Motion Estimation in Static Magnetic Resonance Elastography

Elastography is the imaging of the biomechanical properties of a tissue to detect and diagnose abnormal pathologies in a variety of disease conditions. Static Magnetic Resonance Elastography (MRE) is a modality of elastography that uses Magnetic Resonance Imaging (MRI) principles for data acquisition from a biological sample under external loading. An estimation of the mechanical deformation of the loaded sample from its Magnetic Resonance (MR) images constitutes a key component of the static MRE. Efforts in this area of research have mainly been focused on developing data acquisition protocols and motion estimation algorithms for producing high quality elastography images. So far, however, progress made in static MRE remains limited in both clinical and experimental fields. This dissertation work performed a comprehensive investigation of the data acquisition, pre-processing, and motion analysis stages of the static MRE modality. First, a mechanical device was introduced to reliably apply repetitive external compression to the sample. The design of this device and how it was interfaced with the scanner for gated data acquisition are described in detail. Next, MRI basics are summarized, and the use of tagged MRI sequence as the data acquisition protocol is justified. Optimal parameters that led to the best quality tagged MRI data were determined by taking the repetitiveness of the compression and the use of tag lines into consideration. Lastly, two reliable motion estimation algorithms were implemented and successfully tested on a variety of synthetic and real MRE data. After adjusting the parameters of the techniques using the prior knowledge of the features of the tagged MR images, both Iterative and One-step Optical Flow (OF) algorithms consistently produced acceptable results. It was found, that while applied to the real data, the Iterative OF algorithm slightly outperforms the One-step OF algorithm. The results of the testing are provided and discussed. This research is interdisciplinary and embraces concepts from the fields of Physics, Image Processing, Computer Vision, Algorithmics, Electrical Engineering, and Biomedical sciences. Future extensions of the research include a variety of studies on phantoms with an inclusion, small oncology animal models, and possibly followed by clinical human research that would contribute to improving the reliability, accuracy, and speed of tumor detection. Other possible applications may involve processing of different types of MRI data, such as cardiac tagged gated MRI

Investigating the Effects of Biochemical and Biophysical Signals on Vascular Smooth Muscle Cell Differentiation

In blood vessel engineering, an optimal bioartifical scaffold can be characterized as a 3D tubular structure with high porosity for nutrient diffusion and enough mechanical strength to sustain in vivo dynamic environment. The luminal surface of the scaffold is supposed to have a continuous layer of endothelial cell that is ideally non-immunogenic and non-thrombogenic while the media layer of the construct is assigned for the ingrowth of vascular smooth muscle cell which can provide structural integrity and contractility. While reconstructing endothelial cell layer has been at the center of interest in most polymeric vascular replacements related research, growing VSMCs has had less attention due to the high risk of their excessive proliferation and unexpected phenotype shifts that can result in vessel restenosis. In addition, finding a reliable source of VSMC can be a formidable task. As such, we believe that if VSMCs can be modulated to remain quiescent and functional over time after they are obtained from an alternative source, they might eventually be considered to incorporate into artificial vascular substitute. To achieve this goal, first we investigated the potential of using stem cell to differentiate into functional VSMCs. Next, we designed a 3D culture construct to mimic blood vessel with distinct layers and analyzed the effect of combining different biochemical and biomechanical signals on modulating VSMCs behavior. Finally, we developed a biomechanical model that can incorporate the mechanical property of differentiated cell and distinct layers with geometrical information acquired from confocal images to predict cellular behavior under different conditions. The results of these studies provide insights from a basic science prospective about the potential of using stem cell to obtain functional VSMCs and the impact of environmental factors on VSMCs behavior. Researchers may use these results to optimize the culture condition of VSMCs in order to modulate its proliferation, phenotype and mechanical property. The model developed in this study might be used to predict cellular behavior under different culture environments without repetitive experiments

Applications of Brillouin Light Scattering within the Biological Environment

Brillouin light scattering (BLS) provides information on micromechanics through the scattering of light from acoustic waves or phonons. It is widely accepted that the mechanical properties within the biological environment are crucial to the health and vitality of the system, and alterations in mechanics can thereby indicate disease. To date, biological applications of BLS have ranged from the measurement of live cells and organisms, to tissues and fibrous proteins, demonstrating potential for diagnosis of pathology and characterisation of mechanics. Despite this, the information contained within the Brillouin spectrum, and its full significance to biological matter, is still a matter of debate, due to fundamental problems in understanding the role of water in biomechanics. This work aimed to explore the development and application of BLS to the biological environment, using gelatin hydrogels as a model system. Tuning the degree of physical and chemical cross-linking within the hydrogels, enabled the macromechanical properties to be controlled, mimicking a variety of biological states. Brillouin measurements of these hydrogels gave a unique insight into the viscoelastic properties across a wide range of physical states, ranging from the highly hydrated to the glassy phase, and the transition between the two. The introduction of Raman spectroscopy as a correlative technique enabled the chemical composition of the sample to be determined, in addition to the mechanical information provided by BLS. As well as this, a calibration curve derived from Raman spectra and refractometry data, enabled the refractive index of the hydrogels to be predicted, a parameter necessary to calculate the longitudinal elastic modulus from Brillouin measurements. The final focus of this work was on the development of a virtually imaged phase array (VIPA) based Brillouin spectrometer, exploring system design and experimental considerations for Brillouin measurements. This enabled comparison with measurements from a tandem Fabry-Pérot based system, as well as some consideration to the analysis methods used for the interpretation of Brillouin data. Throughout this work, gelatin hydrogels have been used as a platform to investigate the development and application of BLS to biological systems. As simple models for a host of biological systems, the viscoelastic properties revealed by Brillouin spectroscopy set the basis for BLS within the biological environment.Cancer Research U

Soft tissue viscoelastic properties: measurements, models and interpretation

The quantification of mechanical properties of soft tissues has been of great interest for more than two decades because they have the potential of being used as biomarkers for disease diagnosis. Indentation techniques, the most recognized techniques for characterizing mechanical properties, are widely used for basic science investigations in research labs. The use of elastography techniques coupled with imaging technologies has been growing rapidly in recent years, which is promising for clinical applications. Each technique produces different mechanical behaviors due to the interaction of the stimuli and the structure of the tissue. An appropriate model will parameterize these behaviors to reflect the corresponding tissue microscopic features with high fidelity. The objective of this thesis is to identify combinations of techniques and models that will yield mechanical parameters with diagnostic interpretations about tissue microenvironment. Three techniques for characterizing tissue viscoelastic properties were developed and validated, each offers strengths in a large variety of applications. Indentation based techniques measure low-frequency force-displacement curves under different loading profiles. Ultrasound-based techniques and optical based techniques measure the dispersion behaviors of the propagating wave velocities at mid-to-high frequency ranges. When a material is linear, isotropic, and contains only elastic components, the “intrinsic” elastic modulus of the material can be obtained independently of the technique used when corrections are properly made to eliminate the bias from boundary effects. If the material includes time-dependent components, models must be included in the analysis to provide parametric estimates. Classical models for viscoelastic solids such as the Kelvin-Voigt model do not fully represent mechanical measurements in tissues because they are not material continua. Tissue properties are determined in part by fluid movement in the open- and closed-cell compartments found within a viscoelastic collagen matrix that is actively maintained by the embedded cells to meet programmed needs. These biphasic (solid/fluid) media exhibit multifaceted deformation responses that are particularly difficult to model using a concise feature set. The Kelvin-Voigt fractional derivative (KVFD) model introduced in this study represents the measurement data of a broad range in both time and frequency domain with a small number of parameters, and it yields stable estimates for many types of phantoms and tissues. It is superior to the integer derivative models for the materials and techniques we used in this study. Moreover, the KVFD model provides a three-dimensional feature space of mechanical properties that properly characterizes the composition and structure of a material. This was validated through measurements on gelatin-cream emulsion samples exhibiting viscoelastic behavior, as well as ex vivo liver tissue samples. For the elastic property, KVFD parameter E_0 mainly represents the elasticity of the solid matrix and is approximately equal to the shear modulus no matter which technique is used. For the viscous property, when combined with different measurement techniques, KVFD model parameter α and τ represent different tissue components. The combination of these techniques and the KVFD model have the potential to be able to distinguish between healthy and pathological tissues described by the histological features

Using Raman Spectroscopy for Intraoperative Margin Analysis in Breast Conserving Surgery

Breast Conserving Surgery (BCS) in the treatment of breast cancer aims to provide optimal oncological results, with minimal tissue excision to optimise cosmetic outcome. Positive margins due to an inadequate resection occurs in 17% of UK patients undergoing BCS and prompts recommendation for further tissue re-excision to reduce recurrence risk. A second operation causes patient anxiety and significant healthcare costs. This issue could be resolved with accurate intra-operative margin analysis (IMA) to enable excision of all cancerous tissue at the index procedure. High wavenumber Raman Spectroscopy (HWN RS) is a vibrational spectroscopy highly sensitive to changes in protein/lipid environment and water content –biochemical differences found between tumour and normal breast tissue. We proposed that HWN RS could be used to differentiate between tumour and non-tumour breast tissue with a view to future IMA. This thesis presents the development of a Raman system to measure the HWN region capable of accurately detecting changes in protein, lipid and water content, in the presence of highly fluorescent surgical pigments such as blue dye that are present in surgically excised specimens. We investigate the relationship between changes in the HWN spectra with changes in water content in constructed breast phantoms to mimic protein and lipid rich environments and biological tissue. Human breast tissue of paired tumour and non-tumour samples were then measured and analysed. We found that breast tumour tissue is a protein rich, high water, low fat environment and that non-tumour is a low protein, fat rich environment with a low water content, and this can be used to identify breast cancer using HWN RS with excellent accuracy of over 90%. This thesis demonstrates a HWN RS Raman system capable of differentiating between tumour and non-tumour tissue in human breast tissue, and this has the potential to provide IMA in BCS

Breast and Skin Cancer Detection and Depth Profiling by Tissue Stiffness Contrasting Using Piezoelectric Fingers (PEFs)

Most imaging techniques project a 3-dimensional (3D) tumor into a 2-dimensional (2D) image that lacks the depth information. The ability to provide not only the lateral dimensions of tumors but also the depth profile is important for accurately sizing the tumor and is crucial for preliminary staging of the tumor prior to surgery, improving biopsy accuracy, and minimizing incomplete surgical removal of the tumors. Although computer tomography (CT) and magnetic resonance imaging (MRI) can provide tumor 3D images CT scans exposes patients to additional radiation risks and MRI is expensive. In addition, these techniques may not be suitable for assessing certain tumors such as skin cancers. Piezoelectric finger (PEF) is a tissue stiffness sensor developed at Shih and Shih's lab that can measure the elastic modulus of tissues both in vitro and in vivo. Because breast tumors are stiffer than surrounding tissues, it is possible to detect and image breast tumors by contrasting the higher-elastic modulus regions with the surrounding tissues. In addition, a PEF with a larger contact area can assess the stiffness of tissues at a larger depth. It is thus possible to use PEFs with different contact areas to probe for depth profiles of tumors. The goal of this study is to develop the methodology to use array PEFs not only to detect breast tumors and skin tumors but also image their locations and sizes in 3D for various applications. In Aim 1, a handheld probe containing an array of four PEFs of the same contact area (6.5 mm) is developed together with a custom-built circuit board to detect breast tumors in 40 patients. The results show that PEF detected 96% of breast tumors, including 100% of palpable and 67% non-palpable malignant tumors. Among the 28 patients with mammography records, PEF detected 92% malignant tumors while mammography only detected 80%. Furthermore, PEF detection was not affected by mammography density, indicating that PEF is promising for detecting breast tumors in young women and women with dense breasts for whom mammography is ineffective. In Aim 2, tumor depth profiles was determined using the stiffness measurements by a set of PEFs with contact sizes 4.1 - 9.8 mm on model breast tumors of clays embedded in gelatin coupled with a spring model. The locations of the top of bottom-supported model breast tumors were determined within 1.1 mm of the actual values. For suspended model breast tumors both the top and the bottom margins were determined within 2.1 mm of the actual values, indicating that it is a promising methodology for tumor depth profiling. In addition to the depth accuracy, the current spring model-based methodology has the advantage of being instant as compared to the inversion simulations (IS) using finite element analysis (FEA) which gives similar accuracy but is tedious and time-consuming. In Aim 3, a mechanical model of skin was established as a two-layer structure with the stiffer layer representing the epidermis and dermis (skin) on top of the softer subcutaneous layer. The elastic modulus and thickness of skin were then simultaneously determined using the stiffness measurements obtained with PEFs of different contact sizes of <3 mm coupled with an empirical formula for a two-layer structure derived from Green's function calculations. Both the elastic modulus and the thickness of the skin layer were resolved within <10% of the actual values in skin phantoms, and porcine skins and validated by FEA. In Aim 4, the lateral extent and the depth profile of model skin cancers of clay embedded in porcine skins were determined using the stiffness measurements with PEFs of various contact sizes of <3 mm coupled with a modified spring model taking into account of the two-layer nature of skin. The lateral sizes of model skin cancers determined by PEF were within an error of 1 mm and the estimated depth profiles showed good agreement with the actual thickness with <0.4 mm discrepancy. In conclusion, PEF is capable of detecting breast cancer with sensitivity better than mammography and independent of mammography density. In addition, using a set of PEFs of different contact areas coupled with simple spring-model calculations the depth profiles of both breast cancer and skin cancer can be accurately determined to facilitate 3D breast cancer/skin cancer imaging.Ph.D., Biomedical Engineering -- Drexel University, 201

Biofunctional hydrogels based on elastin-like recombinamers as extracellular matrix analogues

Uno de los objetivos principales de esta tesis consiste en la formación de hidrogeles mediante un proceso citocompatible que permita encapsular células dentro de dichos geles en el momento de su formación y que simulen las propiedades de las matrices extracelulares naturales para su utilización en ingeniería de tejidos. Dichos hidrogeles se obtendrán utilizando Polímeros Recombinantes tipo Elastina (ELRs) por presentar unas excelentes propiedades de partida como son su elevada biocompatibilidad o la posibilidad de incorporar diferentes bioactividades entre otras. Tambien Se quiere desarrollar un sistema fractal de formación de nanogeles mediante tecnología click sin cobre, y comprobar la influencia de la temperatura en dicha fractalidad durante el proceso de formación de estos geles. Se pretende evaluar y caracterizar, mediante el estudio de las dimensiones así como de las propiedades microreológicas y eléctricas, las estructuras formadas para tener un mejor conocimiento de su validez como sistemas de dosificación de fármacos. Por otro lado, se investigará la capacidad de estos hidrogeles para ser utilizados como recubrimiento de distintos materiales como poliestireno, vidrio y titanio mediante la tecnología “capa a capa” (layer by layer); siendo el titanio de especial interés debido a su creciente utilización como implante en procesos quirúrgicos. Se pretende obtener un sistema de formación de capas rápido, reproducible y escalable. Además dicho recubrimiento debe ser totalmente citocompatible y que nos permita incluir diferentes agentes terapéuticos que puedan ser de interés en futuras aplicaciones tanto en ingeniería de tejidos como en dosificación de fármacos. Por último, otro objetivo fundamental de la tesis consistió en demostrar la eficacia de los hidrogeles formados por ELRs y obtenidos mediante tecnología click sin cobre, como “scaffolds” en ingeniería de tejidos y más concretamente en el tratamiento de enfermedades cardiovasculares. Las características, tanto mecánicas como biológicas, de estos hidrogeles podrían convertirlos en biomateriales especialmente útiles en el tratamiento de ciertas afecciones del sistema circulatorio.Departamento de Química AnalíticaDoctorado en Arquitectur