Methods For Coherent Lensless Imaging And X Ray Wavefront Measurement

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Methods For Coherent Lensless Imaging And X Ray Wavefront Measurement

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Author : Manuel Guizar-Sicairos
language : en
Publisher:
Release Date : 2010

Methods For Coherent Lensless Imaging And X Ray Wavefront Measurement written by Manuel Guizar-Sicairos and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.

"Advancement and research on phase retrieval techniques are in large part motivated by their application in high resolution lensless laser imaging and x- ray diffractive imaging. In the former a high resolution image can be obtained from measuring the intensity pattern of the propagated field without the use of any imaging optics, thus providing an imaging system that does not increase its thickness along the optical axis as the aperture diameter is increased. For x- ray coherent diffractive imaging, on the other hand, high-resolution conventional imaging is difficult to achieve at these wavelengths because of the difficulty of manufacturing and aligning x-ray focusing elements with sufficient numerical aperture and precision. Thus, in order to achieve resolutions on the order of a nanometer, a coherent x-ray beam is used to illuminate the object of interest and the object is reconstructed from a measurement of its far-field diffraction intensity without any imaging optics. Thus the advancement and application of lensless imaging techniques has become an increasingly important topic of research. X-ray diffractive imaging is set apart from other high-resolution imaging techniques (e.g. scanning electron or atomic force microscopy) for its high penetration depth, which enables tomographic 3D imaging of thick samples and buried structures. Furthermore, using short x-ray pulses, it enables the capability to take ultrafast snapshots, giving a unique opportunity to probe nanoscale dynamics at femtosecond time scales. In this thesis we present improvements to phase retrieval algorithms, assess their performance through numerical simulations, and develop new methods for both imaging and wavefront measurement. Using numerical simulations we identified and explained the origin of the twin-image problem in iterative transform phase retrieval with a centrosymmetric support constraint. We proposed and numerically demonstrated the effectiveness of a modified phase retrieval algorithm that uses Fourier weighted projections to increase the quality and resolution of the reconstructions by mitigating a problem arising from the finite measurement window and finite support constraint. Such an approach is particularly useful when the object presents large phase variations on a length- scale significantly smaller than the resolution, i.e. reconstruction of fully developed speckled images. In order to accurately and efficiently assess phase retrieval algorithm performance, we have developed algorithms for subpixel image registration. Despite being particularly well suited for comparing images from data collected in the Fourier domain (e.g., phase retrieval and holography), these algorithms have al- ready shown a substantial success in other applications as well. Building on the original work by Faulkner and Rodenburg, we developed an improved reconstruction algorithm for phase retrieval with transverse translations of the object relative to the illumination beam. Based on gradient-based non- linear optimization, this algorithm is capable of estimating the object, and at the same time refining the initial knowledge of the incident illumination and the object translations. The advantages of this algorithm over the original iterative transform approach are shown through numerical simulations. Phase retrieval has already shown substantial success in wavefront sensing at optical wavelengths. Although in principle the algorithms can be used at any wavelength, in practice the focus-diversity mechanism that makes optical phase retrieval robust is not practical to implement for x-rays. In this thesis we also describe the novel application of phase retrieval with transverse translations to the problem of x-ray wavefront sensing. This approach allows the characterization of the complex-valued x-ray field in-situ and at-wavelength and has several practical and algorithmic advantages over conventional focused beam measurement techniques. A few of these advantages include improved robustness through diverse measurements, reconstruction from far-field intensity measurements only, and significant relaxation of experimental requirements over other beam characterization approaches. Furthermore, we show that a one-dimensional version of this technique can be used to characterize an x-ray line focus produced by a cylindrical focusing element. We provide experimental demonstrations of the latter at hard x-ray wavelengths, where we have characterized the beams focused by a kinoform lens and an elliptical mirror. In both experiments the reconstructions exhibited good agreement with independent measurements, and in the latter a small mirror misalignment was inferred from the phase retrieval reconstruction. These experiments pave the way for the application of robust phase retrieval algorithms for in-situ alignment and performance characterization of x-ray optics for nanofocusing. We also present a study on how transverse translations help with the well-known uniqueness problem of one-dimensional phase retrieval. We also present a novel method for x-ray holography that is capable of reconstructing an image using an off-axis extended reference in a non-iterative computation, greatly generalizing an earlier approach by Podorov et.al. The approach, based on the numerical application of derivatives on the field autocorrelation, was developed from first mathematical principles. We conducted a thorough theoret- ical study to develop technical and intuitive understanding of this technique and derived sufficient separation conditions required for an artifact-free reconstruction. We studied the effects of missing information in the Fourier domain, and of an im- perfect reference, and we provide a signal-to-noise ratio comparison with the more traditional approach of Fourier transform holography. We demonstrated this new holographic approach through proof-of-principle optical experiments and later ex- perimentally at soft x-ray wavelengths, where we compared its performance to Fourier transform holography, iterative phase retrieval and state-of-the-art zone-plate x-ray imaging techniques (scanning and full-field). Finally, we present a demonstration of the technique using a single 20 fs pulse from a high-harmonic table-top source. Holography with an extended reference is shown to provide fast, good quality images that are robust to noise and artifacts that arise from missing information due to a beam stop."--Leaves viii-xi.

Lensless Holography Methods For Soft X Ray Resonant Coherent Imaging

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Author : Diling Zhu
language : en
Publisher: Stanford University
Release Date : 2010

Lensless Holography Methods For Soft X Ray Resonant Coherent Imaging written by Diling Zhu and has been published by Stanford University this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.

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.

Coherent X Ray Diffractive Imaging On The Single Cell Level Of Microbial Samples

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Author : Robin Niklas Wilke
language : en
Publisher: Göttingen University Press
Release Date : 2015

Coherent X Ray Diffractive Imaging On The Single Cell Level Of Microbial Samples written by Robin Niklas Wilke and has been published by Göttingen University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.

Since its first experimental demonstration in 1999, Coherent X-Ray Diffractive Imaging has become one of the most promising high resolution X-Ray imaging techniques using coherent radiation produced by brilliant synchrotron storage rings. The ability to directly invert diffraction data with the help of advanced algorithms has paved the way for microscopic investigations and wave-field analyses on the spatial scale of nanometres without the need for inefficient imaging lenses. X-Ray phase contrast which is a measure of the electron density is an important contrast mode of soft biological specimens. For the case of many dominant elements of soft biological matter, the electron density can be converted into an effective mass density offering a unique quantitative information channel which may shed light on important questions such as DNA compaction in the bacterial nucleoid through ‚weighing with light‘. In this work X-Ray phase contrast maps have been obtained from different biological samples by exploring different methods. In particular, the techniques Ptychography and Waveguide-Holographic-Imaging have been used to obtain twodimensional and three-dimensional mass density maps on the single-cell-level of freeze-dried cells of the bacteria Deinococcus radiodurans, Bacillus subtilis and Bacillus thuringiensis allowing, for instance, to estimate the dry weight of the bacterial genome in a near native state. On top of this, reciprocal space information from coherent small angle X-Ray scattering (cellular Nano-Diffraction) of the fine structure of the bacterial cells has been recorded in a synergistic manner and has been analysed down to a resolution of about 2.3/nm exceeding current limits of direct imaging approaches. Furthermore, the dynamic range of present detector technology being one of the major limiting factors of ptychographic phasing of farfield diffraction data has been significantly increased. Overcoming this problem for the case of the very intense X-Ray beam produced by Kirkpatrick-Baez mirrors has been explored by using semi-transparent central stops.

Optimization Of Waveguide Optics For Lensless X Ray Imaging

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Author : Sven Philip Krüger
language : en
Publisher: Universitätsverlag Göttingen
Release Date : 2011

Optimization Of Waveguide Optics For Lensless X Ray Imaging written by Sven Philip Krüger and has been published by Universitätsverlag Göttingen this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.

Lensless x-ray imaging is a promising method to determine the three-dimensional structure of material science and biological specimens at the nanoscale. The development of this technique is strongly related to the optimization of x-ray optics since the image formation and object reconstruction depend significantly on the properties of the illumination wave-field. Waveguide optics act as quasi-point sources and enable the spatial and coherent filtering of x-ray beams. Up to now, x-ray waveguides were severely limited in transmission and flux, restricting their use to high-contrast test structures with moderate resolution and long accumulation times. To overcome these limitations, a novel waveguide design with an optimized refractive index profile is presented which significantly minimizes the absorption of the modes propagating inside the waveguide. Experimental results along with simulations show that these two-component planar x-ray waveguides provide small beam cross-sections along with a high photon flux at the exit. By a serial arrangement of two waveguide slices an optimized illumination source has been developed for high-resolution microscopy, as demonstrated in proof-of-concept imaging experiments.

Structural Dynamics With X Ray And Electron Scattering

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Author : Kasra Amini
language : en
Publisher: Royal Society of Chemistry
Release Date : 2023-12-20

Structural Dynamics With X Ray And Electron Scattering written by Kasra Amini and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-12-20 with Science categories.

Since the early 20th century, X-ray and electron scattering has provided a powerful means by which the location of atoms can be identified in gas-phase molecules and condensed matter with sub-atomic spatial resolution. Scattering techniques can also provide valuable observables of the fundamental properties of electrons in matter such as an electron’s spin and its energy. In recent years, significant technological developments in both X-ray and electron scattering have paved the way to time-resolved analogues capable of capturing real-time snapshots of transient structures undergoing a photochemical reaction. Structural Dynamics with X-ray and Electron Scattering is a two-part book that firstly introduces the fundamental background to scattering theory and photochemical phenomena of interest. The second part discusses the latest advances and research results from the application of ultrafast scattering techniques to imaging the structure and dynamics of gas-phase molecules and condensed matter. This book aims to provide a unifying platform for X-ray and electron scattering.

X Ray Near Field Holography Beyond Idealized Assumptions Of The Probe

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Author : Johannes Hagemann
language : en
Publisher: Göttingen University Press
Release Date : 2017

X Ray Near Field Holography Beyond Idealized Assumptions Of The Probe written by Johannes Hagemann and has been published by Göttingen University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.

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.

An Introduction To Synchrotron Radiation

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Author : Philip Willmott, PhD
language : en
Publisher: John Wiley & Sons
Release Date : 2019-04-29

An Introduction To Synchrotron Radiation written by Philip Willmott, PhD and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-29 with Science categories.

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

Investigating Cellular Nanoscale With X Rays

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Author : Clément Hémonnot
language : en
Publisher: Göttingen University Press
Release Date : 2016

Investigating Cellular Nanoscale With X Rays written by Clément Hémonnot and has been published by Göttingen University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.

The advances and technical improvements of X-ray imaging techniques, taking advantage of X-ray focussing optics and high intensity synchrotron sources, nowadays allow for the use of X-rays to probe the cellular nanoscale. Importantly, X-rays permit thick samples to be imaged without sectioning or slicing. In this work, two macromolecules, namely keratin intermediate filament (IF) proteins and DNA, both essential components of cells, were studied by X-ray techniques. Keratin IF proteins make up an integral part of the cytoskeleton of epithelial cells and form a dense intracellular network of bundles. This network is built from monomers in a hierarchical fashion. Thus, the keratin structure formation spans a large range of length scales from a few nanometres (monomers) to micrometres (networks). Here, keratin was studied at three different scales: i) filaments, ii) bundles and iii) networks. Solution small-angle X-ray scattering revealed distinct structural and organisational characteristics of these highly charged polyelectrolyte filaments, such as increasing radius with increasing salt concentration and spatial accumulation of ions depending on the salt concentration. The results are quantified by employing advanced modelling of keratin IFs by a core cylinder fl anked with Gaussian chains. Scanning micro- diffraction was used to study keratin at the bundle scale. Very different morphologies of keratin bundles were observed at different salt conditions. At the network scale, new imaging approaches and analyses were applied to the study of whole cells. Ptychography and scanning X-ray nano-diffraction imaging were performed on the same cells, allowing for high resolution in real and reciprocal space, thereby revealing the internal structure of these networks. By using a fitting routine based on simulations of IFs packed on a hexagonal lattice, the radius of each fi lament and distance between fi laments were retrieved. In mammalian cells, each nucleus contains 2 nm-thick DNA double helices with a total length of about 2 m. The DNA strands are packed in a highly hierarchical manner into individual chromosomes. DNA was studied in intact cells by visible light microscopy and scanning X-ray nano-diffraction, unveiling the compaction und decompaction of DNA during the cell cycle. Thus, we obtained information on the aggregation state of the nuclear DNA at a real space resolution on the order of few hundreds nm. To exploit to the reciprocal space information, individual diffraction patterns were analysed according to a generalised Porod’s law at a resolution down to 10 nm. We were able to distinguish nucleoli, heterochromatin and euchromatin in the nuclei and follow the compaction and decompaction during the cell division cycle.

X Ray Waveguide Optics

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Author : Sarah Hoffmann-Urlaub
language : en
Publisher: Göttingen University Press
Release Date : 2017

X Ray Waveguide Optics written by Sarah Hoffmann-Urlaub and has been published by Göttingen University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.

Modern x-ray sources and analysis techniques such as lens less imaging combined with phase retrieval algorithms allow for resolving structure sizes in the nanometer range. For this purpose optics have to be employed, ensuring small focal spot dimensions simultaneously with high photon densities. Furthermore, the wave front behind the optics is required to be smooth enabling for high resolution imaging. Combining all these properties, x-ray waveguides are well suited to perform this task, since the intensity distribution behind the guide is restricted in two dimensions serving as a secondary quasi point-source without wave-front aberrations, showing also a high divergence, suitable for resolving fine features. Importantly, the radiation provided by the waveguide reveals a high degree of coherence, required by many imaging techniques. The waveguide itself consists of an air-filled channel embedded in a solid matrix; typical materials are silicon, germanium or quartz. While the entrance area is nano-sized, the channel length is in the millimeter-range, this way posing challenges to fabricate high aspect ratio geometries. Since the functioning of x-ray waveguides is based on the total reflection at small incident angles, the surface roughness of the channel walls must be as low as possible to avoid scattering and hence loss of intensity. To fulfill these demanding conditions, a process scheme involving spin-coating, electron beam lithography, wet development, reactive ion etching and wafer bonding is optimized within this work. To gain deeper insights into the principle of wave guiding finite difference simulations are performed, also opening access for advanced design considerations such as gratings, tapered and curved channels, or beamsplitters, enabling for constructing novel x-ray tools as for example time delay devices or interferometers. Waveguides in all geometries are tested at synchrotron sources, accomplishing new benchmarks in x-ray optical performance. Here, the x-ray beam leaving the channel, propagates out to a pixel array detector in the far-field region. From the recorded data the intensity distribution in the near-field directly behind the waveguide is reconstructed, revealing an outstanding agreement with the simulations and electron micrographs. Since the radiation field of the waveguide is well-characterized and also tunable to meet the requirements of both the measurement setup and the sample, they are suited of a broad field of applications in coherent x-ray imaging.

Chemical Imaging Analysis

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Author : Freddy Adams
language : en
Publisher: Elsevier
Release Date : 2015-06-06

Chemical Imaging Analysis written by Freddy Adams and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-06-06 with Science categories.

Chemical Imaging Analysis covers the advancements made over the last 50 years in chemical imaging analysis, including different analytical techniques and the ways they were developed and refined to link the composition and structure of manmade and natural materials at the nano/micro scale to the functional behavior at the macroscopic scale. In a development process that started in the early 1960s, a variety of specialized analytical techniques was developed – or adapted from existing techniques – and these techniques have matured into versatile and powerful tools for visualizing structural and compositional heterogeneity. This text explores that journey, providing a general overview of imaging techniques in diverse fields, including mass spectrometry, optical spectrometry including X-rays, electron microscopy, and beam techniques. - Provides comprehensive coverage of analytical techniques used in chemical imaging analysis - Explores a variety of specialized techniques - Provides a general overview of imaging techniques in diverse fields