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
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Author : Martin Krenkel
language : en
Publisher: Göttingen University Press
Release Date : 2015
Cone Beam X Ray Phase Contrast Tomography For The Observation Of Single Cells In Whole Organs written by Martin Krenkel 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.
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
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Author : Martin Krenkel
language : en
Publisher:
Release Date : 2015
Cone Beam X Ray Phase Contrast Tomography For The Observation Of Single Cells In Whole Organs written by Martin Krenkel and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
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 ...
Cone Beam X Ray Phase Contrast Tomography Of Biological Samples
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Author : Matthias Bartels
language : en
Publisher: Universitätsverlag Göttingen
Release Date : 2013
Cone Beam X Ray Phase Contrast Tomography Of Biological Samples written by Matthias Bartels and has been published by Universitätsverlag Göttingen this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
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.
Nanoscale Photonic Imaging
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Author : Tim Salditt
language : en
Publisher: Springer Nature
Release Date : 2020-06-09
Nanoscale Photonic Imaging written by Tim Salditt and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-06-09 with Science categories.
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
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Author : Mareike Töpperwien
language : en
Publisher: Göttingen University Press
Release Date : 2018
3d Virtual Histology Of Neuronal Tissue By Propagation Based X Ray Phase Contrast Tomography written by Mareike Töpperwien 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 2018 with categories.
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
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Author : Tim Salditt
language : en
Publisher: Walter de Gruyter GmbH & Co KG
Release Date : 2017-10-23
Biomedical Imaging written by Tim Salditt and has been published by Walter de Gruyter GmbH & Co KG this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-23 with Science categories.
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
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Author : Jan-David Nicolas
language : en
Publisher: Göttingen University Press
Release Date : 2019
Multiscale X Ray Analysis Of Biological Cells And Tissues By Scanning Diffraction And Coherent Imaging written by Jan-David Nicolas 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 2019 with categories.
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
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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.
Cone Beam Computed Tomography
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Author : Chris C. Shaw
language : en
Publisher: Taylor & Francis
Release Date : 2014-02-14
Cone Beam Computed Tomography written by Chris C. Shaw and has been published by Taylor & Francis this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-02-14 with Medical categories.
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 technique using a large area detector and cone-shaped x-ray beam to produce 3D images of a thick section of the body with one full angle (360 degree or 180 degree plus detector coverage) rotation. It finds applications in situations where bulky, conventional CT systems would interfere with clinical procedures or cannot be integrated with the primary treatments or imaging systems. Cone Beam Computed Tomography explores the past, present, and future state of medical x-ray imaging while explaining how cone beam CT, with its superior spatial resolution and compact configuration, is used in clinical applications and animal research. The book: Supplies a detailed introduction to cone beam CT, covering basic principles and applications as well as advanced techniques Explores state-of-the-art research and future developments while examining the fundamental limitations of the technology Addresses issues related to implementation and system characteristics, including image quality, artifacts, radiation dose, and perception Reviews the historical development of medical x-ray imaging, from conventional CT techniques to volumetric 3D imaging Discusses the major components of cone beam CT: image acquisition, reconstruction, processing, and display A reference work for scientists, engineers, students, and imaging professionals, Cone Beam Computed Tomography provides a solid understanding of the theory and implementation of this revolutionary technology.
Construction And Evaluation Of Differential Phase Contrast Cone Beam Ct Imaging System
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Author : Jiangkun Liu
language : en
Publisher:
Release Date : 2015
Construction And Evaluation Of Differential Phase Contrast Cone Beam Ct Imaging System written by Jiangkun Liu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
"When X-rays travel through an object, both the intensity and phase status are varied. The amount of variation depends on the attenuation coefficients and phase coefficients of the materials that the object consists of. In recent years, cone beam breast computed tomography (CBBCT) has emerged as a cutting-edge X-ray imaging modality by reconstructing the attenuation contrast. It is an effective method for screening and diagnosis for breast cancer by providing isotropic three-dimensional images with high resolution and high contrast-to-noise ratio (CNR). However, because the variation of attenuation coefficients among soft tissues is subtle, CBBCT is limited in further characterizing breast lesions. Phase contrast CT technology has been attracting research interests recently. It provides new insight into an object by imaging the phase coefficient, which is more sensitive than the attenuation coefficient. Therefore, it has the potential to overcome the limitations of CBBCT and deliver complementary information. Several phase contrast imaging methods have been developed in the past years. However, the requirement of a coherent X-ray source with a sufficiently small dimension impairs their application as a standard method in hospital-based medical imaging. In this thesis, a grating-based bench-top differential phase contrast cone beam CT (DPC-CBCT) system was designed and constructed. Based on the attenuation-based CBCT imaging system setup, it deploys three more major components: a source grating, a phase grating and an analyzer grating. The source grating enables the system to use a hospital-grade X-ray tube and together they provide sufficient X-ray output power and spatial coherence. The phase grating and the analyzer grating transform the phase shift into intensity contrast based on Talbot interferometry so that a high-resolution detector is not necessary. One of the major challenges of the system construction is grating fabrication because of their high aspect ratio and high precision requirements. This work presents designs for robust recipes that produced gratings meeting our demanding criteria. Another challenge is that the system requires highly precise grating alignment to produce the best contrast effect. An effective method is presented in this work that aligns the phase grating the analyzer grating precisely. The second part of this thesis is to evaluate our DPC-CBCT imaging system in terms of uniformity, CNR, noise property and contrast resolution using a cylinder phantom. As the field of view of the imaging system is limited due to the current grating fabrication technique, it is necessary to investigate the performance of volume of interest (VOI) imaging. The VOI imaging experiment was carried out by scanning a large cylinder phantom. In order to evaluate the performance of DPC-CBCT on actual soft tissues, human breast specimen and small animal experiments were carried out. Phantom experiment results indicate that, compared with attenuation imaging, phase contrast imaging provides higher CNR and contrast resolution. However, in specimen and small animal experiments, phase contrast image quality was greatly degraded. The coherence property of an X-ray beam is critical in phase contrast imaging because the image formation mechanism is based on X-ray beam diffraction. Inhomogeneous objects, such as bones and soft tissues, have a large amount of internal density fluctuations or small structures on a micrometer scale. These small structures produce strong small-angle scattering and greatly reduce the coherence of X-ray beams reaching the detector. In order to evaluate the coherence loss caused by an object quantitatively, the last part of this thesis introduces dark-field imaging, which forms an image by computing small-angle scattering power. Dark-field imaging is also based on grating interferometry and the data can be obtained from the same scan with phase contrast imaging. It can be used to characterize the distribution of micro-structures and to investigate coherence loss in DPC-CBCT imaging. Besides coherence loss, several other factors affect the performance of DPC-CBCT, such as polychromatic X-ray spectrum and imperfect gratings. We believe that phase contrast imaging has the potential to be a more powerful imaging tool and more work will be dedicated to the improvement of DPC-CBCT"--Pages vi-viii.