Ovarian follicles are spherical structures inside the ovaries which contain developing eggs. Monitoring the development of follicles is necessary for both gynecological medicine (ovarian diseases diagnosis and infertility treatment), and veterinary medicine (determining when to introduce superstimulation in cattle, or dividing herds into different stages in the estrous cycle).<p>Ultrasound imaging provides a non-invasive method for monitoring follicles. However, manually detecting follicles from ovarian ultrasound images is time consuming and sensitive to the observer's experience. Existing (semi-) automatic follicle segmentation techniques show the power of automation, but are not widely used due to their limited success.<p>A new automated follicle segmentation method is introduced in this thesis. Human ovarian images acquired <i>in vivo</i> were smoothed using an adaptive neighbourhood median filter. Dark regions were initially segmented using geometric active contour models. Only part of these segmented dark regions were true follicles. A naïve Bayes classifier was applied to determine whether each segmented dark region was a true follicle or not. <p>The Hausdorff distance between contours of the automatically segmented regions and the gold standard was 2.43 ± 1.46 mm per follicle, and the average root mean square distance per follicle was 0.86 ± 0.49 mm. Both the average Hausdorff distance and the root mean square distance were larger than those reported in other follicle segmentation algorithms. The mean absolute distance between contours of the automatically segmented regions and the gold standard was 0.75 ± 0.32 mm, which was below that reported in other follicle segmentation algorithms.<p>The overall follicle recognition rate was 33% to 35%; and the overall image misidentification rate was 23% to 33%. If only follicles with diameter greater than or equal to 3 mm were considered, the follicle recognition rate increased to 60% to 63%, and the follicle misidentification rate increased slightly to 24% to 34%. The proposed follicle segmentation method is proved to be accurate in detecting a large number of follicles with diameter greater than or equal to 3 mm.

In this thesis five different protection harnesses for hunting dogs against canidae attacks were assessed. Hunting dogs can be attacked and severely injured or killed by wolves (Canis lupus) when released during hunting. So far there is no effective protection method. Similar problems are reported with African wild dogs (Lycaon pictus) and dholes (Cuon alpinus) with other domestic animals. In this study the experimental harnesses were presented on a dummy to lure the animals to attack them. The harnesses with physical (screws or spikes on the back) and ultrasound (immediate bite controlled and 19 second continuous ultrasound) deterrents were only assessed during wolf attacks, whereas the harness with electric shocks was also tested on the other two species. Neither physical nor ultrasound deterrents showed a large enough aversive response in the wolves. Electric shocks, given to the animals when biting the dummy, triggered an immediate release of the dummy in all three species. Long term effects differed between species and individuals. The exposed wolf did not touch the dummy again after a second exposure, whereas all except one African wild dog bit the dummy again in consecutive trials. Some individuals returned to bite a second time even in the same trial. An assessment of the long term effect on dholes was not possible, as the individuals were undistinguishable. Based on the data obtained in this study a harness with electric deterrent seems the most promising.

<p>Cardiovascular disease is the leading cause of death for developed countries, including the United States. In order to diagnose and detect certain cardiac diseases, it is necessary to assess myocardial performance and function. One mechanical property that has been shown to reflect myocardial performance is myocardial stiffness. Acoustic radiation force impulse (ARFI) imaging has been demonstrated to be capable of visualizing variations in local stiffness within soft tissue. </p><p>In this thesis, the initial investigations into the visualization of myocardial performance with ARFI imaging are presented. <italic>In vivo</italic> ARFI images were acquired with a linear array placed on exposed <italic>canine</italic> hearts. When co-registered with the electrocardiogram (ECG), ARFI images of the heart reflected the expected changes in myocardial stiffness through the cardiac cycle. With the implementation of a quadratic motion filter, motion artifacts within the ARFI images were reduced to below 1.5 &mu m at all points of the cardiac cycle. The inclusion of pre-excitation displacement estimates in the quadratic motion filter further reduced physiological motion artifacts at all points of the cardiac cycle to below 0.5 &mu m. </p><p>In order for cardiac ARFI imaging to more quantitatively assess myocardial performance, novel ARFI imaging sequences and methods were developed to address challenges specifically related to cardiac imaging. These improvements provided finer sampling and improved spatial and temporal resolution within the ARFI images. <italic>In vivo</italic> epicardial ARFI images of an <italic>ovine</italic> heart were formed using these sequences, and the quality and utility of the resultant ARFI-induced displacement curves were examined.</p><p><italic>In vivo</italic> cardiac ARFI images were formed of <italic>canine</italic> left ventricular free walls while the hearts were externally paced by one of two electrodes positioned epicardially on either side of the imaging plane. Directions and speeds of myocardial stiffness propagation were measured within the ARFI imaging field of view. In all images, the myocardial stiffness waves were seen to be traveling away from the stimulating electrode. The stiffness propagation velocities were also shown to be consistent with propagation velocities measured from elastography and tissue velocity imaging as well as the local epicardial ECG.</p><p>ARFI-induced displacement curves of an <italic>ovine</italic> heart were formed and temporally registered with left ventricular pressure and volume measurements. From these plots, the synchronization of myocardial stiffening and relaxation with the four phases (isovolumic contraction, ejection, isovolumic relaxation, and filling) of the cardiac cycle was determined. These ARFI imaging sequences were also used to correlate changes in left ventricular performance with changes in myocardial stiffness. These preliminary results indicated that changes in the ARFI imaging-derived stiffnesses were consistent with those predicted by current, clinically accepted theories of myocardial performance and function.</p><p>These results demonstrate the ability of ARFI imaging to visualize changes in myocardial stiffness through the cardiac cycle and its feasibility to provide clinically useful insight into myocardial performance.</p> / Dissertation

<p>Prostate cancer (PCa) is the most common non-cutaneous cancer in men in the United States. Early detection of PCa is essential for improving treatment outcomes and survival rates. However, diagnosis of PCa at an early stage is challenged by the lack of an imaging method that can accurately visualize PCas. Because pathological processes change the mechanical properties of the tissue, elasticity imaging methods have the potential to differentiate PCas from other prostatic tissues. Acoustic radiation force impulse (ARFI) imaging is a relatively new elasticity imaging method that visualizes the local stiffness variations inside soft tissue.</p><p>The work presented in this dissertation investigates the feasibility of prostate ARFI imaging. Volumetric ARFI data acquisition and display methods were developed to visualize anatomic structures and pathologies in <italic>ex vivo </italic>human prostates. The characteristic appearances of various prostatic tissues in ARFI images were identified by correlating ARFI images with McNeal's zonal anatomy and the correlated histological slides, in which prostatic pathologies were delineated by a pathologist blinded to the ARFI images. The results suggest ARFI imaging is able to differentiate anatomic structures and identify suspicious PCa regions in the prostate.</p><p>To investigate the correlation between ARFI displacement amplitudes and the underlying tissue stiffness in the prostate ARFI images, the mechanical properties of prostatic tissues were characterized using a quantitative method, based upon shear wave elasticity imaging (SWEI). Co-registered ARFI and SWEI datasets were acquired in excised prostate specimens to reconstruct the shear moduli of prostatic tissues. The results demonstrated that variations in ARFI displacement amplitudes were inversely related to the underlying tissue stiffness; and the reconstructed shear moduli of prostatic tissues had good agreements with those reported in literature. The study suggests the matched ARFI and SWEI datasets provide complementary</p><p> information about tissue's elasticity. </p><p>To increase the efficiency of the data acquisition, a novel imaging sequence was developed to acquired matched ARFI-SWEI datasets without increasing the number of excitations compared to a conventional ARFI imaging sequence. Imaging parameters were analyzed both theoretically and experimentally. An analytical model was derived to quantify the fundamental accuracy limit in the reconstructed shear modulus, and demonstrated good agreement with the experimental data. The novel sequence was demonstrated in tissue-mimicking phantoms.</p><p>Finally, ARFI imaging sequences were developed in a transrectal probe, and ARFI images were presented from <italic>in vivo</italic> data acquired in patients under radical prostatectomy. The <italic>in vivo</italic> ARFI images demonstrated decreased contrast and resolution as compared to the matched <italic>ex vivo</italic> ARFI data. However, prostate anatomy and some PCa were successfully visualized in the <italic>in vivo</italic> ARFI images. Thus, we conclude that ARFI imaging has the potential to provide image guidance for locating cancerous regions during PCa diagnosis and treatment.</p> / Dissertation

<p>This dissertation aims to demonstrate the feasibility of direct infarct visualization using 3D medical ultrasound. The dissertation proceeds by providing the first ever demonstration of fully-sampled 3D ultrasonic speckle tracking using raw B-Mode data of the heart. The initial demonstration uses a Cramer-Rao lower bound limited displacement estimator. The dissertation then proceeds to develop an implementable method for biased time-delay estimation. Biased time-delay estimation is shown to surpass the traditional limits described by the Cramer-Rao lower bound in a mean square error sense. Additional characterization of this new class of estimator is performed to demonstrate that with easily obtainable levels of prior information it is possible to estimate displacements that do surpass the Cramer-Rao lower bound. Finally, using 2D and 3D realizations of biased displacement estimation (Bayesian speckle tracking) the passive strain induced in the ventricle walls during atrial systole is shown to be sufficient to distinguish healthy and chronically infarcted myocardium.</p> / Dissertation

Ultrasound is a valuable tool to monitor wound healing. In this report, ultrasound is used to determine the features in the B-scans that correspond to a bruise. High frequency ultrasound scans show clear and distinct features that correspond to a laceration or a late stage pressure ulcer. This is because of the extensive damage and the rupture of the epidermis in both the cases. This study assumes significance because it is an effort to find such artifacts in the ultrasound scans of bruises caused by blunt forces where the epidermis remains intact. In this study, the structure of the skin was visualized using a 20 MHz ultrasound scanner. Skin thickness and echogenicity changes may result due to blood extravasations or edema. The thickness and the echogenicity values are plotted against time to determine the trend in the variation of these parameters. We see an intraday and a daily fluctuation of skin thickness and echogenicity albeit with no distinct trend on a day to day basis or between subjects. The results also give us a good estimation of the variation observable in these parameters in the event of an injury. A snapshot analysis is also performed, which describes qualitatively the structural changes in the B-scan of the bruise site compared to the control site. There are six different types of qualitative changes which can appear in the B-scan of a bruised site compared to the control. In the event of an injury, usually, more than one of these changes is manifested in the scan of a bruise. Skin thickness and echogenicity vary considerably due to a number of physiological factors which can seldom be controlled. Therefore, these parameters can give conclusive evidence of a bruise only if the change between a bruised region and a control region is much greater than the daily, normal variations. Snapshot analysis can help detect a bruise or a deep tissue injury. Further work involves the application of pattern recognition or face recognition algorithms to automate the detection.

Targeted intracellular delivery is a goal of many novel drug delivery systems to treat site-specific diseases thereby increasing the effectiveness of drugs and reducing side effects associated with current drug administration. The development of ultrasound-enhanced delivery is aimed at providing a targeted means to deliver drugs and genes intracellularly by utilizing ultrasound s ability to non-invasively focus energy into the body and generate cavitation, which has been found to cause transient poration of cells. To address some of the current issues in this field, the goals of this study were (i) to develop a measurement of cavitation to correlate with cellular bioeffects and (ii) to evaluate the ability of ultrasound to target delivery into cells in viable tissue. In addition, this study sought to exploit the shear-based mechanism of cavitation by (iii) developing a simplified device to expose cells to shear stress and cause intracellular uptake of molecules. This study has shown that broadband noise levels of frequency spectra processed from cavitation sound emissions can be used to quantify the kinetic activity of cavitation and provide a unifying parameter to correlate with the cellular bioeffects. We further demonstrated that ultrasound can target delivery of molecules into endothelial and smooth muscle cells in viable arterial tissue and determined approximate acoustic energies relevant to drug delivery applications. Lastly, we developed a novel device to expose cells to high-magnitude shear stress for short durations by using microfluidics and demonstrated the ability of this method to cause delivery of small and macromolecules into cells. In conclusion, this work has advanced the field of ultrasound-enhanced delivery in two major areas: (i) developing a real-time non-invasive measurement to correlate with intracellular uptake and viability that can be used as means to predict and control bioeffects in the lab and potentially the clinic and (ii) quantitatively evaluating the intracellular uptake into viable cells in tissue due to ultrasound that suggest applications to treat cardiovascular diseases and dysfunctions. Finally, by using shear forces generated in microchannels, we have fabricated a simple and inexpensive device to cause intracellular uptake of small and large molecules, which may have applications in biotechnology.

Two similarly managed trials were conducted to investigate serial ultrasound measures of body composition (longissimus muscle area (ULMA), 12th - rib fat thickness (UFAT), and percentage of intramuscular fat (UIMF)) early in the lives of feeder calves as they compared to carcass traits. Group 1 cattle were Charolais-sired by Brahman-British crossbred dams whereas Group 2 cattle were purebred Beefmaster. Both groups were fed at the same commercial feedlot (Graham Land and Cattle Co.) in Gonzales, Texas. In both data sets classifications were developed for ribeye area of Lower (less than 70.95 cm2, Middle (between 70.95 cm2 and 90.3 cm2) and Upper (over 90.3 cm2) based on a range that fit within the ribeye specifications of such branded beef programs as Certified Angus Beef and Nolan Ryan?s Tender Aged Beef. Differences among ribeye area and quality grade (Choice vs. Select) categories were evaluated for ultrasound and carcass traits. As reported previously, correlations between ultrasound measures and carcass traits became larger at times closer to harvest. In both sets of cattle, there were no differences in fat thickness or intramuscular fat at the ultrasound scan sessions or in these carcass traits due to ribeye area category. The same trend for quality grade classification was not seen across both groups of cattle however. In Group 1, there were no differences in early measures of body composition between carcass quality grade classes except for ultrasound fat thickness at weaning. However, in Group 2 cattle there were differences in ultrasound fat at times 1 and 2, IMF at time 1, and ribeye area at time 2 between cattle that graded choice verses those that graded select. Correlations between ultrasound measures of REA (r of .26 to .50) and ultrasound REA and carcass REA (r of .16 to .81) appeared to be lower in Group 1 vs. Group 2 (r of .55, and .64 to 81 respectively). Results from this project imply that changes in ribeye area will not automatically result in changes of marbling and vice versa. Furthermore, these results also show that ultrasound is useful to help predict beef carcass traits, but that early measures of body composition used alone do not explain a large portion of the variation in the carcass measures and specific methods should be developed by different biological cattle types.

Optical imaging of soft biological tissue is highly desirable since it is nonionizing and provides sensitive contrast information which enables the detection of physiological functions and abnormalities, including potentially early cancer detection. However, due to the diffusive nature of light in soft biological tissue, it is difficult to achieve simultaneously good spatial resolution and good imaging depth with pure optical imaging modalities. This work focuses on the ultrasound-modulated optical tomography (UOT): a hybrid technique which combines the advantages of ultrasonic resolution and optical contrast. In this technique, focused ultrasound and optical radiation of high temporal coherence are simultaneously applied to soft biological tissue. The intensity of the sideband, or ultrasound ‗tagged‘ photons depends on the optical absorption in the region of interest where the ultrasound is focused. Demodulation of the optical speckle pattern yields the intensity of tagged photons for each location of the ultrasonic focal spot. Thus UOT yields an image with spatial resolution of the focused ultrasound — typically submillimeter — whose contrast is related to local optical absorption and the diffusive properties of light in the organ. Thus it extends all the advantages of optical imaging deep into highly scattering tissue. However lack of efficient tagged light detection techniques has so far prevented ultrasound-modulated optical tomography from achieving maturity. The signal-to-noise ratio (SNR) and imaging speed are two of the most important figures of merit and need further improvement for UOT to become widely applicable. In the first part of this work, nonlinear optics detection methods have been implemented to demodulate the ―tagged‖ photons. The most common of these is photorefractive (PR) two wave mixing (TWM) interferometry, which is a time-domain filtering technique. When used for UOT, it is found that this approach extracts not only optical properties but also mechanical properties for the area of interest. To improve on TWM, PR four wave mixing (FWM) experiments were performed to read out only the modulated light and at the same time strongly suppressing the ‗untagged‘ light. Spectral-hole burning (SHB) in a rare-earth-ion-doped crystal has been developed for UOT more recently. Experiments in Tm3 :Y3Al5O12 (Tm:YAG) show the outstanding features of SHB: large angle acceptance (etendue), light speckle processing in parallel (insensitive to the diffusive light nature) and real-time signal collection (immune to light speckle decorrelation). With the help of advanced laser stabilization techniques, two orders of magnitude improvement of SNR have been achieved in a persistent SHB material (Pr^3 :Y2SiO5) compared to Tm:YAG. Also slow light with PSHB further reduces noise in Pr:YSO UOT that is caused by polarization leakage by performing time-domain filtering.

In this dissertation, two recent problems from tomographic imaging are studied, and results from numerical simulations with synthetic data are presented. The first part deals with ultrasound modulated optical tomography, a method for imaging interior optical properties of partially translucent media that combines optical contrast with ultrasound resolution. The primary application is the optical imaging of soft tissue, for which scattering and absorption rates contain important functional and structural information about the physiological state of tissue cells. We developed a mathematical model based on the diffusion approximation for photon propagation in highly scattering media. Simple reconstruction schemes for recovering optical absorption rates from boundary measurements with focused ultrasound are presented. We show numerical reconstructions from synthetic data generated for mathematical absorption phantoms. The results indicate that high resolution imaging with quantitatively correct values of absorption is possible. Synthetic focusing techniques are suggested that allow reconstruction from measurements with certain types of non-focused ultrasound signals. A preliminary stability analysis for a linearized model is given that provides an initial explanation for the observed stability of reconstruction. In the second part, backprojection schemes are proposed for the detection of small amounts of highly enriched nuclear material inside 3D volumes. These schemes rely on the geometrically singular structure that small radioactive sources represent, compared to natural background radiation. The details of the detection problem are explained, and two types of measurements, collimated and Compton-type measurements, are discussed. Computationally, we implemented backprojection by counting the number of particle trajectories intersecting each voxel of a regular rectangular grid covering the domain of detection. For collimated measurements, we derived confidence estimates indicating when voxel trajectory counts are deviating significantly from what is expected from background radiation. Monte Carlo simulations of random background radiation confirm the estimated confidence values. Numerical results for backprojection applied to synthetic measurements are shown that indicate that small sources can be detected for signal-to-noise ratios as low as 0.1%.