Browsing by Subject "Optical imaging"
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Item Fiber Optic Micro-endoscopy for Detection of Bacteria in Early Stages of Infection(2012-02-14) Mufti, Nooman SadatMycobacterium tuberculosis, the bacterium that causes tuberculosis, has an incubation period ranging from a few months to several years following infection via inhalation into the lungs. Whole body fluorescence scanners are used to image and monitor the growth of fluorescent protein expressing strains of M. tuberculosis in the lungs of animal models. Accurate quantitative analysis of bacterial growth during the early stages of infection inside lungs remains elusive, due to tissue absorption and scattering of photons emitted by the low numbers of bacteria deep in tissue. Fiber optic micro-endoscopy is uniquely suited to provide a novel solution to this problem by delivering light excitation directly to and collecting fluorescence from the infection site located in the lungs of an animal model, thereby enabling detection of fluorescent bacteria during the early stages of infection. In this thesis, I present a contact probe fiber bundle fluorescence micro-endoscope with a range of LED based excitation wavelengths, 4 ?m resolution, a 750 ?m field of view, and a 1 mm outer diameter. This system has detected tdTomato and GFP expressing Bacillus Calmette-Gu?rin (BCG) bacteria in vitro. Additionally, images of bacterial regions of infection obtained in mice subcutaneously infected with tdTomato expressing bacteria at concentrations ranging from 106 to 101 Colony Forming Units (CFU) and intra-tracheally infected mice at 106 CFU demonstrate the micro-endoscope?s capability to detect and resolve regions of bacterial infection in vivo. By relaying the bacterial fluorescence image from the infection site to an external detector, we are able to increase the sensitivity to early stages of infection.Item Hyper-spectral diffuse reflectance spectroscopy imaging towards the identification of non-melanoma skin cancers(2013-05) Bish, Sheldon Floyd; Tunnell, James W.Non-melanoma skin cancer is the most prevalent malignancy in the world, with over a million annual positive diagnoses in the United States. If left untreated, these cancers cause morbidity and in rare cases, can become life threatening. The key to identifying and characterizing these tumors in the earliest stages, where they are most treatable lie in margin delineation in order to prevent recurrence. The visual obscurity of tumor morphology and physiology can make early detection a difficult task for dermatologists, particularly in the initial stages of cancer development. Tumor resection is a common course of action once they are discovered; however, there is a high recurrence rate due to incomplete removal of the malignant tissue. This dissertation presents an imaging system that can capture the spectral signatures correlating with morphological and physiological changes that accompany skin dysplasia. With this system, we may improve tumor margin delineation, reducing the number of incomplete tumor biopsies and false negative screenings. As an initial step of this process, we begin with a non-contact point sampling diffuse reflectance probe that mitigates the adverse effects of traditional contact probing. Validation of this probe is performed using tissue simulating phantoms spanning a biologically relevant range of optical and physiological properties to ensure that the non-contact format will not hinder performance relative to the contact probe. Cross polarization and auto-focus mechanisms were included in the design to reduce specular reflections and movement artifacts from in vivo measurements. This non-contact design was further developed into a platform for investigating the role of sampling geometry on diffuse reflectance measurements with the addition of a DMD spatial filter. Finally, we developed a hyperspectral DRSi system for the acquisition of wide-field maps of optical and physiological properties that is currently being tested on patients undergoing skin cancer screenings. The spectral output of this system has been validated for scattering and absorption across biologically relevant ranges using tissue simulating phantoms. The DRSi system was optimized for portability, ergonomics and resolution.Item Nanocomposite particles as theranostic agents for cancer(2012-08) Larson, Timothy Arne; Sokolov, Konstantin V. (Associate professor); Ellington, Andrew D.The exploration of nanoparticles for applications in medicine has grown dramatically in recent years. Due to their size, nanoparticles provide an ideal platform for combining multiple functionalities and interfacing directly with the biological realm. Additionally, nanoparticles can have physical properties that don't naturally exist in biology. Metal nanoparticles in particular have unique optical and magnetic properties which have driven nanomaterials research. The optical properties of gold nanoparticles and the magnetic properties of iron nanoparticles make them suitable for use as contrast agents in diagnostics and for radiation enhancement in therapeutic applications. The strong optical absorption and scattering and the nature of the conduction electrons of gold particles makes them ideal contrast agents for two-photon microscopy, photoacoustic imaging, and photothermal therapy. The superparamagnetic nature of iron oxide nanoparticles is clearly visible in magnetic resonance imaging, rendering them suitable as whole-body imaging contrast agents. All nanoparticle types can serve as delivery vehicles for drugs consisting of small molecules, peptides, or nucleic acids. This multiplicity of characteristics renders nanoparticles suitable for use in combining diagnosis and therapy, such as using particles to first detect the spatial extent of a cancer, and then to enhance near-infrared radiation in the tissue optical window to induce localized heating of diseased tissue. This combined approach requires both a mechanism of enhanced imaging contrast and a localized therapeutic mechanism, and the studies presented in this dissertation present work both on these aspects. By coating iron oxide nanoparticle cores with gold shells, it is possible to obtain a nanoparticle with both magnetic and optical properties. While individual gold nanoparticles do not absorb light in the infrared, receptor-mediated aggregation and the plasmon coupling effect lead to enhanced optical absorption only in diseased tissue. In addition to exploring these advanced applications, this work presents a fundamental investigation into the stability of gold nanoparticles in biological media. A previously unknown mechanism of gold nanoparticle destabilization and opsonization is presented and supported, along with a technique for reducing this opsonization and greatly enhancing the stability of gold particles in biological applications. This work will provide guidance to future designs of nanoparticle systems.Item Novel optical techniques for imaging oxygen and other hemodynamic parameters during physiological events(2010-12) Ponticorvo, Adrien; Dunn, Andrew Kenneth, 1970-; Jones, Theresa; Ress, David; Rylander, Grady; Tunnell, JamesThis dissertation presents the development and use of a novel optical imaging system capable of monitoring changes in blood flow, oxygenated hemoglobin, deoxygenated hemoglobin, and absolute pO₂ in the brain. There are several imaging modalities capable of monitoring these parameters separately. Laser speckle contrast imaging (LSCI) and multi-spectral reflectance imaging (MSRI) have been used to monitor relative blood flow and hemoglobin changes respectively. Phosphorescence quenching, while not typically used for imaging, is capable of noninvasive measurements of pO₂. Combining these three techniques has led to the development of an imaging system that could ultimately lead to a better understanding of brain physiology. By combining techniques such as LSCI and MSRI, it becomes possible to estimate the cerebral metabolic rate of oxygen (CMRO₂), an important indicator of neuronal function. It is equally important to understand absolute pO₂ levels so that oxygen metabolism can be examined in context. Integrating phosphorescence quenching and a spatial light modulator into the imaging system allowed absolute pO₂ to be simultaneously measured in distinct regions. This new combined system was used to investigate pathophysiological conditions such as cortical spreading depression (CSD) and ischemia. The observed hemodynamic changes associated with these events were largely dictated by baseline oxygen levels and varied significantly in different regions. This finding highlighted the importance of having a system capable of monitoring hemodynamic changes and absolute pO₂ simultaneously while maintaining enough spatial resolution to distinguish the changes in different regions. It was found that animals with low baseline pO₂ were unable to deliver enough oxygen to the brain during events like CSD because of the high metabolic demand. In order for this technique to become more prevalent among researchers, it is essential to make it cost effective and simple to use. This was accomplished by replacing the expensive excitation sources with cheaper light emitting diodes (LEDs) and redesigning the software interface so that it was easier to control the entire device. The final system shows the potential to become a key tool for researchers studying the role of absolute pO₂ and other hemodynamic parameters during pathophysiological conditions such as CSD and ischemia.Item Numerical algorithms for inverse problems in acoustics and optics(2014-05) Ding, Tian, 1986-; Ren, Kui; Engquist, Bjorn; Gamba, Irene Martínez; Ghattas, Omar; Gonzalez, Oscar; Wheeler, Mary FanettThe objective of this dissertation is to develop computational algorithms for solving inverse coefficient problems for partial differential equations that appear in two medical imaging modalities. The aim of these inverse problems is to reconstruct optical properties of scattering media, such as biological tissues, from measured data collected on the surface of the media. In the first part of the dissertation, we study an inverse boundary value problems for the radiative transport equation. This inverse problem plays important roles in optics-based medical imaging techniques such as diffuse optical tomography and fluorescence optical tomography. We propose a robust reconstruction method that is based on subspace minimization techniques. The method splits the unknowns, both the unknown coefficient and the corresponding transport solutions (or a functional of it) into low-frequency and high-frequency components, and uses singular value decomposition to analytically recover part of low-frequency information. Minimization is then applied to recover part of the high-frequency components of the unknowns. We present some numerical simulations with synthetic data to demonstrate the performance of the proposed algorithm. In the second part of the dissertation, we develop a three-dimensional reconstruction algorithm for photoacoustic tomography in isotropic elastic media. There have been extensive study of photoacoustic tomography in recent years. However, all existing numerical reconstructions are developed for acoustic media in which case the model for wave propagation is the acoustic wave equation. We develop here a two-step reconstruction algorithm to reconstruct quantitatively optical properties, mainly the absorption coefficient and the Gr\"uneisen coefficient using measured elastic wave data. The algorithm consists of an inverse source step where we reconstruct the source function in the elastic wave equation from boundary data and an inverse coefficient step where we reconstruct the coefficients of the diffusion equation using the result of the previous step as interior data. We present some numerical reconstruction results with synthetic data to demonstrate the performance of our algorithm. This is, to the best of our knowledge, the first reconstruction algorithm developed for quantitative photoacoustic imaging in elastic media. Despite the fact that we separate the dissertation into these two different parts to make each part more focused, the algorithms we developed in the two parts are closely related. In fact, if we replace the diffusion model for light propagation in photoacoustic imaging by the radiative transport model, which is often done in the literature, the algorithm we developed in the first part can be integrated into the algorithm in the second part after some minor modifications.Item Optical Lithography and Atom Localization beyond the Diffraction Limit via Rabi Gradient(2014-07-28) Liao, ZeyangThe resolution of traditional optical microscope and optical lithography is limited by about half wavelength of the light source, which is well known as the diffraction limit or Abbe limit. The resolution limit is due to the missing of high spatial frequency components in the far-field. One way to achieve high resolution is to move the detector into the near-field region where the evanescent wave can be collected. However, these methods are surface-bound and usually very slow which have limited applications. It has long been an interesting and important question about how to overcome the diffraction limit in the far-field. For optical lithography, a number of methods have been proposed to overcome the diffraction limit such as multi-photon scanning, quantum entanglement, quantum inspired process (e.g., dopperlon), and quantum dark state. However, these methods either require multi-photon absorber, quantum entanglement, or multi-energy levels, which restrict them from extending to higher resolution in practice. In this thesis, we showed that sub-diffraction-limited resolution can be generated by the coherent Rabi gradient. This method does not require multi-photon absorber or quantum entanglement but just quantum coherence of the medium. Extension from lower resolution to higher resolution is very straightforward where we just need to increase the pulse intensity or pulse duration. We also proposed two atom lithography experiments based on the Rabi gradient. The first one uses Rubidium Rydberg atom and microwave where we showed that sub-micrometer line spacing is possible. The second one uses Chromium atom and optical field where we showed that sub-10nm line spacing is possible while the wavelength of the light is about 400nm. For optical imaging, a number of methods have also been proposed to achieve super-resolution such as multi-photon microscope, stimulated-emission-depletion, structured illumination microscopy, centroid-based techniques and metamaterial-based lens. Here, we will show a new method to achieve resolution beyond the diffraction limit which we called it resonance fluorescence microscopy. Resonance fluorescence has been proposed to localize a single atom with resolution beyond the diffraction limit. The separation between two atoms can also be extracted from the resonance fluorescence spectrum. To develop it as microscopy, we need to evaluate the resonance fluorescence spectrum of multiple-atom system. We analytically solved the general feature of the spectrum when the Rabi frequency is much larger than the dipole-dipole interaction and showed how to extract the spatial information of the atoms with resolution far beyond the diffraction limit. This method is entirely based on far-field techniques and it does not require point-by-point scanning.Item Quantitative optical imaging of hemodynamics as platforms for studying neuro-vascular physiology and disease(2014-08) Kazmi, Syed Mohammad Shams; Dunn, Andrew Kenneth, 1970-; Milner, Thomas E; Tunnell, James W; Rylander, H. Grady; Jones, Theresa ABlood flow and its payload of molecular oxygen are two parameters of most physiological interest. Systemic tissue health is routinely gauged through measurements of vitals and oxygen saturation to estimate the state of these physiological parameters. We design, develop, and deploy optical imaging systems for examining perfusion and oxygenation at the local tissue level and apply these techniques for elucidating the normal and pathological processes associated with neurovascular disease. Specifically, we develop and validate the ability to use Multi-Exposure Speckle Imaging (MESI) to estimate microvascular flow dynamics in rodents over acute and chronic periods. Next, we pose significant optimizations to improve the efficacy of the widefield imaging technique for adoption by bench-side and clinical perfusion studies. We also introduce re-interpretations of the underlying physics to advance the theory that quantifies motion from the imaged speckle patterns. Finally, the technique is deployed for chronic monitoring of cortical flow dynamics before after focal ischemia of the motor cortex as part of a behavioral study in rodents. At the microscale, we develop and validate Two Photon Phosphorescence Lifetime Microscopy (2PLM) to examine dissolved oxygen concentration in microvasculature in three dimensions. We examine the technique’s ability for functional mapping of the rodent cortical microvascular network by quantifying the partial pressure of oxygen (pO₂) before and after occlusion of critical arterioles. Automation of acquisitions and processing for robust oxygen mapping within the micro-vascular network are developed and evaluated. The in vivo results are presented in light of those from studies utilizing more invasive mapping electrodes to provide independent corroboration of the observed neurovascular oxygen distributions. The technique is deployed for examining high resolution functional and structural remodeling after focal cerebral ischemia.