Bioimaging and Biomedical Optics Commons^™

Early Detection And Objective Assessment Of Neonatal Hypoxic-Ischemic Encephalopathy Severity, Soheila Norasteh

Bioengineering Dissertations

Hypoxic–ischemic encephalopathy (HIE) is a neonatal brain injury caused by reduced oxygen and blood flow to the brain around the time of birth. It remains a major cause of neonatal mortality and long-term neurodevelopmental impairment worldwide. Therapeutic hypothermia is the standard treatment for moderate-to severe HIE and improves outcomes when initiated within the first six hours of life. Therefore, accurate assessment of injury severity during this period is essential. Cur rently, HIE severity is determined primarily through neurological examination and classified as mild, moderate, or severe. However, these examinations are subjective, cannot provide continuous monitoring of brain function, and may …

Susceptibility To High-Fidelity Misinformation: An Eye-Tracking Analysis, Yasasi Abeysinghe, Gavindya Jayawardena, Enkelejda Kasneci, Sampath Jayarathna

Computer Science Faculty Publications

With the rise of online misinformation and AI-generated text, understanding human perception of news truthfulness is critical. In this study, we examine visual attention and cognitive processing using eye-tracking measures as individuals read fake and real news articles sharing nearly identical structure and imagery, differing only in subtle textual changes. Using the public FakeNewsPerception dataset, we analyze advanced gaze measures, including scanpaths, AOI transitions, and luminance-corrected pupil measures, beyond basic gaze features, in relation to news truthfulness and perceived believability. Results show that, given the high fidelity of the fake news, readers exhibited comparable visual scanning patterns, attention allocation across …

Volumetric Fluorescence Microscopy For High-Throughput And High-Sensitivity Imaging: From Single Molecules To Tissues, Le-Mei Wang

Graduate Studies Theses and Dissertations 2026

Fluorescence microscopy is an indispensable tool in the biological sciences, enabling researchers to investigate intricate subcellular structures, particularly for volumetric studies. However, conventional optical microscopy for volumetric imaging remains fundamentally constrained by imaging speed and throughput. To bypass traditional serial z-scanning, we introduce an axially scan-free method using a phase layer cake to modulate the system's point spread function. This approach projects volumetric information onto a 2D plane in a single shot, offering high flexibility in tuning axial depth alongside simultaneous multicolor imaging with high spatial resolution and sensitivity. This dissertation divides these technical advancements into cellular and tissue imaging …

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 …

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 …