Bioimaging and Biomedical Optics Commons^™

On The Scalability Of Anisotropic Mesh Adaptation On Distributed And Shared Memory Architectures For Numerical Approximations, Kevin Mark Garner Jr.

Computer Science Theses & Dissertations

Mesh generation is a critical component in numerical approximations of Partial Differential Equations (PDEs). One such example includes Computational Fluid Dynamics (CFD), as CFD simulations in turn are crucial for applications in many industries, such as personalized healthcare and the design of aerospace vehicles. Generating high quality meshes for large-scale CFD problems presents a significant bottleneck in the CFD workflow. This dissertation proposes “fast,” parallel 3D mesh generation methodologies that are designed to leverage the concurrency offered by emerging High-Performance Computing (HPC) architectures. First, a distributed memory method is presented that integrates a sequential state-of-the-art isotropic, advancing front local reconnection-based …

Reproducibility In Modeling Of Knee Joint Mechanics, Maryam Nazem

Electronic Theses and Dissertations

Computational modeling of knee joint biomechanics can provide valuable insights into joint function, injury mechanisms, and patient outcomes, and can support surgical planning and informed clinical decision-making. However, achieving consistent and repeatable results, or reproducibility, is a significant challenge that affects the credibility of these models. This thesis addresses reproducibility through two studies related to the KneeHub Project, which is a multi-institutional collaboration designed to investigate reproducibility in finite-element modeling of the knee.

The first study involved model benchmarking, where predicted results of the calibrated models were compared with the experimental data to evaluate model reproducibility. While all models replicated …

A Convolutional Neural Network Approach To Breast Cancer Tumor Boundary Detection, James Leah Matlosz

Master's Theses

Breast cancer is the second most common form of cancer and often goes undetected in its initial stages due to its subtle symptoms. As the tumors grow, they become more difficult to surgically remove with clean borders. To minimize the chance of recurrence, a 2D convolutional neural network is developed in this work for delineating tumor boundaries. Specifically, the U-shaped network model is trained, validated, and tested with longitudinal MRI scans of patients diagnosed with breast cancer and undergoing neoadjuvant therapy. For training, image masks were generated as ground truths using signal enhancement ratio segmentation, thresholding, and contour detection. The …

Single-Molecule Orientation And Localization Microscopy, Sophie Brasselet, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Single-molecule localization microscopy (SMLM) offers enhanced spatial resolution in optical microscopy, providing detailed insights into the spatial organization of proteins in cells at the nanoscale. Over the past decade, SMLM has progressively incorporated the capability to retrieve the orientations of single molecules using their polarized dipolar emission pattern. Here we explore recent advancements in single-molecule orientation and localization microscopy (SMOLM), which yields super-resolved images of molecular three-dimensional (3D) orientations, wobble and 3D positions. This advancement opens possibilities to explore the nanoscale organization and conformation of biological molecules as well as to monitor and design local 3D optical fields in nanophotonics. …

Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel

Graduate Masters Theses

Background: Photodynamic Therapy (PDT) utilizes specific wavelengths of light to activate photosensitizing chemical compounds, known as photosensitizers, which induce the generation of cytotoxic reactive oxygen species (ROS) for the targeted destruction of cancer cells. Among various photosensitizers for PDT, Protoporphyrin IX (PpIX) is widely employed in oncology and dermatology due to its natural in situ generation via the metabolic conversion of 5- aminolevulinic acid (ALA), a non-phototoxic prodrug. Systemic administration of ALA after 3-6 hr drug delay leads to peak PpIX accumulation in tissues, facilitating therapeutic and diagnostic applications. However, PpIX can persist in the skin for 24–48 hours post-treatment, …

Design And Development Of A Standalone Digital Holographic Microscope Employing Phase-Driven Reconstruction And Classification For Biomedical Imaging And Optical Diagnostics, Charlotte Kyeremah

Graduate Doctoral Dissertations

Access to advanced biomedical imaging technologies remains a significant challenge in resource-limited settings, especially for early disease detection and monitoring of diseases such as malaria, HIV, and other blood-borne diseases. Although point-of-care (POC) devices have gained popularity in global health, many rely on antibody-based tests, lateral flow strips, or optical readouts that often lack quantitative capabilities, sensitivity to early infections, or versatility in different diagnostic targets. In addition, these systems are typically dependent on disposable reagents or manual interpretation, which limits their effectiveness in remote areas. Digital Holographic Microscopy (DHM) presents a promising alternative as a label-free imaging method capable …

Volumetric Imaging Of Cellular Dynamics Using Light-Sheet Microscopy: From Subcellular Structures To Whole Organisms, Md Nasful Huda Prince

Optical Science and Engineering ETDs

Advancing biomedical imaging requires platforms that combine high-resolution, speed, and stability across biological scales. This dissertation presents three innovations designed to address limitations of conventional light-sheet and oblique plane imaging. First, we introduce Reflected Inline Detection in Epi-Oblique Plane Microscopy (RIDE-OPM), a compact and drift-resistant system that eliminates a tertiary detection path while maintaining alignment flexibility, enabling robust long-term live imaging. Second, we present a high-speed Axially Swept Light-Sheet Microscopy (ASLM) platform for cleared tissues, using dual foci and synchronized sweeping to achieve isotropic sub-micron resolution at up to 40 frames-per-second, a fourfold improvement over standard ASLM. Integrated with a …

Sex-Dependent Differences In Cardiac Function And Strain In Doxorubicin-Induced Cardiomyopathy, Anna J. A. Webb, Bea O. Cabot, Aasish Chowdary, Wilhelm S. Smith, Benjamin Zeidler, Cortland H. Johns, Craig J. Goergen

Discovery Undergraduate Interdisciplinary Research Internship

Doxorubicin is a chemotherapeutic agent used to treat many types of cancer. While effective, doxorubicin can cause cardiomyopathy, a disease affecting the heart muscle. Although the effects of doxorubicin on the heart are well studied, the mechanisms leading to cardiomyopathy are not well understood. Previous studies have used murine models to study the cardiotoxicity of doxorubicin. These reports showed that cardiac dysfunction is more pronounced in male compared to female mice. The goal of this study is to further evaluate sex differences in doxorubicin induced cardiomyopathy using 4-dimensional strain mapping techniques. In this study, both female and male C57Bl/6J mice …

Ac Electric Fields Manipulate And Concentrate Dna Molecules On Electrodes, Akila Wijesinghe, Dharmakeerthi Nawarathna

Graduate Student Government Association Research Conference

Point-of-care (POC) electric field-based biosensors have emerged as a promising tool to detect early cancer biomarkers such as circulating tumor DNA (ctDNA), microRNA (miRNA), and proteins. To be effective in screening in clinical settings, these biosensors must be simple and easy to use. In this study, we have studied the manipulation of short DNA molecules suspended in a sessile drop to achieve this goal. Alternative current (AC) electric fields were used to polarize DNA molecules and produce dielectrophoretic (DEP) force on DNA molecules. DEP force is used to manipulate polarized DNA molecules towards the higher electric field gradients (toward the …

Advancing Novel Contrast Agents For Applications In Fluorescence-Guided Neurosurgery Using Fluorescence Cryotomography, Augustino Vittorio Scorzo

Dartmouth College Ph.D Dissertations

Fluorescence guided surgery (FGS) is an emerging surgical technique that aims to help surgeons identify tissue types to assist in surgical decision making - ideally providing “cut-by-color” guidance. A primary application for this approach is the identification of tumor tissue to achieve more accurate and complete tumor removal while simultaneously minimizing damage to surrounding normal tissue. The cornerstone of tumor visualization for FGS is the administration of fluorescent contrast agents, or in some cases metabolic precursors, designed to accumulate specifically in tumor tissue, and a wide range of agents that use different targeting mechanisms are currently under investigation. Although these …

Computational Fluid Dynamics And Fluid Structure Interaction Modeling In Healthy Vertebral Arteries: A Comparative Study, Bryce Clinkenbeard

Electronic Theses and Dissertations

Cerebral perfusion is critical for maintaining proper brain function, with each cerebrovascular artery playing an integral role in the overall cerebrovascular system. When these arteries become damaged or develop plaque, cardiovascular disease (CVDs) such as atherosclerosis can arise, leading to conditions like arterial stenosis. While CVDs are most prevalent in older individuals, they are also observed in young adults, particularly those engaged in high-endurance occupations such as military service. Diagnosis and prediction of CVDs often rely on imaging modalities supported by computational fluid dynamics (CFD) which account for low resolution in fluid flow. CFD models assume rigid arterial walls, which …

Acoustic And Hemodynamic Analysis Of Phantoms: Roughness And Flow Dynamics, Ethan Erik Olof Sundberg

Master's Theses

The purpose of this study was to determine whether different vascular phantoms, with and without a surrogate arm, could serve as effective analogs to the human brachial artery for assessing endothelial dysfunction, an early indicator of cardiovascular disease, particularly atherosclerosis. Atherosclerosis is characterized by plaque buildup and endothelial damage, which precede more severe clinical events and are often detectable through changes in vascular function. A 40” water tower was used to simulate diastolic pressure, enabling water flow through each phantom. Strain gauge pressure transducers were placed at both ends of the phantoms to measure pressure drop, while a microphone captured …

Intraoperative Dynamic Contrast-Enhanced Fluorescence Imaging For Navigating Open Orthopedic Surgeries, Yue Tang

Dartmouth College Ph.D Dissertations

Infection following trauma is one of the most prevalent and challenging complications faced by orthopedic surgeons. Inadequate tissue perfusion plays a critical role in this complication, as poorly perfused bone can be a nidus for bacterial biofilm formation and promote resistance to antibiotic treatments. Consequently, the management of open fractures and fracture-related infections relies on aggressive and thorough debridement to remove all poorly perfused bone. This thesis focuses on developing an indocyanine green (ICG)-based dynamic contrast-enhanced fluorescence imaging (DCE-FI) to objectively measure bone perfusion during open orthopedic surgeries and guide surgical debridement of devitalized bone.

Novel methodologies were developed to …

Development Of A Light-Based Platform To Assess Cervical Mucus Barrier Function And Physical Mucus Properties, Elizabeth J. Buzbee

McKelvey School of Engineering Graduate Student Theses & Dissertations

Preterm birth is the leading cause of neonatal morbidity and mortality worldwide, yet current clinical tools for predicting its risk lack specificity and reliability. Cervical mucus plays a crucial role in maintaining pregnancy by forming a barrier that protects the uterus against infection. This study investigates the use of laser speckle rheology as a noninvasive technique to assess cervical mucus biomechanics. Synthetic cervical mucus was fabricated at varying hydration levels and tested using a conventional rheometer that confirmed that the mechanical properties of the synthetic mucus samples were representative of physiological cervical mucus. These results were compared to the complex …

Multi-Modal Mri For The Pre-Clinical Evaluation Of Hiv-Linked Changes In The Central Nervous System, Gabriel Gauthier

Theses & Dissertations

Though the inception of anti-retroviral therapy (ART) has fundamentally changed the life expectancy of human immunodeficiency virus (HIV) patients, accessibility and outcomes vary enormously along demographic lines. Even for people living with HIV (PLWH) with perfect access and adherence to anti-retroviral drugs (ARVs), modern treatment plans are fundamentally unable to secure complete viral remission for patients. The cause of this perpetual infection is the persistence of viral reservoirs in the central nervous system (CNS), hidden beyond the reach of modern ARVs, leaving patients to deal with lifelong medication side-effects and risks of developing HIV-associated neurodegenerative disorders (HAND). Despite improving outcomes …

Alterations And Improvements Of The Photoacoustic Flow Cytometry Method, Nicholas J. Taylor

Electronic Theses and Dissertations

The emergence and proliferation of antibiotic-resistant bacteria present a significant and growing challenge to global public health, with the potential to render many existing antibiotics ineffective. Infections caused by these resistant pathogens are difficult to treat, resulting in higher morbidity, mortality, and healthcare costs. A major obstacle in combating these infections is the slow pace of traditional diagnostic methods, such as blood cultures, which typically take 2-3 days to identify the causative bacteria and determine their antibiotic resistance profiles. This delay in diagnosis hinders timely interventions and appropriate treatment, further contributing to the spread of resistant infections. As such, there …

Automated Beam Stitching And Segmentation Procedure For Space Division Multiplexing Optical Coherence Tomography Angiography, Andrew J. Song

McKelvey School of Engineering Graduate Student Theses & Dissertations

Optical Coherence Tomography Angiography (OCTA) has revolutionized ophthalmic imaging and its capability to produce high-resolution 3D maps of the retinal microvasculature is instrumental in diagnosing retinovascular diseases such as diabetic retinopathy and age-related macular degeneration; However, the existing OCTA devices often suffer from slow acquisition speed limiting the field-of-view (FOV) in the clinic. Space Division Multiplexing OCTA (SDM-OCTA) address these limitations by acquiring multiple beams simultaneously, achieving manyfold faster acquisition speeds than single beam OCTA systems. But as each beam contains only part of the image, SDM-OCTA requires additional processing steps to produce coherent wide-field images. Though manual stitching and …

Towards The Performance Characterization Of A Robotic Multimodal Diagnostic Imaging System, George Papaioannou, Christos Mitrogiannis, Mark Schweitzer, Nikolaos Michailidis, Maria Pappa, Pegah Khosravi, Apostolos Karantanas, Sean Starling, Christian Ruberg

Publications and Research

Characterizing imaging performance requires a multidisciplinary approach that evaluates various interconnected parameters, including dosage optimization and dynamic accuracy. Radiation dose and dynamic accuracy are challenged by patient motion that results in poor image quality. These challenges are more prevalent in the brain/cardiac pediatric patient imaging, as they relate to excess radiation dose that may be associated with various complications. Scanning vulnerable pediatric patients ought to eliminate anesthesia due to critical risks associated in some cases with intracranial hemorrhages, brain strokes, and congenital heart disease. Some pediatric imaging, however, requires prolonged scanning under anesthesia. It can often be a laborious, suboptimal …

Development Of Translational Microscale Systems To Interrogate How Biophysical And Biochemical Cues Alter The Phenotype Of Hormone Positive Breast Cancer, Braulio Ortega Quesada

All Dissertations

Cancer is a complicated disease and one in every three diagnoses are women with breast cancer. Recent research shows that the progression of cancer depends strongly on interactions with other non-cancerous cells and non-cellular components. Metastasis, the spread of cancer to other parts of the body, is a key step in cancer progression and makes treatment harder, leading to poor response to treatments culminating in death in ~90% of patients. This dissertation focused on creating a series of microdevices as novel pre-clinical models of breast cancer. Two different devices were fabricated to (1) study how exposing cancer cells to the …

Impact Of Shear Flow On Marine Biofilms Using Hyperspectral Imaging, Shantanu Mahesh Kore

All Theses

Various microbial communities in marine biofilms cause biofouling on submerged surfaces, posing challenges to marine industries. Despite their ecological and economic importance, biofilms' biomechanical and biochemical responses to hydrodynamic shear stress are insufficiently understood, particularly in dynamic flow conditions. To fill this gap, our study uses an innovative fiber-optic hyperspectral imaging (HSI) system and a supercontinuum laser source to examine marine biofilms' structure, composition, and detachment behavior at different shear stress levels.

To detect spectral and spatial heterogeneity in live biofilms without labeling, we created a custom imaging pipeline that captures reflectance spectra in the 600-850 nm range, targeting microbial …

Deep Learning In Lung Cancer Pre- And Post-Radiation Therapy: Diagnosis Of Malignancy And Radiation-Induced Lung Injury From 3d X-Ray Ct., Benjamin Peter Veasey

Electronic Theses and Dissertations

Lung cancer remains the leading cause of cancer-related mortality worldwide, with early detection and accurate diagnosis being critical for improving patient outcomes. Additionally, the progression of Radiation-Induced Lung Injury (RILI) following Stereotactic Body Radiation Therapy (SBRT) for lung cancer presents a significant diagnostic challenge. This dissertation addresses these challenges by developing deep learning-based diagnostic tools for both pre-treatment lung nodule malignancy classification and post-treatment RILI identification using 3D X-ray CT imaging. The research is divided into two primary objectives. First, for lung nodule malignancy classification, we developed a biopsy-confirmed dataset, called NLSTx, to train and evaluate deep learning models while …

Painting Rich Six-Dimensional Pictures Using Polarized Fluorescence Microscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

No abstract provided.

Multimodal Ai-Driven Biomarker For Early Detection Of Cancer Cachexia, Sabeen Ahmed

USF Tampa Graduate Theses and Dissertations

Cancer cachexia is a metabolic syndrome characterized by substantial skeletal muscle loss, impacting cancer patients' survival and quality of life. Despite its clinical significance, early detection remains a challenge due to the lack of standardized diagnostic criteria and the reliance on indirect markers. This work presents an AI-driven approach to enhance cachexia detection and monitoring by integrating multiple deep learning methodologies. We explore transformer architectures for time-series analysis to model sequential medical data, enabling disease prediction and progression modeling. To ensure robust and reliable decision-making in clinical settings, we explore Bayesian deep neural networks for uncertainty estimation. Additionally, we introduce …

Investigating Spatial Mapping Of Lipid And Protein Alterations Within Cells And Tissues Using Raman Microspectroscopy, Elnaz Sheikh

LSU Doctoral Dissertations

The progression of various diseases is associated with alterations in the microenvironment of cells, consisting of a variety of metabolites like lipids and proteins. It is well known that lipids and proteins are potential biomarkers for indicating alterations within the cell microenvironment induced by disease, and various methods are frequently used for their examination. To understand the chemical composition and spatial distribution of constituents in tissues and cells, confocal Raman spectroscopy and microscopy, as non-destructive tools, have shown potential for monitoring abnormalities at the cellular level with high resolution and can facilitate detection through targeting multiple biomarkers. The application of …

Unified Adaptive Cross-Attention Multimodal Network, Mahesh Sunuwar

Shelby Hall Graduate Research Forum Posters

Accurately diagnosing appendicitis remains a significant challenge in emergency medicine due to its varied clinical presentation and overlap with other abdominal conditions. Existing diagnostic models often rely on unimodal data, such as computed tomography (CT) images or clinical notes, limiting their ability to capture the full complexity of patient information. This study proposes a novel multimodal framework, a Unified Adaptive Cross-Attention Multimodal Framework (u-ACM), that integrates CT images and clinical notes using hybrid fusion strategies to improve diagnostic accuracy for appendicitis. The u-ACM leverages adaptive contextual filtering to dynamically remove irrelevant features, crossattention mechanisms to align features between modalities, and …

Optimal Tissue Clearing Of Gastric Cancerous Organoids Imaged Via High Resolution Light Sheet Microscopy, Lauren D. Lieu

2025 Fall Honors Capstones Projects - Archive

While the rate of surviving a myocardial infarction has increased in the past 60 years from 60% to 90%, the rate of Americans developing chronic heart disease such as heart failure, arrhythmias, and hypertensive heart disease has risen. This has led to the development of imaging technology such as Light Sheet Microscopy (LSM) and Light Field Microscopy (LFM) to study heart contractility and congenital heart disease via models such as cancerous organoids or Zebrafish. However, LSM and LFM results are highly dependent on the quality of the staining and cleared samples. This study looks to add to the growing field …

Emotion Processing In Adolescents With Epilepsy And Healthy Controls Using Multi-Modal Neuroimaging, Frances Kathryn E. King

Bioengineering Dissertations - Archive

Epilepsy is increasingly recognized as a disorder not only of seizures but also of widespread network dysfunction, impacting cognitive and emotional processing. One critical cognitive process affected in epilepsy is emotional conflict processing, which relies on the interplay of multiple brain networks. However, the spatiotemporal dynamics of emotional conflict processing in epilepsy, particularly in adolescents, have remained poorly understood. This dissertation investigated the neural mechanisms underlying emotional conflict processing in typically developing adolescents and adolescents with epilepsy using magnetoencephalography (MEG). The first study elucidated the spatiotemporal profile of emotional conflict processing in 24 typically developing adolescents using magnetoencephalography (MEG). Cluster-based …

Deep Learning-Assisted Diagnostic System: Apices And Odontogenic Sinus Floor Level Analysis In Dental Panoramic Radiographs, Pei Yi Wu, Yuan-Jin Lin, Yu-Jen Chang, Sung-Tsun Wei, Chiung An Chen, Kuo-Chen Li, Wei-Chen Tu, Patricia Angela R. Abu

Department of Information Systems & Computer Science Faculty Publications

Odontogenic sinusitis is a type of sinusitis caused by apical lesions of teeth near the maxillary sinus floor. Its clinical symptoms are highly like other types of sinusitis, often leading to misdiagnosis as general sinusitis by dentists in the early stages. This misdiagnosis delays treatment and may be accompanied by toothache. Therefore, using artificial intelligence to assist dentists in accurately diagnosing odontogenic sinusitis is crucial. This study introduces an innovative odontogenic sinusitis image processing technique, which is fused with common contrast limited adaptive histogram equalization, Min-Max normalization, and the RGB mapping method. Moreover, this study combined various deep learning models …

Precision Medicine Assessment Of The Radiographic Defect Angle Of The Intrabony Defect In Periodontal Lesions By Deep Learning Of Bitewing Radiographs, Patricia Angela R. Abu, Yi Cheng Mao, Yuan Jin Lin, Chien Kai Chao, Yi He Lin, Bo Siang Wang, Chiung An Chen, Shih Lun Chen, Tsung Yi Chen, Kuo Chen Li

Department of Information Systems & Computer Science Faculty Publications

In dental diagnosis, evaluating the severity of periodontal disease by analyzing the radiographic defect angle of the intrabony defect is essential for effective treatment planning. However, dentists often rely on clinical examinations and manual analysis, which can be time-consuming and labor-intensive. Due to the high recurrence rate of periodontal disease after treatment, accurately evaluating the radiographic defect angle of the intrabony defect is vital for implementing targeted interventions, which can improve treatment outcomes and reduce recurrence. This study aims to streamline clinical practices and enhance patient care in managing periodontal disease by determining its severity based on the analysis of …

Multimodal Imaging Of Protein-Based Biomaterials For Delivering Chemo-Agent Cargo For Glioblastoma Treatment In A Murine Model, Orin Mishkit

Dissertations and Theses

Protein-based self-assembling biomaterials, known as Thermo-Responsive Assembled Proteins (TRAP), present meaningful potential as drug delivery carriers. These materials enable the controlled, slow release of poorly soluble chemotherapeutic agents, such as doxorubicin (Dox), while potentially reducing systemic off-target effects. In collaboration with multiple NYU labs, this study evaluated the efficacy of two TRAP variants—TRAP and F-TRAP—as drug delivery carriers in a xenograft mouse model of glioblastoma multiforme (GBM).

The primary objective was to compare the effectiveness of TRAP-loaded Dox (TRAP-DOX) to free Dox in achieving tumor extravasation and accumulation, facilitating sustained drug release. We hypothesized that the leaky vasculature of GBM …