Bioimaging and Biomedical Optics Commons^™

Session 12: Active Learning To Minimize The Possible Risk From Future Epidemics, Kc Santosh

SDSU Data Science Symposium

In medical imaging informatics, for any future epidemics (e.g., Covid-19), deep learning (DL) models are of no use as they require a large dataset as they take months and even years to collect enough data (with annotations). In such a context, active learning (or human/expert-in-the-loop) is the must, where a machine can learn from the first day with minimum possible labeled data. In unsupervised learning, we propose to build pre-trained DL models that iteratively learn independently over time, where human/expert intervenes only when it makes mistakes and for only a limited data. In our work, deep features are used to …

Small-Separation Speckle Contrast Optical Spectroscopy For Intraoperative Assessment Of Parathyroid Glands Viability During Thyroid Surgery, Connor Berger

Symposium of Student Scholars

The parathyroid glands (PTGs) are often damaged during thyroid surgeries due to a lack of methods identifying PTGs and assessing their viability. Damage to PTGs can cause hypocalcemia, a deficiency of calcium in the body. This complication can lead to detrimental consequences with economic burden. The surgeon’s current method of viability assessment is qualitative and subjective. Our technical solution is to employ an optical technique called speckle contrast optical spectroscopy (SCOS) that noninvasively quantifies the blood flow index (Db) of biological tissues at deep tissue levels (>1cm). The goal of this project is to verify SCOS at small source-detector-separation …

Seeing The Big Picture: System Architecture Trends In Endoscopy And Led-Based Hyperspectral Subsystem Intergration, Craig M. Browning

Theses and Dissertations

Early-stage colorectal lesions remain difficult to detect. Early development of neoplasia tends to be small (less than 10 mm) and flat and difficult to distinguish from surrounding mucosa. Additionally, optical diagnosis of neoplasia as benign or malignant is problematic. Low rates of detection of these lesions allow for continued growth in the colorectum and increased risk of cancer formation. Therefore, it is crucial to detect neoplasia and other non-neoplastic lesions to determine risk and guide future treatment. Technology for detection needs to enhance contrast of subtle tissue differences in the colorectum and track multiple biomarkers simultaneously. This work implements one …

System Of System Integration For Hyperspectral Imaging Microscopy, Marina Parker

Theses and Dissertations

Hyperspectral imaging (HSI) has become a leading tool in the medical field due to its capabilities for providing assessments of tissue pathology and separation of fluorescence signals. Acquisition speeds have been slow due to the need to acquire signal in many spectral bands and the light losses associated with technologies of spectral filtering. Traditional methods resulted in limited signal strength which placed limitations on time sensitive and photosensitive assays. For example, the distribution of cyclic adenosine monophosphate (cAMP) is largely undetermined because current microscope technologies lack the combination of speed, resolution, and spectral ability to accurately measure Forster resonance energy …

Iron Nanoparticles For Magnetic Imaging Applications, Aleia Williams

Masters Theses

Extensive research on iron oxide nanoparticles for various applications including nanomedicine, energy applications, environmental remediation, and magnetic imaging have previously been performed. Many are currently FDA approved as magnetic resonance imaging contrast agents and tracers for magnetic particle imaging applications. Magnetic properties of such materials are crucial to obtain good contrast and resolution. However, studies have shown the magnetic properties of iron oxide nanoparticles are less in comparison to those found in pure iron nanoparticle.

This research involves the synthesis and characterization of iron nanoparticles for applications in magnetic resonance imaging contrast agents, magnetic particle imaging tracers, and therapeutic agents …

Neroimaging Of Brain Activaion Using Diffuse Optical Tomography, Jingyu Huang

USF Tampa Graduate Theses and Dissertations

This research has two parts. The first part focuses on the use of non-invasive imaging technique, diffuse optical tomography (DOT), to study the brain activation during the stimulation in the clinical room. It further extends the application of DOT by using it to monitor the hemodynamic response during the TMS stimulation in different parameters. Diffuse optical tomography (DOT) is based on NIR light that exploits the relative transparency of biological tissue. The part two and three extends the application in the hospital for delirium patient study and arm muscle dystrophy by adding the sources and detectors to monitor the brain …

Model-Based Determination Of The Synchronization Delay Between Mri And Trajectory Data., Paul Ioan Dubovan, Corey Allan Baron

Robarts Imaging Publications

PURPOSE: Real-time monitoring of dynamic magnetic fields has recently become a commercially available option for measuring MRI k-space trajectories and magnetic fields induced by eddy currents in real time. However, for accurate image reconstructions, sub-microsecond synchronization between the MRI data and field dynamics (ie, k-space trajectory plus other spatially varying fields) is required. In this work, we introduce a new model-based algorithm to automatically perform this synchronization using only the MRI data and field dynamics.

METHODS: The algorithm works by enforcing consistency among the MRI data, field dynamics, and receiver sensitivity profiles by iteratively alternating between convex optimizations for (a) …

Using Shg Directionality To Characterize Collagen Alteration In Breast Cancer Tumor Microenvironment And Its Prognostic Applications, Betelhem Solomon Abay

Electronic Theses and Dissertations

Although breast cancer is a growing health concern worldwide, the challenge to minimize mortality rate partly comes from the heterogeneity in its pathological characteristics. The tumor microenvironment is a complex hub of signaling cascades that plays a key role for the progression of cancer to develop to metastatic stage. The extracellular matrix (ECM), as a major component of the tumor microenvironment, contains signatures that have cues to understand tumor progression. Here, the unique microstructural collagen alterations specific to reactive stromal/tumor cell interactions and interactions of reactive stromal fibroblasts with different tumor cell types MCF7A and MDA-MB-231 were investigated. Early alterations …

Labeling Melanoma Cells With Black Microspheres For Improved Sensitivity In Detection Via Photoacoustic Flow Cytometry, Tori Kocsis

Electronic Theses and Dissertations

Melanoma is an aggressive form of skin cancer known for developing into metastatic disease. Current clinical diagnostics, including medical imaging and tissue biopsy, provide a poor prognosis since the cancer is in the late stages of disease progression. In recent years, photoacoustic flow cytometry has allowed for the detection of circulating melanoma cells within patient blood samples in vitro. Although this method exploits the naturally-produced melanin within the cells, it has only successfully detected highly-pigmented melanoma cell lines. Since various forms of melanoma exist, each with varying melanin concentrations, this research aims to provide a novel method for detecting lightly-pigmented …

Noncontact Liquid Crystalline Broadband Optoacoustic Sensors [U.S. Patent Us11366054b2], Hengky Chandrahalim, Michael T. Dela Cruz

Faculty Publications

An optoacoustic sensor includes a liquid crystal (LC) cell formed between top and bottom plates of transparent material. A transverse grating formed across the LC cell that forms an optical transmission bandgap. A CL is aligned to form a spring-like, tunable Bragg grating that is naturally responsive to external agitations providing a spectral transition regime, or edge, in the optical transmission bandgap of the transverse grating that respond to broadband acoustic waves. The optoacoustic sensor includes a narrowband light source that is oriented to transmit light through the top plate, the LC cell, and the bottom plate. The optoacoustic sensor …

Improving The Performance And Evaluation Of Computer-Assisted Semen Analysis, Ji-Won Choi

Dissertations

Semen analysis is performed routinely in fertility clinics to analyze the quality of semen and sperm cells of male patients. The analysis is typically performed by trained technicians or by Computer-Assisted Semen Analysis (CASA) systems. Manual semen analysis performed by technicians is subjective, time-consuming, and laborious, and yet most fertility clinics perform semen analysis in this manner. CASA systems, which are designed to perform the same tasks automatically, have a considerable market share, yet many studies still express concerns about their accuracy and consistency. In this dissertation, the focus is on detection, tracking, and classification of sperm cells in semen …

Hinged Temperature-Immune Self-Referencing Fabry–Pérot Cavity Sensors [Us Patent Us11320596b2], Jeremiah C. Williams, Hengky Chandrahalim

Faculty Publications

A passive microscopic Fabry-Pérot Interferometer (FPI) sensor includes a three-dimensional microscopic optical structure formed on a cleaved tip of the optical fighter using a two-photon polymerization process on a photosensitive polymer by a three-dimensional micromachining device. The three-dimensional microscopic optical structure having a hinged optical layer pivotally connected to a distal portion of a suspended structure. A reflective layer is deposited on a mirror surface of the hinged optical layer while in an open position. The hinged optical layer is subsequently positioned in the closed position to align the mirror surface to at least partially reflect a light signal back …

Determination Of Tissue-Level Changes In Tumors That Are Indicative Of Metastasis Using Optical Spectroscopy, Sanidhya D. Tripathi

Biomedical Engineering Undergraduate Honors Theses

Breast cancer, accounting for 12% of all new cancer cases, is one of the leading causes of death in women worldwide. Although patient survival has improved over the years, metastatic spread to other organ sites and not due to the primary tumor is the most common form of tumor recurrence, accounting for 90% deaths. Hypoxia is a common hallmark of solid tumors and is linked with metastasis, therapeutic resistance, and poor patient survival. Defined as a state of decreased oxygen availability, cells under hypoxia have an increased rate of genetic mutation, local invasion, and resistance to treatment such as radiation …

Investigating The Impact Of Hypoxia On Reactive Oxygen Species Generation Within Murine Breast Cancer Cells, Jared Mcpeake

Biomedical Engineering Undergraduate Honors Theses

When cancer metastasizes from a primary tumor site to secondary site through the bloodstream or lymph, the cancer becomes more difficult to treat. For this reason, it is vital to study what indicates the metastatic potential of a tumor. Current research has shown that cell lines with high metastatic potential display increased levels of metabolic adaptability over their nonmetastatic counterparts after undergoing hypoxic conditions. One method of assessing this adaptability is to measure the concentration of reactive oxygen species (ROS) produced by the cells while undergoing oxidative stress. In highly adaptable metastatic cells, an increase of ROS buildup within the …

Machine Learning Approaches For Early Prediction Of Hypertension., Heba Elsayed Mohamed Kandil

Electronic Theses and Dissertations

Hypertension afflicts one in every three adults and is a leading cause of mortality in 516, 955 patients in USA. The chronic elevation of cerebral perfusion pressure (CPP) changes the cerebrovasculature of the brain and disrupts its vasoregulation mechanisms. Reported correlations between changes in smaller cerebrovascular vessels and hypertension may be used to diagnose hypertension in its early stages, 10-15 years before the appearance of symptoms such as cognitive impairment and memory loss. Specifically, recent studies hypothesized that changes in the cerebrovasculature and CPP precede the systemic elevation of blood pressure. Currently, sphygmomanometers are used to measure repeated brachial artery …

Wavelet-Based Automatic Breast Segmentation For Mammograms, Basel White

Honors College

As part of a first of its kind analysis of longitudinal mammograms, there are thousands of mammograms that need to be analyzed computationally. As a pre- processing step, each mammogram needs to be converted into a binary (black or white) spatial representation in order to delineate breast tissue from the pectoral muscle and image background, which is called a mammographic mask. The current methodology for completing this task is for a lab member to manually trace the outline of the breast, which takes approximately three minutes per mammogram. Thus, reducing the time cost and human subjectivity when completing this task …

Analysis Of An Existing Method In Refinement Of Protein Structure Predictions Using Cryo-Em Images, Maytha Alshammari, Jing He, Willy Wriggers, Jiangwen Sun

College of Sciences Posters

Protein structure prediction produces atomic models from its amino acid sequence. Three-dimensional structures are important for understanding the function mechanism of proteins. Knowing the structure of a given protein is crucial in drug development design of novel enzymes. AlphaFold2 is a protein structure prediction tool with good performance in recent CASP competitions. Phenix is a tool for determination of a protein structure from a high-resolution 3D molecular image. Recent development of Phenix shows that it is capable to refine predicted models from AlphaFold2, specifically the poorly predicted regions, by incorporating information from the 3D image of the protein. The goal …

Two-Stage Transfer Learning For Facial Expression Classification In Children, Gregory Hubbard, Megan Witherow, Khan Iftekharuddin

Undergraduate Research Symposium

Studying facial expressions can provide insight into the development of social skills in children and provide support to individuals with developmental disorders. In afflicted individuals, such as children with Autism Spectrum Disorder (ASD), atypical interpretations of facial expressions are well-documented. In computer vision, many popular and state-of-the-art deep learning architectures (VGG16, EfficientNet, ResNet, etc.) are readily available with pre-trained weights for general object recognition. Transfer learning utilizes these pre-trained models to improve generalization on a new task. In this project, transfer learning is implemented to leverage the pretrained model (general object recognition) on facial expression classification. Though this method, the …

Characterizing Mechanical Regulation Of Bone Metastatic Breast Cancer Cells, Boyuan Liu

Doctoral Dissertations

Breast cancer most frequently metastasizes to the skeleton. Bone metastatic cancer is incurable and induces wide-spread bone osteolysis, resulting in significant patient morbidity and mortality. Mechanical stimuli in the skeleton are an important microenvironmental parameter that modulates tumor formation, osteolysis, and tumor cell-bone cell signaling, but which mechanical signals are the most beneficial and the corresponding molecular mechanisms are unknown. This work focused on bone matrix deformation and interstitial fluid flow based on their well-known roles in bone remodeling and in primary breast cancer. The goal of our research was to establish a platform that could define the relationship between …

Bayesian Network-Based Diagnostic Support Tool With Limited Point-Of-Care Ultrasound For Work-Related Elbow Injuries, Cristina Maria Franceschini Sánchez

USF Tampa Graduate Theses and Dissertations

The upper extremity is commonly injured at the workplace, frequently involving the elbow. Currently, there are not many diagnostic support tools for elbow injuries. Developing a clinical decision support tool would allow for narrowing differential diagnoses and guide management steps in a timely and cost-effective manner. In a descriptive retrospective cohort study, 85 non-contrast elbow MRIs were obtained from a large Workers Compensation insurer database. MRIs were either (a) greater than 2 weeks after first clinic visit, or (b) more than 6 weeks after injury, but (c) not more than 3 months after injury. A Bayesian network-based diagnostic support tool …