3D spatio-temporal analysis for compressive sensing in magnetic resonance imaging of the murine cardiac cycle

This thesis consists of two major contributions, each of which has been prepared in a conference paper. These papers will be submitted for publication in the SPIE 2013 Medical Imaging Conference and the ASEE 2013 Annual Conference. The first paper explores a three-dimensional compressive sensing (CS) technique for reducing measurement time in MR imaging of the murine (mouse) cardiac cycle. By randomly undersampling a single 2D slice of a mouse heart at regular time intervals as it expands and contracts through the stages of a heartbeat, a CS reconstruction algorithm can be made to exploit transform sparsity in time as well as space. For the purposes of measuring the left ventricular volume in the mouse heart, this 3D approach offers significant advantages against classical 2D spatial compressive sensing. The second paper describes the modification and testing of a set of laboratory exercises for developing an undergraduate level understanding of Simulink. An existing partial set of lab exercises for Simulink was obtained and improved considerably in pedagogical utility, and then the completed set of pilot exercises was taught as a part of a communications course at the Missouri University of Science and Technology in order to gauge student responses and learning experiences. In this paper, the content of the laboratory exercises with corresponding educational approaches are discussed, along with student feedback and future improvements. --Abstract, page iv

Cell shape determines gene expression in cardiomyocytes

The fundamental biological processes involve sensing biophysical stress, strain and forces along with conversion of these stimuli into chemical signals. These processes are linked to the atrophic and hypertrophic responses. Deficiencies in these biological processes are associated with different diseases, particularly in the circulation system. Although cardiomyocytes are exposed to significant hemodynamic stimuli that alter their shapes, it was not known until recently whether changes in cardiomyocyte shape impact gene expression. However, recent progress in single-cell RNA sequencing have enabled the profiling of transcriptomes of individual cardiomyocytes with engineered geometries, which are specific to normal or pathological conditions such as preload or afterload. Cardiomyocytes undergo considerable changes in cell morphology, either due to mutations, causing various cardiomyopathies such as hypertrophic cardiomyopathy or dilated cardiomyopathy or via changes in hemodynamic conditions. Moreover, because of various patterns of contraction-relaxation cycles, the membrane of cardiomyocytes is dynamically reshaped in each beating cycle. The overall aim of this thesis was to investigate the effects of cardiomyocyte geometry on gene expression and signaling. In study I, we engineered a novel platform to study cardiomyocyte morphology. In this article, we presented a single-cardiomyocyte trapping strategy, consisting of a method for growing neonatal rat cardiomyocytes with different aspect ratios. The study also proposes a protocol to sort patterned cardiomyocytes based on their acquired geometrical aspect ratios and pick up these adherent cells from their pattern. The described approach paved the way to profile the transcriptome of single cardiomyocytes with specific geometric aspect ratio. In study II, we employed single-cell RNA sequencing to investigate impacts of cardiomyocyte aspect ratio on its transcriptome, using the approach proposed in study I. We observed that distinct morphotypic cardiomyocytes had noticeably varied gene expression patterns, implying that the shape of a cardiomyocyte plays a role in gene expression. This was apparent from the separate cluster of cells, detected in unsupervised clustering analyses. In study III, we proposed a mathematical model of a sarcomere to examine whether and how signaling activity at the membrane of cardiomyocyte depends on its beating rate. Based on this model, a multiphysics program was designed to simulate the cardiomyocyte dynamic geometry throughout the contraction and relaxation phases. The main finding of this study was that an increase in the rate of cardiomyocyte contraction leads to an increase in the concentration of activated Src kinase, especially underneath the costameres. Since hypertrophy of cardiomyocyte modifies the ratio of surface to volume at the plane of membrane, the finding of this study suggests that hypertrophy might be considered as part of a feedback, equilibrating membrane-mediated signaling cascades. These studies identify the shape of the cardiomyocyte as a significant determinant of its gene expression and signaling. Our findings illustrate a novel and important observation, with potentially far-reaching impacts in medicine and biology

Enhancing Single Walled Carbon Nanotube Deposition For The Study Of Extracellular Analytes

Extracellular signaling is a dynamic process responsible for coordinating large scale biological processes. As such, understanding extracellular signaling is important to our determination of normal function and pathophysiological development. High resolution spatial and temporal information are critical to completely understanding these processes. Unfortunately, current methods of detection are lacking in either spatial or temporal resolution of extracellular products, limiting researchers’ ability to understand complex biological processes. A new group of sensors based on fluorescent single walled carbon nanotubes (SWNT) have shown the potential to provide both high quality spatial and temporal resolution for the sensing of analytes. However, while SWNT has already been used extensively as an intracellular probe, it has seldom been used for intercellular monitoring. In the few instances that SWNT has been used to form extracellular sensor arrays the deposition method has relied on electrostatic or non-specific interactions and is not well characterized. Herein a new method of SWNT deposition based on the avidin-biotin bond was developed, where biotin activity was imparted to SWNT via coupling to its DNA wrapping and avidin was covalently immobilized on the surface of a glass slide. The method of SWNT immobilization produced a twofold enhancement in SWNT deposition over the current standard without negatively impacting SWNT spectral properties, distribution, response time, or degradation rates. These results indicate the effectiveness of this method for increasing SWNT deposition and provide a simple pathway for enhancing the deposition of DNA-SWNT complexes. Advisor: Nicole M. Iverso

Enhancing Single Walled Carbon Nanotube Deposition For The Study Of Extracellular Analytes

Extracellular signaling is a dynamic process responsible for coordinating large scale biological processes. As such, understanding extracellular signaling is important to our determination of normal function and pathophysiological development. High resolution spatial and temporal information are critical to completely understanding these processes. Unfortunately, current methods of detection are lacking in either spatial or temporal resolution of extracellular products, limiting researchers’ ability to understand complex biological processes. A new group of sensors based on fluorescent single walled carbon nanotubes (SWNT) have shown the potential to provide both high quality spatial and temporal resolution for the sensing of analytes. However, while SWNT has already been used extensively as an intracellular probe, it has seldom been used for intercellular monitoring. In the few instances that SWNT has been used to form extracellular sensor arrays the deposition method has relied on electrostatic or non-specific interactions and is not well characterized. Herein a new method of SWNT deposition based on the avidin-biotin bond was developed, where biotin activity was imparted to SWNT via coupling to its DNA wrapping and avidin was covalently immobilized on the surface of a glass slide. The method of SWNT immobilization produced a twofold enhancement in SWNT deposition over the current standard without negatively impacting SWNT spectral properties, distribution, response time, or degradation rates. These results indicate the effectiveness of this method for increasing SWNT deposition and provide a simple pathway for enhancing the deposition of DNA-SWNT complexes. Advisor: Nicole M. Iverso

Advanced acquisition and reconstruction techniques in magnetic resonance imaging

Mención Internacional en el título de doctorMagnetic Resonance Imaging (MRI) is a biomedical imaging modality with outstanding features such as excellent soft tissue contrast and very high spatial resolution. Despite its great properties, MRI suffers from some drawbacks, such as low sensitivity and long acquisition times. This thesis focuses on providing solutions for the second MR drawback, through the use of compressed sensing methodologies. Compressed sensing is a novel technique that enables the reduction of acquisition times and can also improve spatiotemporal resolution and image quality. Compressed sensing surpasses the traditional limits of Nyquist sampling theories by enabling the reconstruction of images from an incomplete number of acquired samples, provided that 1) the images to reconstruct have a sparse representation in a certain domain, 2) the undersampling applied is random and 3) specific non-linear reconstruction algorithms are used. Cardiovascular MRI has to overcome many limitations derived from the respiratory and cardiac cycles, and has very strict requirements in terms of spatiotemporal resolution. Hence, any improvement in terms of reducing acquisition times or increasing image quality by means of compressed sensing will be highly beneficial. This thesis aims to investigate the benefits that compressed sensing may provide in two cardiovascular MR applications: The acquisition of small-animal cardiac cine images and the visualization of human coronary atherosclerotic plaques. Cardiac cine in small-animals is a widely used approach to assess cardiovascular function. In this work we proposed a new compressed sensing methodology to reduce acquisition times in self-gated cardiac cine sequences. This methodology was developed as a modification of the Split Bregman reconstruction algorithm to include the minimization of Total Variation across both spatial and temporal dimensions. We simulated compressed sensing acquisitions by retrospectively undersampling complete acquisitions. The accuracy of the results was evaluated with functional measurements in both healthy animals and animals with myocardial infarction. The method reached accelerations rates of 10-14 for healthy animals and acceleration rates of 10 in the case of unhealthy animals. We verified these theoretically-feasible acceleration factors in practice with the implementation of a real compressed sensing acquisition in a 7 T small-animal MR scanner. We demonstrated that acceleration factors around 10 are achievable in practice, close to those obtained in the previous simulations. However, we found some small differences in image quality between simulated and real undersampled compressed sensing reconstructions at high acceleration rates; this might be explained by differences in their sensitivity to motion contamination during acquisition. The second cardiovascular application explored in this thesis is the visualization of atherosclerotic plaques in coronary arteries in humans. Nowadays, in vivo visualization and classification of plaques by MRI is not yet technically feasible. Acceleration techniques such as compressed sensing may greatly contribute to the feasibility of the application in vivo. However, it is advisable to carry out a systematic study of the basic technical requirements for the coronary plaque visualization prior to designing specific acquisition techniques. On simulation studies we assessed spatial resolution, SNR and motion limits required for the proper visualization of coronary plaques and we proposed a new hybrid acquisition scheme that reduces sensitivity to motion. In order to evaluate the benefits that acceleration techniques might provide, we evaluated different parallel imaging algorithms and we also implemented a compressed sensing methodology that incorporates information from the coil sensitivity profile of the phased-array coil used. We found that, with the coil setup analyzed, acceleration benefits were greatly limited by the small size of the FOV of interest. Thus, dedicated phased-arrays need to be designed to enhance the benefits that accelerating techniques may provide on coronary artery plaque imaging in vivo.La Imagen por Resonancia Magnética (IRM) es una modalidad de imagen biomédica con notables características tales como un excelente contraste en tejidos blandos y una muy alta resolución espacial. Sin embargo, a pesar de estas importantes propiedades, la IRM tiene algunos inconvenientes, como una baja sensibilidad y tiempos de adquisición muy largos. Esta tesis se centra en buscar soluciones para el segundo inconveniente mencionado a través del uso de metodologías de compressed sensing. Compressed sensing es una técnica novedosa que permite la reducción de los tiempos de adquisición y también la mejora de la resolución espacio-temporal y la calidad de las imágenes. La teoría de compressed sensing va más allá los límites tradicionales de la teoría de muestreo de Nyquist, permitiendo la reconstrucción de imágenes a partir de un número incompleto de muestras siempre que se cumpla que 1) las imágenes a reconstruir tengan una representación dispersa (sparse) en un determinado dominio, 2) el submuestreo aplicado sea aleatorio y 3) se usen algoritmos de reconstrucción no lineales específicos. La resonancia magnética cardiovascular tiene que superar muchas limitaciones derivadas de los ciclos respiratorios y cardiacos, y además tiene que cumplir unos requisitos de resolución espacio-temporal muy estrictos. De ahí que cualquier mejora que se pueda conseguir bien reduciendo tiempos de adquisición o bien aumentando la calidad de las imágenes resultaría altamente beneficiosa. Esta tesis tiene como objetivo investigar los beneficios que la técnica de compressed sensing puede proporcionar a dos aplicaciones punteras en RM cardiovascular, la adquisición de cines cardiacos de pequeño animal y la visualización de placas ateroscleróticas en arterias coronarias en humano. La adquisición de cines cardiacos en pequeño animal es una aplicación ampliamente usada para evaluar función cardiovascular. En esta tesis, proponemos una metodología de compressed sensing para reducir los tiempos de adquisición de secuencias de cine cardiaco denominadas self-gated. Desarrollamos esta metodología modificando el algoritmo de reconstrucción de Split-Bregman para incluir la minimización de la Variación Total a través de la dimensión temporal además de la espacial. Para ello, simulamos adquisiciones de compressed sensing submuestreando retrospectivamente adquisiciones completas. La calidad de los resultados se evaluó con medidas funcionales tanto en animales sanos como en animales a los que se les produjo un infarto cardiaco. El método propuesto mostró que factores de aceleración de 10-14 son posibles para animales sanos y en torno a 10 para animales infartados. Estos factores de aceleración teóricos se verificaron en la práctica mediante la implementación de una adquisición submuestreada en un escáner de IRM de pequeño animal de 7 T. Se demostró que aceleraciones en torno a 10 son factibles en la práctica, valor muy cercano a los obtenidos en las simulaciones previas. Sin embargo para factores de aceleración muy altos, se apreciaron algunas diferencias entre la calidad de las imágenes con submuestreo simulado y las realmente submuestreadas; esto puede ser debido a una mayor sensibilidad a la contaminación por movimiento durante la adquisición. La segunda aplicación cardiovascular explorada en esta tesis es la visualización de placas ateroscleróticas en arterias coronarias en humanos. Hoy en día, la visualización y clasificación in vivo de es te tipo de placas mediante IRM aún no es técnicamente posible. Pero no hay duda de que técnicas de aceleración, como compressed sensing, pueden contribuir enormemente a la consecución de la aplicación in vivo. Sin embargo, como paso previo a la evaluación de las técnicas de aceleración, es conveniente hacer un estudio sistemático de los requerimientos técnicos necesarios para la correcta visualización y caracterización de las placas coronarias. Mediante simulaciones establecimos los límites de señal a ruido, resolución espacial y movimiento requeridos para la correcta visualización de las placas y propusimos un nuevo esquema de adquisición híbrido que reduce la sensibilidad al movimiento. Para valorar los beneficios que las técnicas de aceleración pueden aportar, evaluamos diferentes algoritmos de imagen en paralelo e implementamos una metodología de compresed sensing que tiene en cuenta la información de los mapas de sensibilidad de las antenas utilizadas. En este estudio se encontró, que para la configuración de antenas analizadas, los beneficios de la aceleración están muy limitados por el pequeño campo de visón utilizado. Por tanto, para incrementar los beneficios que estas técnicas de aceleración pueden aportar la imagen de placas coronarias in vivo, es necesario diseñar antenas específicas para esta aplicación.Programa Oficial de Doctorado en Multimedia y ComunicacionesPresidente: Elfar Adalsteinsson.- Secretario: Juan Miguel Parra Robles.- Vocal: Pedro Ramos Cabre

Photoacoustic Elastography and Next-generation Photoacoustic Tomography Techniques Towards Clinical Translation

Ultrasonically probing optical absorption, photoacoustic tomography (PAT) combines rich optical contrast with high ultrasonic resolution at depths beyond the optical diffusion limit. With consistent optical absorption contrast at different scales and highly scalable spatial resolution and penetration depth, PAT holds great promise as an important tool for both fundamental research and clinical application. Despite tremendous progress, PAT still encounters certain limitations that prevent it from becoming readily adopted in the clinical settings. This dissertation aims to advance both the technical development and application of PAT towards its clinical translation. The first part of this dissertation describes the development of photoacoustic elastography techniques, which complement PAT with the capability to image the elastic properties of biological tissue and detect pathological conditions associated with its alterations. First, I demonstrated vascular-elastic PAT (VE-PAT), capable of quantifying blood vessel compliance changes due to thrombosis and occlusions. Then, I developed photoacoustic elastography to noninvasively map the elasticity distribution in biological tissue. Third, I further enhanced its performance by combing conventional photoacoustic elastography with a stress sensor having known stress–strain behavior to achieve quantitative photoacoustic elastography (QPAE). QPAE can quantify the Young’s modulus of biological tissues on an absolute scale. The second part of this dissertation introduces technical improvements of photoacoustic microscopy (PAM). First, by employing near-infrared (NIR) light for illumination, a greater imaging depth and finer lateral resolution were achieved by near-infrared optical-resolution PAM (NIR-OR-PAM). In addition, NIR-OR-PAM was capable of imaging other tissue components, including lipid and melanin. Second, I upgraded a high-speed functional OR-PAM (HF-OR-PAM) system and applied it to image neurovascular coupling during epileptic seizure propagation in mouse brains in vivo with high spatio-temporal resolution. Last, I developed a single-cell metabolic PAM (SCM-PAM) system, which improves the current single-cell oxygen consumption rate (OCR) measurement throughput from ~30 cells over 15 minutes to ~3000 cells over 15 minutes. This throughput enhancement of two orders of magnitude achieves modeling of single-cell OCR distribution with a statistically meaningful cell count. SCM-PAM enables imaging of intratumoral metabolic heterogeneity with single-cell resolution. The third part of this dissertation introduces the application of linear-array-based PAT (LA-PAT) in label-free high-throughput imaging of melanoma circulating tumor cells (CTCs) in patients in vivo. Taking advantage of the strong optical absorption of melanin and the unique capability of PAT to image optical absorption, with 100% relative sensitivity, at depths with high ultrasonic spatial resolution, LA-PAT is inherently suitable for melanoma CTC imaging. First, with a center ultrasonic frequency of 21 MHz, the LA-PAT system was able to detect melanoma CTCs clusters and quantify their sizes based on the contrast-to-noise ratio (CNR). Second, I developed an LA-PAT system with a center ultrasonic frequency of 40 MHz and imaged melanoma CTCs in patients in vivo with a CNR greater than 12. We successfully imaged 16 melanoma patients and detected melanoma CTCs in 3 of them. Among the CTC-positive patients, 67% had disease progression despite systemic therapy. In contrast, only 23% of the CTC-negative patients showed disease progression. This study lays a solid foundation for translating CTC detection to bedside for clinical care and decision-making