Cone Beam X Ray Phase Contrast Tomography For The Observation Of Single Cells In Whole Organs

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Cone-beam x-ray phase-contrast tomography for the observation of single cells in whole organs

Martin Krenkel
Cone beam x ray phase contrast tomography for the observation of single cells in whole organs Book PDF

Author : Martin Krenkel
Publisher : Göttingen University Press
Page : 238 pages
File Size : 40,6 Mb
Release : 2015
Category : Electronic
ISBN : 9783863952518

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Cone-beam x-ray phase-contrast tomography for the observation of single cells in whole organs by Martin Krenkel Pdf

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.

Cone-beam X-ray Phase-contrast Tomography for the Observation of Single Cells in Whole Organs

Martin Krenkel
Cone beam X ray Phase contrast Tomography for the Observation of Single Cells in Whole Organs Book PDF

Author : Martin Krenkel
Publisher : Unknown
Page : 128 pages
File Size : 45,5 Mb
Release : 2015
Category : Electronic
ISBN : OCLC:928655724

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Cone-beam X-ray Phase-contrast Tomography for the Observation of Single Cells in Whole Organs by Martin Krenkel Pdf

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 reco ...

Nanoscale Photonic Imaging

Tim Salditt,Alexander Egner,D. Russell Luke
Nanoscale Photonic Imaging Book PDF

Author : Tim Salditt,Alexander Egner,D. Russell Luke
Publisher : Springer Nature
Page : 634 pages
File Size : 45,6 Mb
Release : 2020-06-09
Category : Science
ISBN : 9783030344139

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Nanoscale Photonic Imaging by Tim Salditt,Alexander Egner,D. Russell Luke Pdf

This open access book, edited and authored by a team of world-leading researchers, provides a broad overview of advanced photonic methods for nanoscale visualization, as well as describing a range of fascinating in-depth studies. Introductory chapters cover the most relevant physics and basic methods that young researchers need to master in order to work effectively in the field of nanoscale photonic imaging, from physical first principles, to instrumentation, to mathematical foundations of imaging and data analysis. Subsequent chapters demonstrate how these cutting edge methods are applied to a variety of systems, including complex fluids and biomolecular systems, for visualizing their structure and dynamics, in space and on timescales extending over many orders of magnitude down to the femtosecond range. Progress in nanoscale photonic imaging in Göttingen has been the sum total of more than a decade of work by a wide range of scientists and mathematicians across disciplines, working together in a vibrant collaboration of a kind rarely matched. This volume presents the highlights of their research achievements and serves as a record of the unique and remarkable constellation of contributors, as well as looking ahead at the future prospects in this field. It will serve not only as a useful reference for experienced researchers but also as a valuable point of entry for newcomers.

3d virtual histology of neuronal tissue by propagation-based x-ray phase-contrast tomography

Mareike Töpperwien
3d virtual histology of neuronal tissue by propagation based x ray phase contrast tomography Book PDF

Author : Mareike Töpperwien
Publisher : Göttingen University Press
Page : 286 pages
File Size : 49,8 Mb
Release : 2018
Category : Electronic
ISBN : 9783863953645

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3d virtual histology of neuronal tissue by propagation-based x-ray phase-contrast tomography by Mareike Töpperwien Pdf

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.

Biomedical Imaging

Tim Salditt,Timo Aspelmeier,Sebastian Aeffner
Biomedical Imaging Book PDF

Author : Tim Salditt,Timo Aspelmeier,Sebastian Aeffner
Publisher : Walter de Gruyter GmbH & Co KG
Page : 358 pages
File Size : 48,8 Mb
Release : 2017-10-23
Category : Science
ISBN : 9783110426694

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Biomedical Imaging by Tim Salditt,Timo Aspelmeier,Sebastian Aeffner Pdf

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

Multiscale X-Ray Analysis of Biological Cells and Tissues by Scanning Diffraction and Coherent Imaging

Jan-David Nicolas
Multiscale X Ray Analysis of Biological Cells and Tissues by Scanning Diffraction and Coherent Imaging Book PDF

Author : Jan-David Nicolas
Publisher : Göttingen University Press
Page : 183 pages
File Size : 45,7 Mb
Release : 2019
Category : Electronic
ISBN : 9783863954208

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Multiscale X-Ray Analysis of Biological Cells and Tissues by Scanning Diffraction and Coherent Imaging by Jan-David Nicolas Pdf

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.

X-Ray Near-Field Holography: Beyond Idealized Assumptions of the Probe

Johannes Hagemann
X Ray Near Field Holography Beyond Idealized Assumptions of the Probe Book PDF

Author : Johannes Hagemann
Publisher : Göttingen University Press
Page : 152 pages
File Size : 54,9 Mb
Release : 2017
Category : Electronic
ISBN : 9783863953324

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X-Ray Near-Field Holography: Beyond Idealized Assumptions of the Probe by Johannes Hagemann Pdf

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.

Cone Beam Computed Tomography

Chris C. Shaw
Cone Beam Computed Tomography Book PDF

Author : Chris C. Shaw
Publisher : Taylor & Francis
Page : 266 pages
File Size : 53,9 Mb
Release : 2014-02-14
Category : Medical
ISBN : 9781439846278

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Cone Beam Computed Tomography by Chris C. Shaw Pdf

Conventional computed tomography (CT) techniques employ a narrow array of x-ray detectors and a fan-shaped x-ray beam to rotate around the patient to produce images of thin sections of the patient. Large sections of the body are covered by moving the patient into the rotating x-ray detector and x-ray source gantry. Cone beam CT is an alternative te

Coherent X-Ray Optics

David Paganin
Coherent X Ray Optics Book PDF

Author : David Paganin
Publisher : OUP Oxford
Page : 424 pages
File Size : 50,5 Mb
Release : 2006-01-12
Category : Science
ISBN : 9780191524318

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Coherent X-Ray Optics by David Paganin Pdf

This book gives a thorough treatment of the rapidly-expanding field of coherent x-ray optics, which has recently experienced something of a renaissance with the availability of third-generation synchrotron sources. It is the first book of its kind. The author begins with a treatment of the fundamentals of x-ray diffraction for both coherent and partially coherent radiation, together with the interactions of x-rays with matter. X-ray sources, optics elements and detectors are then discussed, with an emphasis on their role in coherent x-ray optics. Various facets of coherent x-ray imaging are then discussed, including holography, interferometry, self imaging, phase contrast and phase retrieval. Lastly, the foundations of the new field of singular x-ray optics are examined. Most topics are developed from first principles, with numerous references given to the contemporary research literature. This book will be useful to x-ray physicists and students, together with optical physicists and engineers who wish to learn more about the fascinating subject of coherent x-ray optics.

MicroComputed Tomography

Stuart R. Stock
MicroComputed Tomography Book PDF

Author : Stuart R. Stock
Publisher : CRC Press
Page : 299 pages
File Size : 49,9 Mb
Release : 2018-10-03
Category : Technology & Engineering
ISBN : 9781351835077

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MicroComputed Tomography by Stuart R. Stock Pdf

Due to the availability of commercial laboratory systems and the emergence of user facilities at synchrotron radiation sources, studies of microcomputed tomography or microCT have increased exponentially. MicroComputed Technology provides a complete introduction to the technology, describing how to use it effectively and understand its results. The first part of the book focuses on methodology, covering experimental methods, data analysis, and visualization approaches. The second part addresses various microCT applications, including porous solids, microstructural evolution, soft tissue studies, multimode studies, and indirect analyses. The author presents a sufficient amount of fundamental material so that those new to the field can develop a relative understanding of how to design their own microCT studies. One of the first full-length references dedicated to microCT, this book provides an accessible introduction to field, supplemented with application examples and color images.

Machine Learning for Tomographic Imaging

Ge Wang,Yi Du Zhang,Xiaojing Ye
Machine Learning for Tomographic Imaging Book PDF

Author : Ge Wang,Yi Du Zhang,Xiaojing Ye
Publisher : Programme: Iop Expanding Physi
Page : 250 pages
File Size : 51,8 Mb
Release : 2019-12-30
Category : Technology & Engineering
ISBN : 0750322144

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Machine Learning for Tomographic Imaging by Ge Wang,Yi Du Zhang,Xiaojing Ye Pdf

Machine learning represents a paradigm shift in tomographic imaging, and image reconstruction is a new frontier of machine learning. This book will meet the needs of those who want to catch the wave of smart imaging. The book targets graduate students and researchers in the imaging community. Open network software, working datasets, and multimedia will be included. The first of its kind in the emerging field of deep reconstruction and deep imaging, Machine Learning for Tomographic Imaging presents the most essential elements, latest progresses and an in-depth perspective on this important topic.

Medical Imaging Systems

Andreas Maier,Stefan Steidl,Vincent Christlein,Joachim Hornegger
Medical Imaging Systems Book PDF

Author : Andreas Maier,Stefan Steidl,Vincent Christlein,Joachim Hornegger
Publisher : Springer
Page : 263 pages
File Size : 49,6 Mb
Release : 2018-08-02
Category : Computers
ISBN : 9783319965208

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Medical Imaging Systems by Andreas Maier,Stefan Steidl,Vincent Christlein,Joachim Hornegger Pdf

This open access book gives a complete and comprehensive introduction to the fields of medical imaging systems, as designed for a broad range of applications. The authors of the book first explain the foundations of system theory and image processing, before highlighting several modalities in a dedicated chapter. The initial focus is on modalities that are closely related to traditional camera systems such as endoscopy and microscopy. This is followed by more complex image formation processes: magnetic resonance imaging, X-ray projection imaging, computed tomography, X-ray phase-contrast imaging, nuclear imaging, ultrasound, and optical coherence tomography.

X-ray waveguide optics

Sarah Hoffmann-Urlaub
X ray waveguide optics Book PDF

Author : Sarah Hoffmann-Urlaub
Publisher : Göttingen University Press
Page : 134 pages
File Size : 51,7 Mb
Release : 2017
Category : Electronic
ISBN : 9783863953089

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X-ray waveguide optics by Sarah Hoffmann-Urlaub Pdf

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.

Atlas of Plant Cell Structure

Tetsuko Noguchi,Shigeyuki Kawano,Hirokazu Tsukaya,Sachihiro Matsunaga,Atsushi Sakai,Ichirou Karahara,Yasuko Hayashi
Atlas of Plant Cell Structure Book PDF

Author : Tetsuko Noguchi,Shigeyuki Kawano,Hirokazu Tsukaya,Sachihiro Matsunaga,Atsushi Sakai,Ichirou Karahara,Yasuko Hayashi
Publisher : Springer
Page : 228 pages
File Size : 48,6 Mb
Release : 2014-08-27
Category : Science
ISBN : 9784431549413

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Atlas of Plant Cell Structure by Tetsuko Noguchi,Shigeyuki Kawano,Hirokazu Tsukaya,Sachihiro Matsunaga,Atsushi Sakai,Ichirou Karahara,Yasuko Hayashi Pdf

This atlas presents beautiful photographs and 3D-reconstruction images of cellular structures in plants, algae, fungi, and related organisms taken by a variety of microscopes and visualization techniques. Much of the knowledge described here has been gathered only in the past quarter of a century and represents the frontier of research. The book is divided into nine chapters: Nuclei and Chromosomes; Mitochondria; Chloroplasts; The Endoplasmic Reticulum, Golgi Apparatuses, and Endocytic Organelles; Vacuoles and Storage Organelles; Cytoskeletons; Cell Walls; Generative Cells; and Meristems. Each chapter includes several illustrative photographs accompanied by a short text explaining the background and meaning of the image and the method by which it was obtained, with references. Readers can enjoy the visual tour within cells and will obtain new insights into plant cell structure. This atlas is recommended for plant scientists, students, their teachers, and anyone else who is curious about the extraordinary variety of living things.

Springer Handbook of Microscopy

Peter W. Hawkes,John C.H. Spence
Springer Handbook of Microscopy Book PDF

Author : Peter W. Hawkes,John C.H. Spence
Publisher : Springer Nature
Page : 1561 pages
File Size : 54,7 Mb
Release : 2019-11-02
Category : Technology & Engineering
ISBN : 9783030000691

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Springer Handbook of Microscopy by Peter W. Hawkes,John C.H. Spence Pdf

This book features reviews by leading experts on the methods and applications of modern forms of microscopy. The recent awards of Nobel Prizes awarded for super-resolution optical microscopy and cryo-electron microscopy have demonstrated the rich scientific opportunities for research in novel microscopies. Earlier Nobel Prizes for electron microscopy (the instrument itself and applications to biology), scanning probe microscopy and holography are a reminder of the central role of microscopy in modern science, from the study of nanostructures in materials science, physics and chemistry to structural biology. Separate chapters are devoted to confocal, fluorescent and related novel optical microscopies, coherent diffractive imaging, scanning probe microscopy, transmission electron microscopy in all its modes from aberration corrected and analytical to in-situ and time-resolved, low energy electron microscopy, photoelectron microscopy, cryo-electron microscopy in biology, and also ion microscopy. In addition to serving as an essential reference for researchers and teachers in the fields such as materials science, condensed matter physics, solid-state chemistry, structural biology and the molecular sciences generally, the Springer Handbook of Microscopy is a unified, coherent and pedagogically attractive text for advanced students who need an authoritative yet accessible guide to the science and practice of microscopy.