Browsing by Author "Das, Mini"
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Item (I) The Significance of Incorporating a 3D Point Source in Inverse Scattering Series (ISS) Multiple Removal for a 1D/2D Subsurface; (II) an Alternative ISS Internal Multiple Elimination Algorithm for the First-Order Internal Multiples Having Their Downward Reflection at the Ocean Bottom(2016-08) Lin, Xinglu 1989-; Weglein, Arthur B.; Das, Mini; Liu, Fang; Francis, David J.; Zhang, Jingfeng; Liang, DongInverse scattering series (ISS) de-multiple methods do not require any subsurface information to achieve seismic processing objectives. In specific applications of the ISS de-multiple methods, the subsurface is assumed to 1D, 2D, or 3D and the dimension of the source is typically chosen to agree with the dimension of the subsurface, for example, choosing a 2D line source for a 2D subsurface. And often in deriving a 1D subsurface theory from a 2D algorithm the 2D line source is brought along into the 1D subsurface theory. However, field data are generated by a locally 3D source and realistic synthetic data need to incorporate a 3D source. The lesson is that there are times when a 1D or 2D subsurface can be a reasonable approximation, but it is always important to incorporate a 3D source to have an effective multiple predictor and removal. This dissertation describes how to incorporate a 3D source in ISS de-multiple methods for a 1D and 2D subsurface. We then evaluate the positive added value of incorporating a 3D source in the distinct 1D subsurface algorithms, using synthetic data generated by a 3D source. The second part provides an approach to address the challenge of current internal multiple attenuator. The current algorithm provides accurate time and approximate amplitude of all internal multiples. For complex circumstances, where internal multiples are often proximal to or interfering with primaries, the current ISS internal multiple attenuator plus an adaptive subtraction can fail to remove multiples without damaging primaries. This challenge demands an internal multiple eliminator, in which both time and amplitude of internal multiples can be accurately predicted. There are circumstances where it is possible to provide reliable subsurface information to transform the internal multiple attenuator into an eliminator. For example, in marine exploration, the earth properties down to and across the ocean bottom can often be estimated from a velocity analysis. With that information, the ISS internal multiple attenuator can eliminate all internal multiples having their shallowest downward reflection at the ocean bottom. The effectiveness of the proposed method is evaluated by a 1D normal incidence test.Item I. THE FIRST MULTI-DIMENSIONAL INVERSE-SCATTERING-SERIES INTERNAL-MULTIPLE-ELIMINATION METHOD: A NEW TOOLBOX OPTION FOR REMOVING INTERNAL MULTIPLES THAT INTERFERE WITH A PRIMARY, WITHOUT DAMAGING THE PRIMARY, AND WITHOUT ANY KNOWLEDGE OF SUBSURFACE PROPERTIES II. TESTS AND ANALYSIS FOR RESOLUTION COMPARISONS BETWEEN REVERSE TIME MIGRATION (RTM) AND THE FIRST MIGRATION METHOD THAT IS EQUALLY EFFECTIVE AT ALL FREQUENCIES AT THE TARGET(2017-08) Zou, Yanglei 1989-; Weglein, Arthur B.; Chemingui, Nizar; Das, Mini; Liu, Fang; Meier, Mark A.; Melo, Federico Xavier de; Ordonez, CarlosThe general goal of seismic exploration is to develop new capabilities in the seismic toolbox to increase our ability to locate hydrocarbons. There is a seismic processing chain of linked tasks that processes the data recorded by the receivers and produces subsurface images to serve that goal and objective. This thesis represents progress in two different links in this chain, (1) the internal-multiple removal and (2) the first migration method that is equally effective at all frequencies at the target. The organization of the thesis is as follows. First, we provide an introduction to the new internal-multiple-elimination method. Then a similar introduction is provided for the rst migration method that is equally e ective at all frequencies at the target. Chapters 2, 3 and 4 discuss the internal-multiple-elimination algorithm and provide numerical tests for: (1) a 1D normal incidence plane wave on an acoustic medium, (2) pre-stack 1D acoustic and elastic model data and (3) a multi-dimensional acoustic earth. Chapters 5 and 6 discuss the first migration method that is equally effective at all frequencies at the target and compare this method (for structural resolution) with current industry leading edge RTM. Chapter 7 summarizes this thesis.Item Interactions between Phenotypic Switching, Gene Network Dynamics and Evolutionary Dynamics in Growing Cell Populations(2016-05) Belete, Merzu Kebede 1982-; Balazsi, Gabor; Gunaratne, Gemunu H.; Bassler, Kevin E.; Das, Mini; Cooper, Timothy F.Gene expression is a stochastic biological processes that controls the different phenotypes of an organism depending on the environment. High-resolution single cell measurements show that genetically identical cells can be different from each other even in a homogeneous environment, leading a spectrum of phenotypes with different cellular fitnesses that can reversibly switch between phenotypes. How population-level properties emerge from single cell behavior and how mutants emerge and spread in such populations is unclear. In this thesis, we developed mathematical models to study (i) the effect of time-delay needed for a mutation in a regulator gene influence an effector protein and the long term population fitness, (ii) how optimum population fitness behaves as a function of the growth rates of the various phenotypes for different durations in fluctuating environments. Our work shows a paradoxical outcome of evolution where mutations in a regulator gene interact with gene network dynamics and evolutionary dynamics, giving rise to permanent decrease in population fitness. In the other scenario of fluctuating environments, a previously predicted optimum exists for wider parameter regime if the environmental durations are long and narrow regime for short environmental durations. We also find that a mutant, which randomly evolved to match its phenotypic switching rates with environmental switching rates, can sweep the population if the predicted optimum matches with the assumed one, but not otherwise.Item LASER MULTI-SPECTRAL CONFOCAL MICROSCOPY FOR STRUCTURED ILLUMINATION IMAGING(2013-12) Sukumari, Abhilash; Le, Han Q.; Charlson, Earl J.; Das, MiniConfocal laser scanning microscopy is a powerful and well-established technique with a wide range of applications. Structured illumination microscopy is a technique to extend the spatial resolution by a factor of two or potentially more beyond Abbe’s microscopy limit by using patterned illumination light. Certain aspects of each technique can be combined to give a new approach with advantageous features of each. Theoretical work has been done to demonstrate the applicability of SIM principle to CLSM. This research focuses on experimental investigation and developing a state-of-the-art instrumentation that can be deployed to demonstrate this concept. Research challenges are expected for all aspects of the proposed work. The anticipated ultimate impact of this research is a new feature that can be added to existing and future CLSM systems that can double the spatial resolution of these systems. Given the large number of existing CLSM for numerous applications, this feature may have a substantial commercial market.Item Laser Optoacoustic Imaging System for Molecular and Functional Imaging Research in Small Animal Models(2021-05) Su, Richard; Oraevsky, Alexander A.; Larin, Kirill V.; Gifford, Howard C.; Roysam, Badrinath; Das, Mini; Emelianov, Stanislav Y.Optoacoustic tomography is an emerging field of medical imaging that is rapidly developing due to its unique capability to visualize and display molecular content of biological tissues with quantitative accuracy and excellent spatial resolution scalable with depth within live tissues. The main merit of optoacoustic tomography is in deep tissue imaging where resolution and contrast of pure optical imaging methods are limited by the strong optical scattering. The dominating tissue chromophores in the spectral range of laser wavelengths (650 nm to 1100 nm) that penetrate deep within tissues are hemoglobin and oxyhemoglobin of blood. Potential capability of functional optoacoustic tomography systems to measure concentrations of hemoglobin and oxyhemoglobin in humans provides for a variety of medical applications in the fields of diagnostics, therapeutic interventions and surgery. Using the methods of molecular imaging, it is also possible to visualize distribution of molecules that do not possess strong optical absorption in the near infrared spectral range, but can be targeted by special molecular and nano-particular contrast agents designed with strong optical absorption and high efficiency of acoustic wave emission through thermal expansion. In spite of great promises the full potential of optoacoustic tomography in functional and molecular imaging has not been realized yet. In order to achieve capabilities of functional and molecular imaging, the optoacoustic tomography system has to overcome the tradeoff between high sensitivity of detection and ultrawide-bandwidth of ultrasonic frequency detection. Furthermore, quantitative imaging is only possible with knowledge of the optical fluence distribution through the entire volume of interest at each of the multiple wavelengths of laser illumination. We took on a challenging task to develop such an advanced tomography system and enhance it with the methods of quantitative data analysis and image reconstruction. We designed and assembled a full view three-dimensional Laser Optoacoustic Imaging System (LOIS-3D) based on a 96-channel array of ultrawide band ultrasonic transducers and demonstrated its highest sensitivity to changes in the optical absorption coefficient ~0.03/cm compared with any academic or industrial system. We proposed and implemented a signal processing method of transducer impulse response deconvolution that enabled reversal of distortions in the detected optoacoustic signals, which in turn allowed the experimental approach to functional and molecular imaging in live laboratory animals. The system technical specifications were characterized in a number of molecular imaging experiments. Finally, we proposed and implemented a practical method of the optical fluence normalization through the entire imaged volume based on measurements of the voxel brightness in blood vessels with known optical absorption and without computations of light propagation through tissues with unknown optical properties. We reconstructed previously unattainable functional images of the total hemoglobin and blood oxygen saturation in a volume of live tissue showing separately arteries, veins and tissues.Item Material Decomposition Using Multi-Energy Imaging with Photon Counting Detectors(2017) Torrico, Raul; Fredette, Nathaniel; Das, MiniThe current screening tool for breast cancer is digital mammography (DM). DM is based on the principle that x-ray photons are absorbed by materials differently. Breast cancer screening relies on the detection of tumors and micro calcifications. One of the primary challenges in breast imaging is to differentiate healthy, glandular and adipose, versus unhealthy tissues in the breast. Certain plastics can be used as a substitute to mimic the x-ray absorption of breast tissue. Micro calcifications can be replaced with hydroxyapatite (HA). To improve diagnosis, contrast agents, like iodine, could be used in DM. Iodine is injected intravenously and the tumor will temporarily absorb it. Dual energy subtraction techniques are used for enhanced iodine contrast imaging. In order to separate iodine from calcification, multi-energy imaging is desired. Multi-energy imaging is the acquisition of three or more different images at different energies. This data can be used for material decomposition where the distribution of each of the materials is found simultaneously.Item Multi-Material Discrimination Using Photon Counting Spectral Computed Tomography(2020-12) Fredette, Nathaniel Raymond; Das, Mini; Gifford, Howard C.; Zhang, Yingchun; Ince, Nuri F.; Hebert, Thomas J.Quantitative volumetric mapping of multiple materials with spectral computed tomography (CT) has applications in many areas including biomedical imaging, defense and security, geophysical imaging of rock composition and in materials and chemical imaging. Dual or multi-kVp x-ray exposure when using an energy-integrating detector has been proposed and demonstrated in the past for biomedical imaging. X-ray dose and imaging time, along with insufficient spectral separation, limits dual and multi-kVp applications and their ability for accurate quantitation. When using photon-counting spectral detectors (PCDs), some of these limitations can be overcome. However, low dose and computationally efficient mechanisms to yield volumetric maps of more than two or three materials remain as a significant challenge. Recently, our group has proposed a multi-step method for virtual discernment between the materials of an object termed material decomposition for short. Experimental implementation of this method adds new challenges including reliable detector spectral corrections. This work presents initial simulation studies, experimental validation and detailed methods to successfully implement this multi-material decomposition technique. Here we show examples with virtual separation of up to six materials in simulations and five materials in experiments on our benchtop spectral CT system. For comparison, a conventional single-step decomposition was also performed on the same synthetic and experimental data. Results show a significant reduction in decomposition errors with low noise over the single-step approach. Finally, a biological specimen of a chicken heart was injected with tantalum and gadolinium (likely candidate contrast agent materials) and multi-step decomposition was also successfully conducted on this sample. These studies offer validations required for robust utility of the method in imaging applications requiring separation of multiple materials.Item On the Microscopic Mechanism of Mesoscopic Aggregation in Protein Solutions(2015-08) Chan, Ho Yin 1985-; Lubchenko, Vassiliy; Cheung, Margaret S.; Das, Mini; Miller, John H.; Vekilov, Peter G.Mesoscopic clusters of protein-rich fluid are observed in solutions of several proteins. The molecular origin and thermodynamics underlying the formation of the clusters are poorly understood. Here we test the “complexation” scenario of cluster formation, in which the clusters represent a spatially heterogeneous mixture of protein and protein containing complexes. Two separate aspects of this microscopic picture are addressed in the present work. On the one hand, we have developed a novel coarse-grained model that accounts for anisotropy of the Coulomb component of protein-protein interaction. Solvent-screened Coulomb interactions between protein molecules are approximated at the Debye-Huckel level, with corrections to account for polarization at the protein-solvent interface. We establish that transient complexes formed by folded molecules of the protein lysozyme are too short-lived to give rise to mesoscopic clusters; thus complex formation in lysozyme must involve partial unfolding of individual protein molecules. On the other hand, we develop a complete framework to treat nucleation in fluid mixtures, in the presence of chemical conversion between components of the mixture. We establish an expression for the coordinate-dependent pressure in the Landau-Ginzburg functional theory, which is applicable to mixtures and non-equilibrium situations. We discover that in contrast with nucleation in mixtures with conserved amounts of components, finite-sized metastable phases can be kinetically stabilized in the presence of chemical conversion between the components. Clusters of such metastable minority phases will grow indefinitely, upon reaching a certain critical size; the growth is eventually halted by a mechanical instability. On approach to equilibrium, Ostwald-like ripening is predicted to take place, but with a distinct time-dependence of the cluster size from the Lifshitz-Slyozov-Wagner theory. The present results provide substantial support for the complexation scenario for the formation of the mesoscopic clusters.Item Perceptually Relevant Measurements in Tomosynthesis Imaging(2022-08-15) Kavuri, Amareswararao; Das, Mini; Francis, Joseph T.; Gifford, Howard C.; Hebert, Thomas J.; Zhang, YingchunTissue structures and imaging system parameters are major factors that influence the ability of radiologists to find and identify malignancies. For example, parameters relevant to mammography like radiation dose, breast density and thickness, pixel size, arc span and number of projections in the case of digital breast tomosynthesis (aka 3D mammography) can alter the cancer screening diagnosis. Therefore, it is necessary to find which configuration is best so that least number of malignancies are missed by the radiologists. They examine hundreds of radiographs every day and sometimes there is a potential to misclassify the images. By understanding the image properties in relation to human perceptual mechanisms, we can find the optimal configurations to reduce misdiagnosis. The focus of this thesis is to characterize digital breast tomosynthesis (DBT) images using image quality metrics and eye gaze analysis and to explore how these metrics relate to abnormality detection performance and diagnostic errors. The first part of this thesis evaluates the relevance of noise power spectrum (NPS) based metrics in characterizing the DBT images and their relation to human observer diagnosis performance. The NPS based power-law exponent beta was hypothesized to quantify tissue structural overlap and to use as a surrogate for diagnostic performance in x-ray imaging. We showed that random noise and system configurations influence this parameter and do not correlate with human observer performance in DBT imaging and hence cannot be used as a surrogate for diagnostic performance while the power-law magnitude (K) showed a strong correlation. Next, we investigated the impact of phantom structural variations on the estimation of DBT optimal configurations in virtual imaging trials (VITs). Our results indicate that phantoms should be designed to resemble the patients’ anatomical structures accurately and should be evaluated for their realism and sufficiency in the use of VITs. Finally, to further our understanding of the relation between different system parameters and human perceptual mechanisms, gaze analysis was conducted. To this end, we developed a graphical user interface for an eye-tracking tool to conduct eye-tracking studies and estimate eye gaze metrics and fixation regions. Our results indicate that along with diagnostic performance other perceptual aspects such as image reading time can be considered for system optimization. Our gaze analysis suggests that gaze metrics correlate with diagnostic performance and task difficulty and could help understand the difficulty levels in a VIT.Item Spectral Phase Contrast Imaging and Phase Retrieval(2020-12) Vazquez, Ivan; Das, Mini; Gifford, Howard C.; Li, Liming; Meier, Mark A.Phase-contrast X-ray imaging (PCI) can significantly improve the contrast of small and weakly-absorbing materials. This is because of the sensitivity of PCI measurements to changes in both the attenuation and phase of an X-ray wavefield due to interactions with matter. Yet, quantitative estimates of material properties from PCI measurements require the use of phase retrieval (PR) algorithms. Our team developed a capable PR strategy for propagation-based PCI that estimates a pair of material properties from two or more energy-resolved measurements. Part of this work is dedicated to broadening our understanding of the key advantages and practical limitations of our method. To this end, a comprehensive analysis of the underlying theory and the sensitivity to factors such as noise are provided. Based on our findings, we proposed a set of strategies that can help enhance the quality and accuracy of estimated values. We also examined the performance of the PR method with laboratory measurements of a heterogeneous sample. To simultaneously obtain multiple energy-resolved measurements, we used a polychromatic (laboratory) source in combination with high-resolution photon-counting detectors. Our findings demonstrate that the properties of multiple (more than two) unique materials can be estimated with accuracies above 90\%. Additionally, our strategy produced results with satisfactory accuracy and image quality even when the detected photon counts were as low as 250 photons per pixel. The underpinning theory in our approach relies on the weak object approximation to simplify the transport-of-intensity equation (TIE). Thus, a section of this work is dedicated to examining the errors related to enforcing the weak object approximation when deriving a TIE-based PR algorithm. We also tested other prevalent methods to simplify the TIE. Experimental results revealed that errors introduced by the weak object approximation were below 5\% even for the case of aluminum, which has a relatively high atomic number.Item Spectral Signature and Correction of Scattered Radiation in Energy-Resolved X-ray Imaging(2020-12) Lewis, Cale E.; Das, Mini; Gifford, Howard C.; Koerner, Lisa W.; Varghese, Oomman K.X-ray imaging is a powerful tool for material identification and characterization with applications in a wide range of fields including medicine, biology, geoscience, and security. Since the discovery of x-rays in 1895, gradual improvements to imaging technology have lead to some major milestones such as computed tomography (CT). More recently, pioneering advancements in x-ray detector technology have made possible photon counting detectors (PCDs) with energy-resolving capabilities. Exploiting spectral information of the incident radiation promises revolutionary approaches to material identification and characterization. However, radiation that scatters from the object and reaches the detector is a long-standing problem that reduces image quality and quantitative accuracy. Previous studies to characterize and account for the scattered radiation have been limited to conventional x-ray imaging with energy-integrating detectors (EIDs). The purpose of this research is two-fold: i) determine the spectral characteristics of the scattered radiation and the impact on quantitative spectral imaging and ii) develop an energy-sensitive scatter correction method to compensate for these inaccuracies. Through Monte Carlo simulation and experimental validation, the spectral characteristics of scatter are evaluated for a large scope of imaging parameters including: the object geometry and composition, object-to-detector distance, x-ray source distribution, and detector type. The impact of the scattered radiation was evaluated by estimating the energy-dependent attenuation properties of clinically-relevant materials. When left uncorrected, scattered radiation results in severe quantitative inaccuracies which can limit proper material identification. The next objective was applying these characteristics to develop an energy-sensitive scatter correction that compensates for the inaccuracies due to scatter. Our method derives from the physical understanding of scatter interactions to estimate the spectrally-dependent scatter maps. This method was applied in the context of contrast-enhanced mammography, which showed accurate quantitative restoration of iodine targets in breast-like phantoms. This particular scatter correction technique is appealing as it does not require any modifications to the acquisition process or beam path. The versatility of the energy-sensitive scatter estimation technique also suggests further utility in other x-ray imaging applications such as tomosynthesis and computed tomography.