisfy the canonical assumptions of fully coherent and monochromatic radiation emitted by a point source. The main results of this thesis are compiled as a collection of publications. An approach is shown to reconstruct the probe of a X-ray nano-focus setup by a series of measurements of the probe at varied Fresnel number. The following chapter presents a study concerning the reconstruction efficiency in terms of resolution for near- and far-field based lensless imaging. In the following, the reconstruction scheme for the probe is extended to incorporate the effects of partial coherence in the near field. This enables the recovery of the modal structure of the probe which yields a full description of its coherence properties. Giving up the assumption of temporal stability due to the stochastic pulses, delivered by X-ray free electron lasers, the reconstruction of probe and specimen must be achieved from a single shot. A suitable scheme for this purpose is proposed in this work.
Book Synopsis An Introduction to Synchrotron Radiation by : Philip Willmott, PhD
Download or read book An Introduction to Synchrotron Radiation written by Philip Willmott, PhD and published by John Wiley & Sons. This book was released on 2019-03-07 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: The updated guide to the fundamental concepts, techniques and applications of synchrotron radiation and its applications in this rapidly developing field Synchrotron light is recognized as an invaluable research tool by a broad spectrum of scientists, ranging from physicists to biologists and archaeologists. The comprehensively revised second edition of An Introduction to Synchrotron Radiation offers a guide to the basic concepts of the generation and manipulation of synchrotron light, its interaction with matter and the application of synchrotron light in x-ray scattering, spectroscopy, and imaging. The author, a noted expert in the field, reviews the fundamentals of important experimental methods, and explores the most recent technological advances in both the latest generation of x-ray sources and x-ray instrumentation. Designed to be an accessible resource, the book contains full-colour illustrations of the underlying physics and experimental applications, as well as the most commonly-used synchrotron techniques. In particular, the updated second edition now includes: In-depth descriptions of the latest x-ray-source technologies, notably diffraction-limited storage rings and x-ray free-electron lasers The latest advances in instrumentation, x-ray optics, and experimental methods in synchrotron radiation The most recent developments in macromolecular crystallography, time-resolved studies, and imaging techniques A comprehensive set of problems for each chapter, plus their ideal solutions in the appendices. Written for undergraduate and postgraduate students from all areas of the natural and physical sciences, An Introduction to Synchrotron Radiation, Second Edition is an invaluable up-to-date reference source in this highly multidisciplinary field. PowerPoint slides of all the figures within the text are available for download, for instructors and users of this book, at http://booksupport.wiley.com
Book Synopsis X-ray Free Electron Lasers by : Sébastien Boutet
Download or read book X-ray Free Electron Lasers written by Sébastien Boutet and published by Springer. This book was released on 2018-12-27 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: The timely volume describes recent discoveries and method developments that have revolutionized Structural Biology with the advent of X-ray Free Electron Lasers. It provides, for the first time, a comprehensive examination of this cutting-edge technology. It discusses of-the-moment topics such as growth and detection of nanocrystals, Sample Delivery Techniques for serial femtosecond crystallography, data collection methods at XFELs, and more. This book aims to provide the readers with an overview of the new methods that have been recently developed as well as a prospective on new methods under development. It highlights the most important and novel Structural Discoveries made recently with XFELS, contextualized with a big-picture discussion of future developments.
Book Synopsis Advanced X-ray Imaging of Electrochemical Energy Materials and Devices by : Jiajun Wang
Download or read book Advanced X-ray Imaging of Electrochemical Energy Materials and Devices written by Jiajun Wang and published by Springer Nature. This book was released on 2021-10-02 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprehensively outlines synchrotron-based X-ray imaging technologies and their associated applications in gaining fundamental insights into the physical and chemical properties as well as reaction mechanisms of energy materials. In this book the major X-ray imaging technologies utilised, depending on research goals and sample specifications, are discussed. With X-ray imaging techniques, the morphology, phase, lattice and strain information of energy materials in both 2D and 3D can be obtained in an intuitive way. In addition, due to the high penetration of X-rays, operando/in situ experiments can be designed to track the qualitative and quantitative changes of the samples during operation. This book will broader the reader’s view on X-ray imaging techniques and inspire new ideas and possibilities in energy materials research.
Book Synopsis Synchrotron Radiation Applications by : Xinyi Zhang
Download or read book Synchrotron Radiation Applications written by Xinyi Zhang and published by World Scientific. This book was released on 2018-03-20 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a research-level review volume. It presents both the fundamentals and the advanced research results, covering most part of important aspects of synchrotron radiation applications. Among the broad subjects of synchrotron radiation applications, as the main content of this book we have applications in VUV, soft X-rays, hard X-rays and XFEL (X-ray free electron laser) and important applications by various synchrotron-based techniques and methods, such as ARPES (angle-resolved photoemission spectroscopy), VUV photo-ionization spectroscopy, X-ray absorption/emission spectroscopy and X-ray absorption fine structure, X-ray diffraction, small angle X-ray scattering, X-ray excited optical luminescence, imaging and high pressure techniques.
Book Synopsis Soft X-Ray Spectromicroscopy of Environmental and Biological Samples by : Julia Maria Sedlmair
Download or read book Soft X-Ray Spectromicroscopy of Environmental and Biological Samples written by Julia Maria Sedlmair and published by Universitätsverlag Göttingen. This book was released on 2011 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soft x-ray spectromicroscopy was used to investigate environmental and biological specimens paying particular attention to their carbon content, of organic or anthropogenic origin. To be more specific, energies in the spectral region of the so-called water window, between the K absorption edges of carbon (284 eV) and oxygen (523 eV), were applied. In this region the absorbance of substances of high carbon content such as proteins is ten times higher than the absorbance of water which provides natural contrast and in turn allows for a natural or close to natural environment for such samples. The experiments presented in this thesis were chosen in such a way that either new instruments or new analysis methods are studied on different non-model sample specimens. To understand the effect of nanoparticles on the environment, the interaction between carbon nanotubes and soil was monitored, both in dry and aqueous sample environment. Additionally, for the characterization of heterogeneous samples like soils, spectroscopic experiments with a laser driven plasma source were performed. It demonstrated the feasibility of such a complementary technique, if not sometimes alternative to NEXAFS studies using synchrotron radiation. In the third project the possibility to image vascular smooth muscle cells without the necessity of additional embedding or staining was inquired, but by applying a simple, non-cryo fixation sample preparation.
Book Synopsis Light and Video Microscopy by : Randy O. Wayne
Download or read book Light and Video Microscopy written by Randy O. Wayne and published by Academic Press. This book was released on 2010-07-28 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of this book is to provide the most comprehensive, easy-to-use, and informative guide on light microscopy. Light and Video Microscopy will prepare the reader for the accurate interpretation of an image and understanding of the living cell. With the presentation of geometrical optics, it will assist the reader in understanding image formation and light movement within the microscope. It also provides an explanation of the basic modes of light microscopy and the components of modern electronic imaging systems and guides the reader in determining the physicochemical information of living and developing cells, which influence interpretation. * Brings together mathematics, physics, and biology to provide a broad and deep understanding of the light microscope * Clearly develops all ideas from historical and logical foundations * Laboratory exercises included to assist the reader with practical applications * Microscope discussions include: bright field microscope, dark field microscope, oblique illumination, phase-contrast microscope, photomicrography, fluorescence microscope, polarization microscope, interference microscope, differential interference microscope, and modulation contrast microscope
Book Synopsis Cone-beam x-ray phase-contrast tomography for the observation of single cells in whole organs by : Martin Krenkel
Download or read book Cone-beam x-ray phase-contrast tomography for the observation of single cells in whole organs written by Martin Krenkel and published by Göttingen University Press. This book was released on 2015 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: X-ray imaging enables the nondestructive investigation of interior structures in otherwise opaque samples. In particular the use of computed tomography (CT) allows for arbitrary virtual slices through the object and 3D information about intricate structures can be obtained. However, when it comes to image very small structures like single cells, the classical CT approach is limited by the weak absorption of soft-tissue. The use of phase information, encoded in measureable intensity images by free-space propagation of coherent x-rays, allows a huge increase in contrast, which enables 3D reconstructions at higher resolutions. In this work the application of propagation-based phase-contrast tomography to lung tissue samples is demonstrated in close to in vivo conditions. Reconstructions of the lung structure of whole mice at down to 5 μm resolution are obtained at a selfbuilt CT setup, which is based on a liquid-metal jet x-ray source. To reach even higher resolutions, synchrotron radiation in combination with suitable holographic phase-retrieval algorithms is employed. Due to optimized cone-beam geometry, field of view and resolution can be varied over a wide range of parameters, so that information on different length scales can be achieved, covering several millimeters field of view down to a 3D resolution of 50 nm. Thus, the sub-cellular 3D imaging of single cells embedded in large pieces of tissue is enabled, which paves the way for future biomedical research.
Book Synopsis Computational Methods for Three-Dimensional Microscopy Reconstruction by : Gabor T. Herman
Download or read book Computational Methods for Three-Dimensional Microscopy Reconstruction written by Gabor T. Herman and published by Springer Science & Business Media. This book was released on 2014-01-29 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: Approaches to the recovery of three-dimensional information on a biological object, which are often formulated or implemented initially in an intuitive way, are concisely described here based on physical models of the object and the image-formation process. Both three-dimensional electron microscopy and X-ray tomography can be captured in the same mathematical framework, leading to closely-related computational approaches, but the methodologies differ in detail and hence pose different challenges. The editors of this volume, Gabor T. Herman and Joachim Frank, are experts in the respective methodologies and present research at the forefront of biological imaging and structural biology. Computational Methods for Three-Dimensional Microscopy Reconstruction will serve as a useful resource for scholars interested in the development of computational methods for structural biology and cell biology, particularly in the area of 3D imaging and modeling.
Book Synopsis International Union of Crystallography Newsletter by :
Download or read book International Union of Crystallography Newsletter written by and published by . This book was released on 2007 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis X-Ray Diffraction Imaging of Biological Cells by : Masayoshi Nakasako
Download or read book X-Ray Diffraction Imaging of Biological Cells written by Masayoshi Nakasako and published by Springer. This book was released on 2018-03-29 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, the author describes the development of the experimental diffraction setup and structural analysis of non-crystalline particles from material science and biology. Recent advances in X-ray free electron laser (XFEL)-coherent X-ray diffraction imaging (CXDI) experiments allow for the structural analysis of non-crystalline particles to a resolution of 7 nm, and to a resolution of 20 nm for biological materials. Now XFEL-CXDI marks the dawn of a new era in structural analys of non-crystalline particles with dimensions larger than 100 nm, which was quite impossible in the 20th century. To conduct CXDI experiments in both synchrotron and XFEL facilities, the author has developed apparatuses, named KOTOBUKI-1 and TAKASAGO-6 for cryogenic diffraction experiments on frozen-hydrated non-crystalline particles at around 66 K. At the synchrotron facility, cryogenic diffraction experiments dramatically reduce radiation damage of specimen particles and allow tomography CXDI experiments. In addition, in XFEL experiments, non-crystalline particles scattered on thin support membranes and flash-cooled can be used to efficiently increase the rate of XFEL pulses. The rate, which depends on the number density of scattered particles and the size of X-ray beams, is currently 20-90%, probably the world record in XFEL-CXDI experiments. The experiment setups and results are introduced in this book. The author has also developed software suitable for efficiently processing of diffraction patterns and retrieving electron density maps of specimen particles based on the diffraction theory used in CXDI.
