Biomedical Engineering and Bioengineering Commons^™

Deep Learning And Generative Ai Approaches For Automated Diagnosis And Personalized Treatment: Bridging Machine Learning, Medicine, And Biomechanics In Predicting Tissue Mechanics And Biomaterial Properties., Yasin Shokrollahi

Theses and Dissertations

Machine learning, particularly deep neural networks, has demonstrated significant potential in predicting high-dimensional tasks across various domains. This work encompasses a detailed review of Generative AI in healthcare and three studies integrating machine learning with finite element analysis for predicting biomechanical behaviors and properties. Initially, we provide a comprehensive overview of Generative AI applications in healthcare, focusing on Transformers and Denoising Diffusion models and suggesting potential research avenues to address existing challenges.

Subsequently, we addressed soccer-related ocular injuries by combining finite element analysis and machine learning to predict retinal mechanics following a soccer ball hit rapidly. The prediction errors are …

Efficient Scopeformer: Towards Scalable And Rich Feature Extraction For Intracranial Hemorrhage Detection Using Hybrid Convolution And Vision Transformer Networks, Yassine Barhoumi

Theses and Dissertations

The field of medical imaging has seen significant advancements through the use of artificial intelligence (AI) techniques. The success of deep learning models in this area has led to the need for further research. This study aims to explore the use of various deep learning algorithms and emerging modeling techniques to improve training paradigms in medical imaging. Convolutional neural networks (CNNs) are the go-to architecture for computer vision problems, but they have limitations in mapping long-term dependencies within images. To address these limitations, the study explores the use of techniques such as global average pooling and self-attention mechanisms. Additionally, the …

Image-Based Cancer Diagnosis Using Novel Deep Neural Networks, Hosein Barzekar

Theses and Dissertations

Cancer is the major cause of death in many nations. This serious illness can only be effectivelytreated if it is diagnosed early. In contrast, biomedical imaging presents challenges to both clinical institutions and researchers. Physiological anomalies are often characterized by modest modifications in individual cells or tissues, making them difficult to detect visually. Physiological anomalies are often characterized by slight abnormalities in individual cells or tissues, making them difficult to detect visually. Traditionally, anomalies are diagnosed by radiologists and pathologists with extensive training. This procedure, however, demands the participation of professionals and incurs a substantial expense, making the classification of …

Medical Image Segmentation Using Machine Learning, Masoud Khani

Theses and Dissertations

Image segmentation is the most crucial step in image processing and analysis. It can divide an image into meaningfully descriptive components or pathological structures. The result of the image division helps analyze images and classify objects. Therefore, getting the most accurate segmented image is essential, especially in medical images. Segmentation methods can be divided into three categories: manual, semiautomatic, and automatic. Manual is the most general and straightforward approach. Manual segmentation is not only time-consuming but also is imprecise. However, automatic image segmentation techniques, such as thresholding and edge detection, are not accurate in the presence of artifacts like noise …

Imaging Potential In Saturation Recovery Methods For Sarcoidosis Patients With Medical Devices, Samantha Zhao

Theses and Dissertations

Cardiovascular magnetic resonance (CMR) imaging is a preferred imaging methodology due to its lack of ionizing radiation and ability to detect myocardial inflammation and fibrosis using quantitative T1 mapping techniques. Cardiac sarcoidosis (CS) is characterized as the formation of granulomas in the myocardium. Current methods for detection include measuring non-cardiac specific C-reactive protein (CRP) levels, or PET imaging, which uses ionizing radiation, therefore CMR would make an ideal imaging option. However, many CS patients have implanted cardiac devices which can cause degradation in image. The modified Look-Locker inversion recovery (MOLLI) method is widely used in quantitative T1 mapping with high …

Patients’ Needs And Preferences Regarding Radiology Test Results On Patient Portals, Mansour Abdulaziz Almanaa

Theses and Dissertations

Introduction and significance: Radiology exams are an important part of health care. To enhance the quality of health care, health care services need to be delivered in ways that meet patients’ needs and preferences. Patients were found to be interested in the timely receipt of radiology test results. One of the easiest and fastest ways to deliver radiology test results to patients is via online patient portals. It seems, however, that the method of providing radiology test results through patient portals has not reached its full maturity; it still needs a great deal of improvement. Therefore, participation of the end-readers …

Higher Tensile Forces Across Cellular Junctions And An Intact Nuclear Linc Complex Is Required For Epithelial Function And Stability, Fnu Vani Narayanan

Theses and Dissertations

Recent advances in three-dimensional (3D) cell culture systems have provided key insights into the understanding of biochemical and physiological states of native tissue. A significant progress in the field of mechanobiology involves measuring cellular traction forces in a more native 3D environment. However, the effects of mechanical forces exerted across cellular junctions and the nuclear LINC complex, in an organized 3D system has not been investigated thus far. Epithelial cells spontaneously form acini (also known as cysts or spheroids) with a single, fluid-filled central lumen, when grown in 3D matrices. The size of the lumen is dependent on apical secretion …

Development And Validation Of A Novel Resonant Energy Transfer (Fret) Biosensor To Measure Tensile Forces At The Linc Complex In Live Cells, Paul Arsenovic

Theses and Dissertations

There is a large body of evidence supporting the theory that cell physiology largely depends on the mechanical properties of its surroundings or micro-environment. More recently studies have shown that changes to intra-cellular mechanical properties can also have a meaningful impact on cell function and in some cases lead to the progression of ailments or disease. For example, small changes to the protein sequence of a structural nuclear envelope protein called lamin-A is known to cause a variety of neurological and musculoskeletal diseases referred to as laminopathies. Currently, there is little incite into how these mutations lead to disease progression …

Sensitivity Analysis Of Geometry Changes In The Simulation Of Basilar Aneurysms, Paul Eserkaln

Theses and Dissertations

Computer simulation is a useful tool in the research and treatment of basilar aneurysms. Current technology allows researchers to create 3D models from cerebral vasculature in-vivo, allowing for the investigation of surgical options with minimal risk to the patient. The method used to construct these models overlooks smaller lateral arterial branches which are difficult to discern due to resolution limits of the imaging process. These lateral branches have minimal impact on the overall blood flow through the basilar artery, but they play a significant role in the health of the patient, so it is important to ensure sufficient blood will …

Quantitative Optical Studies Of Oxidative Stress In Rodent Models Of Eye And Lung Injuries, Zahra Ghanian

Theses and Dissertations

Optical imaging techniques have emerged as essential tools for reliable assessment of organ structure, biochemistry, and metabolic function. The recognition of metabolic markers for disease diagnosis has rekindled significant interest in the development of optical methods to measure the metabolism of the organ.

The objective of my research was to employ optical imaging tools and to implement signal and image processing techniques capable of quantifying cellular metabolism for the diagnosis of diseases in human organs such as eyes and lungs. To accomplish this goal, three different tools, cryoimager, fluorescent microscope, and optical coherence tomography system were utilized to study the …

The Effectiveness, Efficiency, And Appeal Of Pediatric Echocardiography Protocol Training For First Year Pediatric Cardiology Fellows, Lynne M. Brown

Theses and Dissertations

Echocardiography training for pediatric cardiology fellows is complex and academic hospitals strive to provide high-quality training using limited resources. The purpose of this embedded single case study design was to evaluate the effectiveness, efficiency, and appeal of a newly developed 10-day echocardiography protocol learning module for first year pediatric cardiology fellows. Using blended learning methods that included didactic lectures, online learning activities, and interactive games, the learning module was the first step in the process of training pediatric cardiology fellows to perform echocardiograms independently with limited supervision during their first year of fellowship. At the end of the 10-day module, …

Spectral And Temporal Interrogation Of Cerebral Hemodynamics Via High Speed Laser Speckle Contrast Imaging, Rex Chin-Hao Chen

Theses and Dissertations

Laser Speckle Contrast Imaging (LSCI) is a non-scanning wide field-of-view optical imaging technique specifically developed for cerebral blood flow (CBF) monitoring. In this project, a versatile Laser speckle contrast imaging system has been designed and developed to monitor CBF changes and examine the physical properties of cerebral vasculature during functional brain activation experiments.

The hardware of the system consists of a high speed CMOS camera, a coherent light source, a trinocular microscope, and a PC that does camera controlling and data storage. The simplicity of the system’s hardware makes it suitable for biological experiments.

In controlled flow experiments using a …

Femtosecond Laser Beam Propagation Through Corneal Tissue: Evaluation Of Therapeutic Laser-Stimulated Second And Third-Harmonic Generation, William R. Calhoun Iii

Theses and Dissertations

One of the most recent advancements in laser technology is the development of ultrashort pulsed femtosecond lasers (FSLs). FSLs are improving many fields due to their unique extreme precision, low energy and ablation characteristics. In the area of laser medicine, ophthalmic surgeries have seen very promising developments. Some of the most commonly performed surgical operations in the world, including laser-assisted in-situ keratomileusis (LASIK), lens replacement (cataract surgery), and keratoplasty (cornea transplant), now employ FSLs for their unique abilities that lead to improved clinical outcome and patient satisfaction.

The application of FSLs in medical therapeutics is a recent development, and although …

Quantitative Object Reconstruction Using Abel Transform Tomography And Mixed Variable Optimization, Kevin R. O'Reilly

Theses and Dissertations

Researchers at the Los Alamos National Laboratory (LANL) are interested in quantitatively reconstructing an object using Abel transform x-ray tomography. Specifically, they obtain a radiograph by x-raying an object and attempt to quantitatively determine the number and types of materials and the thicknesses of each material layer. Their current methodologies either fail to provide a quantitative description of the object or are generally too slow to be useful in practice. As an alternative, the problem is modeled here as a mixed variable programming (MVP) problem, in which some variables are nonnumeric and for which no derivative information is available. The …

Using Kriging To Interpolate Spatially Distributed Volumetric Medical Data, Stephen M. Matechik

Theses and Dissertations

Routine cases in diagnostic radiology require the interpolation of volumetric medical imaging data sets. Inaccurate renditions of interpolated volumes can lead to the misdiagnosis of a patient's condition. It is therefore essential that interpolated modality space estimates accurately portray patient space. Kriging is investigated in this research to interpolate medical imaging volumes. Kriging requires data to be spatially distributed. Therefore, magnetic resonance imaging (MRI) data is shown to exhibit spatially regionalized characteristics such that it can be modeled using regionalized variables and subsequently be interpolated using kriging. A comprehensive, automated, three-dimensional structural analysis of the MRI data is accomplished to …

Pulse Coupled Neural Networks For The Segmentation Of Magnetic Resonance Brain Images, Shane L. Abrahamson

Theses and Dissertations

This research develops an automated method for segmenting Magnetic Resonance (MR) brain images based on Pulse Coupled Neural Networks (PCNN). MR brain image segmentation has proven difficult, primarily due to scanning artifacts such as interscan and intrascan intensity inhomogeneities. The method developed and presented here uses a PCNN to both filter and segment MR brain images. The technique begins by preprocessing images with a PCNN filter to reduce scanning artifacts. Images are then contrast enhanced via histogram equalization. Finally, a PCNN is used to segment the images to arrive at the final result. Modifications to the original PCNN model are …

Evaluation Of Segmentation For Bone Structures In 3d Rendering Of Ultrasound Residual Limb Images, Min C. Baker

Theses and Dissertations

Prosthetists today widely practice manual socket fitting, which produces subjective, inconsistent results. To address this problem, the Computerized Anthropometry Research and Design (CARD) Laboratory is developing a computer-aided socket design system that acquires ultrasound datasets of an amputee's residual limb, creates a 3D model, and helps identify load- bearing and pressure-relief areas. This research project focuses on providing 3D visualization of a residual limb to support the CARD Laboratory's efforts. Creating the 3D model of the skin and two bone contours requires two major steps: segmentation to identify the objects of interest and a surface tracking algorithm to generate the …

Clustered Microcalcification Detection Using Optimized Difference Of Gaussians, Edward M. Ochoa

Theses and Dissertations

The objective of this thesis is to design an automated microcalcification detection system to be used as an aid in radiologic mammogram interpretation. This research proposes the following methodology for clustered microcalcification detection. First, preprocess the digitized film mammogram to reduce digitization noise. Second, spatially filter the image with a difference of Gaussians (DoG) kernel. To detect potential microcalcifications, segment the filtered image using global and local thresholding. Next, cluster and index these detections into regions of interest (ROIs). Identify ROIs on the digitized image (or hardcopy printout) for final radiologic diagnosis.

Computer-Aided Diagnosis Of Mammographic Masses, William E. Polakowski

Theses and Dissertations

A new Model-Based Vision algorithm was developed to find possibly cancerous regions of interest (ROIs) in digitized mammograms and to correctly identify the malignant masses. This work has shown a sensitivity of 92 percent for locating malignant ROIs. The database contained 272 images (12 bit, 1OO microns) with 36 malignant and 53 benign mass images. Of the 53 biopsied benign cases, 74 percent were correctly classified. The Focus of Attention (segmentation) Module algorithm used a physiologically motivated Difference of Gaussians (DoG) filter to highlight mass-like regions in the mammogram. The Index Module labeled the regions by their hypothesized class: large …

Detection Of Clustered Microcalcifications Using Wavelets, Donald A. Mccandless

Theses and Dissertations

An automated method for detecting microcalcification clusters is presented. The algorithm begins with a digitized mammogram and outputs the center coordinates of regions of interest (ROIs) that contain microcalcification clusters. The method presented uses a 12-tap Least Asymmetric Daubechies (LAD12) wavelet in a tree structured filter bank to increase the signal to noise level of microcalcifications. The signal to noise level gain achieved by the filtering allows subsequent thresholding to eliminate on average 90% of the image from further consideration without eliminating actual microcalcifications 95% of the time. A novel approach to isolating individual calcifications from background tissue through non-stationary …

Computer Aided Detection Of Microcalcifications Utilizing Texture Analysis, Ronald C. Dauk

Theses and Dissertations

A comparative study of texture measures for the classification of breast tissue is presented. The texture features investigated include Angular Second Moments, Power Spectrum Analysis and a novel feature, Laws Energy Ratios. The texture study was accomplished as part of the development of a Model Based Vision (MBV) system for the automatic detection of microcalcifications. An overview of the Microcalcification Detection System is presented, which applies image differencing techniques, feature selection methods, and neural networks for locating microcalcification clusters in mammograms. The Power Spectrum Analysis feature set had the best overall performance with an 83% Probability of Detection and an …

Three Dimensional Localization Of Lesions From Digitized Mammograms, Amy L. Magnus

Theses and Dissertations

This thesis describes new algorithms to localize regions-of-interests (ROIs) three dimensionally from a pair of digitized mammograms. This work is intended to add a layer of sophistication to computer aided diagnosis by putting to use the fixed and measurable parameters of mammographic imaging. The fixed parameters are the source to film orientation and the podium-image distance. Measurable parameters are the rotation angle of the x-ray tube from the horizontal and the compression depth (the distance from compression paddle to contact podium distance) at the time of imaging. As an additional benefit, three dimensional localization algorithms alleviate the confusion radiologists may …