Objective To determine the difference in CT values and image quality of abdominal CT images reconstructed by filtered back-projection (FBP), hybrid iterative reconstruction (IR), and deep learning... Show moreObjective To determine the difference in CT values and image quality of abdominal CT images reconstructed by filtered back-projection (FBP), hybrid iterative reconstruction (IR), and deep learning reconstruction (DLR). Methods PubMed and Embase were systematically searched for articles regarding CT densitometry in the abdomen and the image reconstruction techniques FBP, hybrid IR, and DLR. Mean differences in CT values between reconstruction techniques were analyzed. A comparison between signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of FBP, hybrid IR, and DLR was made. A comparison of diagnostic confidence between hybrid IR and DLR was made. Results Sixteen articles were included, six being suitable for meta-analysis. In the liver, the mean difference between hybrid IR and DLR was - 0.633 HU (p = 0.483, SD +/- 0.902 HU). In the spleen, the mean difference between hybrid IR and DLR was - 0.099 HU (p = 0.925, SD +/- 1.061 HU). In the pancreas, the mean difference between hybrid IR and DLR was - 1.372 HU (p = 0.353, SD +/- 1.476 HU). In 14 articles, CNR was described. In all cases, DLR showed a significantly higher CNR. In 9 articles, SNR was described. In all cases but one, DLR showed a significantly higher SNR. In all cases, DLR showed a significantly higher diagnostic confidence. Conclusions There were no significant differences in CT values reconstructed by FBP, hybrid IR, and DLR in abdominal organs. This shows that these reconstruction techniques are consistent in reconstructing CT values. DLR images showed a significantly higher SNR and CNR, compared to FBP and hybrid IR. Show less
Understanding the formation and evolution of planetary systems is one of the most fundamental challenges in astronomy. To directly image and study young exoplanets and the circumstellar disks they... Show moreUnderstanding the formation and evolution of planetary systems is one of the most fundamental challenges in astronomy. To directly image and study young exoplanets and the circumstellar disks they form from, dedicated high-contrast imaging instruments are built. Several of these instruments have polarimetric modes that are particularly powerful to reach the large contrasts required to directly image these objects as well as to characterize them. This thesis aims to improve the polarimetric sensitivity, accuracy, and capabilities of high-contrast imaging polarimeters for the detection and characterization of exoplanets and circumstellar disks. In addition, this thesis presents the first direct detections of linear polarization from self-luminous planetary mass companions. The focus of this thesis is mostly on ground-based high-contrast imaging, in particular with the instrument SPHERE-IRDIS at the Very Large Telescope. This thesis covers many aspects of high-contrast imaging polarimetry, ranging from theoretical work, calibrations, and the development of new observing techniques to actual scientific polarimetric measurements and astrophysical interpretation. Show less
Arterial spin labeling (ASL) has undergone significant development since its inception, with a focus on improving standardization and reproducibility of its acquisition and quantification. In a... Show moreArterial spin labeling (ASL) has undergone significant development since its inception, with a focus on improving standardization and reproducibility of its acquisition and quantification. In a community-wide effort towards robust and reproducible clinical ASL image processing, we developed the software package ExploreASL, allowing standardized analyses across centers and scanners.The procedures used in ExploreASL capitalize on published image processing advancements and address the challenges of multi-center datasets with scanner-specific processing and artifact reduction to limit patient exclusion. ExploreASL is self-contained, written in MATLAB and based on Statistical Parameter Mapping (SPM) and runs on multiple operating systems. To facilitate collaboration and data-exchange, the toolbox follows several standards and recommendations for data structure, provenance, and best analysis practice.ExploreASL was iteratively refined and tested in the analysis of >10,000 ASL scans using different pulse-sequences in a variety of clinical populations, resulting in four processing modules: Import, Structural, ASL, and Population that perform tasks, respectively, for data curation, structural and ASL image processing and quality control, and finally preparing the results for statistical analyses on both single-subject and group level. We illustrate ExploreASL processing results from three cohorts: perinatally HIV-infected children, healthy adults, and elderly at risk for neurodegenerative disease. We show the reproducibility for each cohort when processed at different centers with different operating systems and MATLAB versions, and its effects on the quantification of gray matter cerebral blood flow.ExploreASL facilitates the standardization of image processing and quality control, allowing the pooling of cohorts which may increase statistical power and discover between-group perfusion differences. Ultimately, this workflow may advance ASL for wider adoption in clinical studies, trials, and practice. Show less
In this thesis, we use low-frequency and high-frequency radio observations to address the following questions regarding quasars: is the radio loud/quiet quasar dichotomy real?; can deep low... Show moreIn this thesis, we use low-frequency and high-frequency radio observations to address the following questions regarding quasars: is the radio loud/quiet quasar dichotomy real?; can deep low-frequency radio observations be used to effectively select high-z quasars?; how does the faint radio-selected quasar population evolve with redshift?; is the environment of quasars related to the origin of their radio-emission. For this purpose, we use low-frequency and high-frequency radio imaging, spectroscopic quasar catalogs, and ancillary optical and infrared data. The second chapter of the thesis uses existing radio and spectroscopic catalogs of quasars to study the clustering properties of RQQs and RLQs. The third chapter uses a directional-dependent calibration algorithm known as facet-calibration to obtain a deep LOFAR 150 MHz mosaic of the NOAO Deep Wide-Field Survey Boötes field. The remaining chapters combine the catalog obtained from the deep LOFAR mosaic presented with ancillary optical/infrared data to study the selection of high-z quasars using LOFAR observations, and to investigate the evolution of radio-selected quasars with redshift. Show less
In pre-clinical research, whole-body small-animal imaging is widely used for in vivo visualization of functional and anatomical information to study cancer, neurological and cardiovascular diseases... Show moreIn pre-clinical research, whole-body small-animal imaging is widely used for in vivo visualization of functional and anatomical information to study cancer, neurological and cardiovascular diseases and help with a faster development of new drugs. Functional information is provided by imaging modalities such as PET, SPECT and specialized MRI. Structural imaging modalities like CT, MRI and ultrasound provide detailed depictions of anatomy. Optical imaging modalities, such as BLI and near-infrared-fluorescence offer a high sensitivity in visualizing molecular processes in vivo. Combining these modalities enables to follow the subject(s) and molecular processes in time, in living animals. With these advances in image acquisition, the problem has shifted from data acquisition to data processing: organization, analysis and interpretation of this heterogeneous whole-body imaging data has become a demanding task. Here, our data processing approach is based on an articulated whole-body atlas as a common reference to normalize the geometric heterogeneity caused by postural and anatomical differences between individuals and geometric differences between imaging modalities. Mapping to this atlas has the advantage that all the different imaging modalities can be registered to a common anatomical reference; postural variations can be corrected, and the different animals can be scaled properly while allowing for proper management of this high-throughput data. Show less
Coronary artery disease(CAD) is one of the leading causes of mortality and morbidity worldwide. Clinically, it refers to atherosclerotic changes in the coronary arteries and is usually assessed... Show moreCoronary artery disease(CAD) is one of the leading causes of mortality and morbidity worldwide. Clinically, it refers to atherosclerotic changes in the coronary arteries and is usually assessed with a stress electrocardiogram and conventional coronary angiography(CCA). CCA, however, is an invasive technique and carries a small risk of complications. Non-invasive techniques such as coronary angiography with CT(CTCA), and myocardial perfusion imaging (MPI) with SPECT and MR are therefore used as gatekeeper tests before CCA. These techniques provide valuable information on both the coronary stenoses and their hemodynamic impact on the myocardial function. However, each of these techniques presents only one aspect of CAD. To achieve a higher level of accuracy and precision in CAD assessment, integration of information from different cardiac imaging modalities is essential. The goal of this thesis was therefore to develop techniques to realize this multimodal diagnostic image integration to enhance CAD diagnosis. To this end, we developed novel algorithms for near automated analysis of magnetic resonance based myocardial perfusion images. In addition, we developed and evaluated a new integration framework that allows comprehensive visualization of physiologic information from myocardial perfusion imaging -either with MR or SPECT and anatomical information from CTCA Show less
During gastrulation, the cells, and consequently the organ anlagen, are repositioned according to their future arrangement along the anterio- posterior axis. The movements responsible, the... Show moreDuring gastrulation, the cells, and consequently the organ anlagen, are repositioned according to their future arrangement along the anterio- posterior axis. The movements responsible, the convergence and extension (CE) cell movements, are crucial for normal development and defects in their mechanism underlie human pathologies like spina bifida and Noonan syndrome. Collective polarization of the cells is essential for these morphogenetic. The coordination and regulation are governed by intricate signaling mechanisms. Tyrosine phosphorylation is one of such mechanisms. By either phosphorylation by protein-tyrosine kinases or dephosphorylation by protein-tyrosine phosphatases (PTPs) of tyrosine residues, many signaling proteins can be switched from active to inactive states. In this thesis, we focus on the role of ‘classical’ PTPs. We identified PTP-BL, Ptpn20, RPTPα and RPTPε as components of a system regulating cell polarity. Additionally, we identified via screening one additional PTP, ptprda, as essential for CE movements. Quantitative analysis and clear representation of the data is essential to modern day biology. Studying collective cell migrations requires the analysis of the net effect of cell polarization and/or displacements of a large number of cells within a tissue rather than measurements of a few individuals. An automated cell tracing algorithm was developed and an algorithm for the detection of cell membranes. Additionally, a novel method of graphical data representation is introduced. Show less
This thesis proposes several new algorithms including X-ray angiographic image enhancement, three-dimensional (3D) angiographic reconstruction, angiographic overlap prediction, and the co... Show moreThis thesis proposes several new algorithms including X-ray angiographic image enhancement, three-dimensional (3D) angiographic reconstruction, angiographic overlap prediction, and the co-registration of X-ray angiography with intracoronary imaging devices, such as intravascular ultrasound (IVUS) and optical coherence tomography (OCT). The algorithms were integrated into prototype software packages that were validated at a number of clinical centers. The feasibility of using such software packages in typical clinical population was verified, while the advantages and accuracy of the proposed algorithms were demonstrated by phantoms and in-vivo clinical studies. In addition, based on the proposed approaches and the conducted studies, this thesis reports a number of findings including the impact of acquisition angle difference on 3D quantitative coronary angiography (QCA), the clinical characteristics of bifurcation optimal viewing angles and bifurcation angles, and the discrepancy of lumen dimensions as assessed by 3D QCA and by IVUS or OCT. Show less
With the help of modern techniques of imaging processing and computing, image data obtained by electron cryo-microscopy of biomolecules can be reconstructed to three-dimensional biological models... Show moreWith the help of modern techniques of imaging processing and computing, image data obtained by electron cryo-microscopy of biomolecules can be reconstructed to three-dimensional biological models at sub-nanometer resolution. These models allow answering urgent problems in life science, for instance, the pathways directing the self-recovery system of cell, which certainly has great significance for all our lives. To determine these models, there are two main electron microscopic methods available, corresponding to its two main modes of operation: 3DEM single particle reconstruction and electron diffraction. This thesis focuses on the research and methods of 3DEM and electron diffraction, and its practical application in solving the structure of a 50S ribosomal complex, which clarifies the mechanism of cell recovery in heat shock stress. Preliminary research on a novel structure determination method by using nano-crystals resulted in a novel software suite __ EDiff __ which is a program for unit cell parameter determination, indexing and so on. Show less
Accurate visualization and quantification of atherosclerosis in a non-invasive manner by means of MR is, nowadays, of high importance, not only regarding morphology but also composition of the... Show moreAccurate visualization and quantification of atherosclerosis in a non-invasive manner by means of MR is, nowadays, of high importance, not only regarding morphology but also composition of the atherosclerotic plaques. MR has proven to be capable of detecting early, subclinical vulnerable plaque. However, when the analysis of atherosclerosis is based on visual interpretation of the images or manually delineated structures, the outcome is often not reliable. The main objective of this thesis was to investigate novel image processing techniques to automatically quantify markers of the severity of atherosclerosis in a reproducible manner, by automatically outlining the boundaries of the blood vessel wall, lumen and plaque burden. Different algorithms have been developed and applied to different vascular beds (aorta and carotid arteries) proving to be versatile and powerful tools, that provide quantitative reproducible parameters. These new techniques have been validated in limited populations, proving to be accurate and reproducible. They are, therefore, suitable to be further adapted and to be employed in the clinical vascular research. This assists the physician in making a diagnosis and identifying high-risk patients, who may benefit from treatment. Show less
