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.

Download or read book Coherent X ray diffractive imaging on the single cell level of microbial samples written by Robin Niklas Wilke and published by Göttingen University Press. This book was released on 2015 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Cone beam X ray Phase Contrast Tomography of Biological Samples written by Matthias Bartels and published by Universitätsverlag Göttingen. This book was released on 2013 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Three-dimensional information of entire objects can be obtained by the remarkable technique of computed tomography (CT). In combination with phase sensitive X-ray imaging high contrast for soft tissue structures can be achieved as opposed to CT based on classical radiography. In this work biological samples ranging from micrometer sized single cells over multi-cellular nerve tissue to entire millimeter sized organs are investigated by use of cone-beam propagationbased X-ray phase contrast. Optimization with respect to contrast, resolution and field of view is achieved by addressing instrumentation, sample preparation and phase reconstruction techniques. By using laboratory sources functional soft tissue within the bony capsule of mouse cochleae is visualized in 3D with unprecedented image quality. At synchrotron storage rings the technique reveals more than 1000 axons running in parallel within a mouse nerve and enables doseefficient three-dimensional cellular imaging as well as two-dimensional imaging at high resolutions below 50 nm.

Download or read book Wave Optical Simulations of X ray Nano focusing Optics written by Markus Osterhoff and published by Universitätsverlag Göttingen. This book was released on 2012 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: Curved x-ray multilayer mirrors focus synchrotron beams down to tens of nano metres. A wave-optical theory describing propagation of two waves in an elliptically curved focusing multilayer mirror is developed in this thesis. Using numerical integration, the layer shapes can be optimised for reflectivity and aberrations. Within this framework, performance of both existing and currently upgraded synchrotron beamlines is simulated. Using a more theoretical model case, limits of the theory are studied. A significant part of this work is dedicated to partial spatial coherence, modelled using the method of stochastic superpositions. Coherence propagation and filtering by x-ray waveguides is shown analytically and numerically. This comprehensive model is put forward that shall help in development and testing of new algorithms for a variety of imaging techniques using coherent x-ray beams. Advanced simulations accounting for real structure effects are compared to experimental data obtained at the GINIX instrument at the coherence beamline P10 at PETRA III, DESY. This thesis presents results of a collaboration between the Georg-August-Universität Göttingen and the European Synchrotron Radiation Facility (ESRF) Grenoble.

Download or read book Biomedical Imaging written by Tim Salditt and published by Walter de Gruyter GmbH & Co KG. This book was released on 2017-10-23 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering both physical as well as mathematical and algorithmic foundations, this graduate textbook provides the reader with an introduction into modern biomedical imaging and image processing and reconstruction. These techniques are not only based on advanced instrumentation for image acquisition, but equally on new developments in image processing and reconstruction to extract relevant information from recorded data. To this end, the present book offers a quantitative treatise of radiography, computed tomography, and medical physics. Contents Introduction Digital image processing Essentials of medical x-ray physics Tomography Radiobiology, radiotherapy, and radiation protection Phase contrast radiography Object reconstruction under nonideal conditions

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.

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.

Download or read book A Dedicated Endstation for Waveguide based X ray Imaging written by Sebastian Kalbfleisch and published by Universitätsverlag Göttingen. This book was released on 2013 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book 3d virtual histology of neuronal tissue by propagation based x ray phase contrast tomography written by Mareike Töpperwien and published by Göttingen University Press. This book was released on 2018 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deciphering the three-dimensional (3d) cytoarchitecture of neuronal tissue is an important step towards understanding the connection between tissue function and structure and determining relevant changes in neurodegenerative diseases. The gold standard in pathology is histology, in which the tissue is examined under a light microscope after serial sectioning and subsequent staining. It is an invasive and labor-intensive technique which is prone to artifacts due to the slicing procedure. While it provides excellent results on the 2d slices, the 3d anatomy can only be determined after aligning the individual sections, leading to a non-isotropic resolution within the tissue. X-ray computed tomography (CT) offers a promising alternative due to its potential resolution and large penetration depth which allows for non-invasive imaging of the sample's 3d density distribution. In classical CT, contrast formation is based on absorption of the x-rays as they pass through the sample. However, weakly absorbing samples like soft tissue from the central nervous system give nearly no contrast. By exploiting the much stronger phase shifts for contrast formation, which the sample induces in a (partially) coherent wavefront, it can be substantially increased. During free-space propagation behind the sample, these phase shifts are converted to a measurable intensity image by interference of the disturbed wave fronts. In this thesis, 3d virtual histology is performed by means of propagation-based x-ray phase-contrast tomography on tissue from the central nervous system of humans and mice. A combination of synchrotron-based and laboratory setups is used to visualize the 3d density distribution on varying lengths scales from the whole organ down to single cells. By comparing and optimizing different preparation techniques and phase-retrieval approaches, even sub-cellular resolution can be reached in mm-sized tissue blocks. The development of an automatic cell segmentation workflow provides access to the 3d cellular distribution within the tissue, enabling the quantification of the cellular arrangement and allowing for extensive statistical analysis based on several thousands to millions of cells. This paves the way for biomedical studies aimed at changes in cellular distribution, e.g., in the course of neurodegenerative diseases such as multiple sclerosis, Alzheimer's disease or ischemic stroke.

Download or read book Phase retrieval problems in x ray physics written by Carolin Homann and published by Göttingen University Press. This book was released on 2015 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: In phase retrieval problems that occur in imaging by coherent x-ray diffraction, one tries to reconstruct information about a sample of interest from possibly noisy intensity measurements of the wave fi eld traversing the sample. The mathematical formulation of these problems bases on some assumptions. Usually one of them is that the x-ray wave fi eld is generated by a point source. In order to address this very idealized assumption, it is common to perform a data preprocessing step, the so-called empty beam correction. Within this work, we study the validity of this approach by presenting a quantitative error estimate. Moreover, in order to solve these phase retrieval problems, we want to incorporate a priori knowledge about the structure of the noise and the solution into the reconstruction process. For this reason, the application of a problem adapted iteratively regularized Newton-type method becomes particularly attractive. This method includes the solution of a convex minimization problem in each iteration step. We present a method for solving general optimization problems of this form. Our method is a generalization of a commonly used algorithm which makes it efficiently applicable to a wide class of problems. We also proof convergence results and show the performance of our method by numerical examples.

Download or read book Phase retrieval for object and probe in the optical near field written by Anna-Lena Robisch and published by Göttingen University Press. This book was released on 2016 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lensless, holographic X-ray microscopy is a non-invasive imaging technique that provides resolution on the nanometer scale. Therefore, a divergent, coherent and especially clean wave front impinging on the sample is needed. Yet, focusing X-rays by even the most advanced X-ray mirrors causes so called figure errors of high spatial frequency content. The results are strongly deteriorated intensity profiles that are often even more pronounced than the holographic image of the sample itself. A common strategy to compensate these figure errors is to divide the hologram by the pure intensity profile of the beam (the so called flat field). However, this division is only valid in the limiting case of an illumination focused down to a point source. In reality, as a consequence of a fi nite spot size, one has to accept a loss in resolution when performing the flat field correction. An approach different from the described straightforward procedure is necessary. Here, the simultaneous reconstruction of object and probe is proposed using holograms which were not flat field corrected before phase retrieval. To this end, a method has been developed that allows simultaneously reconstructing object and probe in amplitude and phase from holographic intensity recordings. The experimental way of proceeding was mainly inspired by well-established holographic full-field X-ray imaging techniques that require holograms defocused to different degrees. Consequently, the conclusion seems reasonable that diversity in the optical near-field arises mainly from variation of the propagation distance of light. This so called longitudinal diversity is used to properly phase the transmission function of the sample of interest. The algorithmic strategy of simultaneous phase retrieval for object and probe draws on far-field ptychography where lateral translations of the sample create diverse diffraction patterns. In view of the need for longitudinal diversity realized by shifts of the sample along the optical axis, ptychography has been generalized and adapted for the optical near-field. Hence, translations of the sample in all three dimensions of space need to be exploited to collect enough information about object and probe such that both can be reconstructed simultaneously in amplitude and phase. Concepts have been put into practice by simulations as well as by experiments with coherent visible light and hard X-rays from synchrotron sources. The presented approach offers the opportunity to perform high resolution imaging, to be extended to tomography and to be adapted to super-resolution experiments.

Download or read book X ray Microscopy written by Ping-chin Cheng and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: In 1979, a conference on x-ray microscopy was organized by the New York Academy of Sciences, and in 1983, the Second Interna tional Symposium on X-ray Imaging was organized by the Akademie der Wissenschaften in Gottingen, Federal Republic of Germany. This volume contains the contributions to the symposium "X-ray Microscopy '86", held in Taipei, Taiwan, the Republic of China in August 1986. This is the first volume which intends to provide up-to date information on x-ray imaging to biologists, therefore, emphasis was given to specimen preparation techniques and image interpreta tion. Specimen preparation represents a major part of every microscopy work, therefore, it should be strongly emphasized in this emerging field of x-ray microscopy. Theoretically, x-ray microscopy offers the potential for the study of unfixed, hydrated biological ma terials. Since very few biological system can be directly observed without specimen preparation, we would like to emphasize that new information on biological specimens can only be obtained if the speci men is properly prepared. In the past decade, many of the published x-ray images were obtained from poorly prepared biological speci mens, mainly air-dried materials. Therefore, one of the goals of this conference is to bring the importance of specimen preparation to the attention of x-ray microscopy community. X-ray microscopy can be subdivided into several major areas. They are the classic x-ray projection microscope, x-ray contact imag ing (microradiography) and the more recent x-ray scanning micro scope, x-ray photoelectron microscope and x-ray imaging microscope.

Download or read book Multiscale X Ray Analysis of Biological Cells and Tissues by Scanning Diffraction and Coherent Imaging written by Jan-David Nicolas and published by Göttingen University Press. This book was released on 2019 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the intricate details of muscle contraction has a long-standing tradition in biophysical research. X-ray diffraction has been one of the key techniques to resolve the nanometer-sized molecular machinery involved in force generation. Modern, powerful X-ray sources now provide billions of X-ray photons in time intervals as short as microseconds, enabling fast time-resolved experiments that shed further light on the complex relationship between muscle structure and function. Another approach harnesses this power by repeatedly performing such an experiment at different locations in a sample. With millions of repeated exposures in a single experiment, X-ray diffraction can seamlessly be turned into a raster imaging method, neatly combining real- and reciprocal space information. This thesis has focused on the advancement of this scanning scheme and its application to soft biological tissue, in particular muscle tissue. Special emphasis was placed on the extraction of meaningful, quantitative structural parameters such as the interfilament distance of the actomyosin lattice in cardiac muscle. The method was further adapted to image biological samples on a range of scales, from isolated cells to millimeter-sized tissue sections. Due to the ‘photon-hungry’ nature of the technique, its full potential is often exploited in combination with full-field imaging techniques. From the vast set of microscopic tools available, coherent full-field X-ray imaging has proven to be particularly useful. This multimodal approach allows to correlate two- and three-dimensional images of cells and tissue with diffraction maps of structure parameters. With the set of tools developed in this thesis, scanning X-ray diffraction can now be efficiently used for the structural analysis of soft biological tissues with overarching future applications in biophysical and biomedical research.

Download or read book Hard X ray Microscopy Enhanced by Coherent Image Reconstruction written by Jakob Soltau and published by Universitätsverlag Göttingen. This book was released on 2022 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: X-ray microscopy is used to study the structure, dynamics and bulk properties of matter with high spatial resolutions. It is widely applied, from physics and chemistry to material and life sciences. In the past two decades, progress in X-ray microscopy was driven either by improvements in X-ray optics or by improvements in the image reconstruction by using algorithms as computational lenses. In this work both approaches are combined to exploit the advantages of X-ray imaging with a large numerical aperture and the advantages of coherent image reconstruction. It is shown that a combined X-ray microscope using both, advanced optics and algorithms, is neither limited by flawed optics nor by constraints imposed by reconstruction algorithms, which enables to go beyond current limits in resolution and applications. The thesis is structured in four parts. In the first part hard X-ray lenses, so called multilayer zone plates, are simulated to investigate volume diffraction effects within the multilayer structure, and to study the potential for smaller focus sizes and higher efficiencies. In the second part, the multilayer zone plates are characterized and implemented in an X-ray microscope. In the third part, a new imaging scheme is presented, which combines in-line holography and coherent diffractive imaging. This method overcomes the current resolution limit of in-line holography and can achieve super-resolution with respect to the numerical aperture of the illuminating beam. Finally, in the fourth part a multilayer zone plate is used as an objective lens with a known transfer function in a novel coherent full-field imaging experiment based on iterative phase retrieval, for high resolution and quantitative contrast.

Download or read book X RAY MICROANALYSIS OF BIOLOGICAL SPECIMENS NEW APPROACHES PAPERS written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book High Resolution Extreme Ultraviolet Microscopy written by Michael Werner Zürch and published by Springer. This book was released on 2014-11-07 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis describes novel approaches and implementation of high-resolution microscopy in the extreme ultraviolet light regime. Using coherent ultrafast laser-generated short wavelength radiation for illuminating samples allows imaging beyond the resolution of visible-light microscopes. Michael Zürch gives a comprehensive overview of the fundamentals and techniques involved, starting from the laser-based frequency conversion scheme and its technical implementation as well as general considerations of diffraction-based imaging at nanoscopic spatial resolution. Experiments on digital in-line holography and coherent diffraction imaging of artificial and biologic specimens are demonstrated and discussed in this book. In the field of biologic imaging, a novel award-winning cell classification scheme and its first experimental application for identifying breast cancer cells are introduced. Finally, this book presents a newly developed technique of generating structured illumination by means of so-called optical vortex beams in the extreme ultraviolet regime and proposes its general usability for super-resolution imaging.

Download or read book Biophotonics Science And Technology written by Yin Yeh and published by World Scientific. This book was released on 2018-06-28 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: This lecture volume aims to give students and researchers in this rapidly expanding field of biophotonics an interdisciplinary perspective. Among the primary topics are ultrahigh resolution microscopy, particle tracking, photon correlation spectroscopy, and nonlinear optical methods as used in biological and biomedical research, with a focus on current applications in biophysics and biomedicine.