Bioimaging and Biomedical Optics Commons^™

Expanding Cherenkov Imaging Applications In Radiotherapy: Clinic-Wide In Vivo Treatment Monitoring And Mr-Linac Quality Assurance, Daniel A. Alexander

Dartmouth College Ph.D Dissertations

Radiation therapy treatments have become increasingly complex, striving to improve patient outcomes by delivering sufficient dose for tumor control while sparing more normal tissue. This trend has necessitated the development of additional workflows, such as multilayered incident mitigation strategies and advanced techniques for adapting treatments to account for time-sensitive patient factors. Novel technologies such as optical 3D surface monitoring and magnetic resonance-guided linear accelerators have been developed to assist clinicians in implementing these workflows. We hypothesize that optical imaging methods developed for radiotherapy dose monitoring and measurement can be used to positively impact modern radiation therapy challenges. Cherenkov imaging allows …

Design And Development Of Software With A Graphical User Interface To Display And Convert Multiple Microscopic Histology Images, Sayed Ahmadreza Razian, Majid Jadidi, Alexey Kamenskiy

UNO Student Research and Creative Activity Fair

Histological images are widely used to assess the microscopic anatomy of biological tissues. Recent advancements in image analysis allow the identification of structural features on histological sections that can help advance medical device development, brain and cancer research, drug discovery, vascular mechanobiology, and many other fields. Histological slide scanners create images in SVS and TIFF formats that were designed to archive image blocks and high-resolution textual information. Because these formats were primarily intended for storage, they are often not compatible with conventional image analysis software and require conversion before they can be used in research. We have developed a user-friendly …

Live Cell Imaging Gas Control, Elsa M. Bean, Brady C. Berg, Abby A. Jens

Biomedical Engineering

The following document outlines the entire process for designing and manufacturing a Live Cell Imaging Gas Control subsystem in tandem with the Heated Stage subsystem to make a CO₂ and temperature-controlled chamber for use with the Olympus IX73P2F Microscope. It highlights the current literature and patents surrounding live cell imaging and touches on the existing live cell imaging setups currently being used by other entities. Following this, it defines the scope of the project, key customer requirements, and engineering specifications to ensure the design meets all the needs of its users. This document includes project planning steps to establish …

Cbct In Clinical Practice, Tarunjeet Pabla Bds, Dmd, Ms, Dip. Abomr, Hugo C. Campos Dds, Dmd, Mds, Dip. Abomr, Aruna Ramesh Bds, Dmd, Ms, Dip. Abomr

The Journal of the Michigan Dental Association

This feature explores the integration of Cone Beam Computed Tomography (CBCT) into dental practice, offering guidelines for best practices. Introduced in 2001, CBCT revolutionized dental radiography, impacting various clinical areas. The article emphasizes the need for clinicians to comprehend CBCT technology, its benefits, and potential risks. It delves into CBCT imaging considerations, technical parameters (Field of View, Voxel Size, Spatial and Contrast Resolution), image viewing, artifacts, machine calibration, and service. Addressing radiation dose, risks, and protection, the article outlines decision-making for 2D vs. 3D imaging. It underscores the responsibility of interpreting CBCT images, legal considerations, return on investment, and the …

Therapeutic Treatment With The Anti-Inflammatory Drug Candidate Mw151 May Partially Reduce Memory Impairment And Normalizes Hippocampal Metabolic Markers In A Mouse Model Of Comorbid Amyloid And Vascular Pathology, David J. Braun, David K. Powell, Christopher J. Mclouth, Saktimayee M. Roy, D. Martin Watterson, Linda J. Van Eldik

Neuroscience Faculty Publications

Alzheimer's disease (AD) is the leading cause of dementia in the elderly, but therapeutic options are lacking. Despite long being able to effectively treat the ill-effects of pathology present in various rodent models of AD, translation of these strategies to the clinic has so far been disappointing. One potential contributor to this situation is the fact that the vast majority of AD patients have other dementia-contributing comorbid pathologies, the most common of which are vascular in nature. This situation is modeled relatively infrequently in basic AD research, and almost never in preclinical studies. As part of our efforts to develop …

Resolving The Three-Dimensional Rotational And Translational Dynamics Of Single Molecules Using Radially And Azimuthally Polarized Fluorescence, Oumeng Zhang, Weiyan Zhou, Jin Lu, Tingting Wu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR’s orientational diffusion to be dramatically reduced, but curiously NR’s median lateral displacements drastically increase from 20.8 to …

In Vitro Mitral Valve Model With Unrestricted Ventricular Access: Using Vacuum To Close The Valve And Enable Static Trans-Mitral Pressure, Sam E. Stephens, Alexander J. Kammien, Jacob C. Paris, Alexis P. Applequist, Neil B. Ingels, Hanna K. Jensen, Drew E. Rodgers, Charles R. Cole, Jonathan F. Wenk, Morten O. Jensen

Biomedical Engineering Faculty Publications and Presentations

Current in vitro models of the left heart establish the pressure difference required to close the mitral valve by sealing and pressurizing the ventricular side of the valve, limiting important access to the subvalvular apparatus. This paper describes and evaluates a system that establishes physiological pressure differences across the valve using vacuum on the atrial side. The subvalvular apparatus is open to atmospheric pressure and accessible by tools and sensors, establishing a novel technique for experimentation on atrioventricular valves. Porcine mitral valves were excised and closed by vacuum within the atrial chamber. Images were used to document and analyze closure …

Toward A Multimodal Computer-Aided Diagnostic Tool For Alzheimer’S Disease Conversion, Danilo Pena, Jessika Suescun, Mya Schiess, Timothy M. Ellmore, Luca Giancardo, Alzheimer’S Disease Neuroimaging Initiative

Publications and Research

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder. It is one of the leading sources of morbidity and mortality in the aging population AD cardinal symptoms include memory and executive function impairment that profoundly alters a patient’s ability to perform activities of daily living. People with mild cognitive impairment (MCI) exhibit many of the early clinical symptoms of patients with AD and have a high chance of converting to AD in their lifetime. Diagnostic criteria rely on clinical assessment and brain magnetic resonance imaging (MRI). Many groups are working to help automate this process to improve the clinical workflow. Current …

Towards Fluoro-Free Interventions: Using Radial Intracardiac Ultrasound For Vascular Navigation, Hareem Nisar, Leah Groves, Leandro Cardarelli-Leite, Terry M Peters, Elvis C.S. Chen

Robarts Imaging Publications

Transcatheter cardio-vascular interventions have the advantage of patient safety,reduced surgery time, and minimal trauma to the patient's body. Transcathetherinterventions, which are performed percutaneously, suffer from the lack of direct line-of-sight with the surgical tools and the patient anatomy. Therefore, such interventionalprocedures rely heavily on image guidance for navigating towards and deliveringtherapy at the target site. Vascular navigation via the inferior vena cava (IVC), from thegroin to the heart, is an imperative part of most transcatheter cardiovascularinterventions such as valve repair surgeries and ablation therapy. Traditionally, the IVCis navigated using fluoroscopic techniques such as angiography or CT venography.These X-ray based techniques …

A Radiofrequency Coil To Facilitate Task-Based Fmri Of Awake Marmosets, Kyle Gilbert, Audrey Dureux, Azadeh Jafari, Alessandro Zanini, Peter Zeman, Ravi S. Menon, Stefan Everling

Robarts Imaging Publications

Background: The small common marmoset (Callithrix jacchus) is an ideal nonhuman primate for awake fMRI in ultra-high field small animal MRI scanners. However, it can often be challenging in task-based fMRI experiments to provide a robust stimulus within the MRI environment while using hardware (an RF coil and restraint system) that is compatible with awake imaging. New Method: Here we present an RF coil and restraint system that permits unimpeded access to an awake marmoset’s head subsequent to immobilization, thereby permitting the setup of peripheral devices and stimuli proximal to the head.

Results: As an example application, an …

Towards Ultrasound-Based Navigation: Deep Learning Based Ivc Lumen Segmentation From Intracardiac Echocardiography, Hareem Nisar, Patrick Carnahan, Djalal Fakim, Humayoun Akhunzada, David Hocking, Elvis Chen, Terry Peters

Robarts Imaging Publications

ascular navigation is a prerequisite to transcatheter cardiac interventions. The current standard approach to catheter navigation relies on real-time fluoroscopy, while this technique utilizes ionizing radiation and it places the interventionalist at risk for eye cataracts and cancer. The shielding equipment needed to mitigate these risks is associated with spinal issues and neck and back pain which has led towards the coining of the term "interventionalist's disc disease". A proposed alternative is to have an ultrasound-guided vascular navigation system where a catheter-based ultrasound probe scans the vessel and reconstructs the vascular roadmap, which can then be navigated by tracked guidewire …

Segmentation Of Intracranial Structures From Noncontrast Ct Images With Deep Learning, Evan Porter

Wayne State University Dissertations

Presented in this work is an investigation of the application of artificially intelligent algorithms, namely deep learning, to generate segmentations for the application in functional avoidance radiotherapy treatment planning. Specific applications of deep learning for functional avoidance include generating hippocampus segmentations from computed tomography (CT) images and generating synthetic pulmonary perfusion images from four-dimensional CT (4DCT).A single institution dataset of 390 patients treated with Gamma Knife stereotactic radiosurgery was created. From these patients, the hippocampus was manually segmented on the high-resolution MR image and used for the development of the data processing methodology and model testing. It was determined that …

Biomedical Applications Of Lanthanide Nanomaterials, For Imaging, Sensing And Therapy, Qize Zhang, Stephen O'Brien, Jan Grimm

Publications and Research

The application of nanomaterials made of rare earth elements within biomedical sciences continues to make significant progress. The rare earth elements, also called the lanthanides, play an essential role in modern life through materials and electronics. As we learn more about their utility, function, and underlying physics, we can contemplate extending their applications to biomedicine. This particularly applies to diagnosis and radiation therapy due to their relatively unique features, such as an ultra-wide Stokes shift in the luminescence, variable magnetism and potentially tunable properties, due to the library of lanthanides available and their multivalent oxidation state chemistry. The ability to …

Automated, Robust Radiomics Biomarker Modeling For Glioblastoma, Eric Nathan Carver

Wayne State University Dissertations

Individualized medicine is possible due to the discovery that a patient’s gene expression can serve as a bio-marker and provide prognostic clinical knowledge. The genetic revolution increased interest in the field of “-omics” which investigates differing classifications of patient characteristics to increase clinician knowledge, which directly improves patient care. Glioblastoma (GBM) is the most aggressive brain cancer and very difficult to treat, resulting in a 15 month median survival. Researchers have discovered several patient specific markers, specifically IDH1 and MGMT methylation, which energized further research for GBM patient specific markers. A relatively new subfield of ‘-omics’ is Radiomics; which aims …

Photoacoustic Imaging For Image-Guided Interventions, Samuel John

Wayne State University Dissertations

Image-guided surgeries and therapeutic procedures utilize imaging modalities to enhance the surgeon’s capability of visualizing and guiding the medical instruments within the body. One such application is the endovenous laser ablation (EVLA), which utilizes an ultrasound (US)-guided catheter carrying high power continuous wave (CW) energy for treating varicose veins. Varicose veins, a condition defined by venous insufficiency, affects nearly 40 million people in the United States annually. In EVLA procedures, US limitations including angular dependency, poor contrast-to-noise ratio, poor signal-to-noise ratio, and artifacts limit the ability of the surgeon to detect the catheter tip within the vein. Furthermore, the absence …

Phase-Changing Nanodroplets As Nanotheranostic Platform For Combination Cancer Therapy, Catalina-Paula Spatarelu

Dartmouth College Ph.D Dissertations

Cancer is a cluster of diseases, and 1.8 million Americans are newly diagnosed each year. Treatment issues such as drug instability, the occurrence of severe side effects, as well as resistance make the need for solutions to improve conventional methods, like chemotherapy, apparent. Nano-sized drug-delivery platforms, particles loaded with therapeutic molecules that escape the immune system clearance and accumulate at the tumor site, were proposed as one of these solutions. Despite the expansion of the field, several aspects still need to be addressed: inconsistent delivery of the drugs, inability of measuring the effective dose being delivered to the tumor, lack …

Advancing Combined Radiological And Optical Scanning For Breast-Conserving Surgery Margin Guidance, Samuel Stewart Streeter

Dartmouth College Ph.D Dissertations

Breast cancer is one of the most common types of cancer worldwide, and standard-of-care for early-stage disease typically involves a lumpectomy or breast-conserving surgery (BCS). BCS involves the local resection of cancerous tissue, while sparring as much healthy tissue as possible. State-of-the-art methods for intraoperatively evaluating BCS margins are limited. Approximately 20% of BCS cases result in a tissue resection with cancer at or near the resection surface (i.e., a positive margin). A two-fold increase in ipsilateral breast cancer recurrence is associated with the presence of one or more positive margins. Consequently, positive margins often necessitate costly re-excision procedures to …

Characterizing The Internal Porous Structure Of Equine Proximal Sesamoid Bones Subjected To Race Training Using Fast Fourier Transforms, Joseph Erik Davis

Theses and Dissertations--Biomedical Engineering

The equine racing industry is one of the main proponents in Kentucky’s economic infrastructure. In this industry there has come a need to investigate the nature of the proximal sesamoid bone (PSB). Breakdowns involving the PSBs are the leading cause in racehorse deaths in the industry, with still little known about what causes this bone to fracture. This study seeks to shed insight by investigating the internal structure of the PSB. Using microCT scanning, the internal porous structure was captured. From there, noticeable differences in the pores were noticed and quantified using fast Fourier transform (FFT) analysis.

The dominant peak …

Modulation Of Brain Tissue Transport And Endothelial Glycocalyx And Tight Junctions Of The Blood-Brain Barrier By Transcranial Direct Current Stimulation, Yifan Xia

Dissertations and Theses

Transcranial direct current stimulation (tDCS) is a non-invasive approach to treat a broad range of brain disorders and to enhance memory and cognition in healthy individuals. In addition to directly acting on neurons by modulating the membrane potential, inducing neuronal polarization and changing cortical excitability in the brain to achieve its therapeutic effects, prior studies found that tDCS can transiently enhance the permeability (P) of the blood-brain barrier (BBB), the interface between blood circulation and brain tissue. Brain extracellular space (ECS) is a narrow microenvironment which surrounds every cell in the central nervous system (CNS). ECS occupies ~20% of brain …

Gan-Based Super-Resolution And Segmentation Of Retinal Layers In Optical Coherence Tomography Scans, Paria Jeihouni

Graduate Theses, Dissertations, and Problem Reports (ETD)

Optical Coherence Tomography (OCT) has been identified as a noninvasive and cost-effective imaging modality for identifying potential biomarkers for Alzheimer's diagnosis and progress detection. Current hypotheses indicate that retinal layer thickness, which can be assessed via OCT scans, is an efficient biomarker for identifying Alzheimer's disease. Due to factors such as speckle noise, a small target region, and unfavorable imaging conditions manual segmentation of retina layers is a challenging task. Therefore, as a reasonable first step, this study focuses on automatically segmenting retinal layers to separate them for subsequent investigations. Another important challenge commonly faced is the lack of clarity …

Nano-, Encapsulated Manganese Oxide (Nemo) Particles For Mri Enhancement In Microfluidic Tumor Models, Kasey Alexis Freshwater

Graduate Theses, Dissertations, and Problem Reports (ETD)

Breast cancer is among the deadliest cancers in women, with approximately 2.3 million new cases and 685,000 deaths reported globally in 2020 alone. Magnetic Resonance Imaging (MRI) is commonly used to diagnose, stage, and develop treatment plans for patients predisposed to breast cancer. However, current MRI-based screening of breast cancer has high false-positive rates up to 25%, leading to unnecessary invasive follow-up screening and testing. The gold-standard intravenous gadolinium (Gd)-based contrast agents (GBCAs) account for false-positive rates because they are always “ON”, providing a constant MRI signal that highlights both benign and malignant tumors. The work detailed in this thesis …

Tumor-Targeted Ph-Sensitive Manganese Oxide Nanoparticle For Enhanced Detection Of Breast Cancer Using Mri, Celia Martinez De La Torre

Graduate Theses, Dissertations, and Problem Reports (ETD)

In the United States, approximately 287,850 new cases of invasive breast cancer will be diagnosed, and over 43,000 women will die because of it in 2022. Currently, mammography is the gold standard for breast cancer surveillance. Although this detection technique is relatively cheap and fast, it misses about 1 in 5 breast cancers in younger women with dense breast tissue, causing a delay in treatment. Compared to mammography, magnetic resonance imaging (MRI) has superior soft-tissue contrast that elucidates structural differences within soft tissue to detect more breast cancers. However, MRI still misses

NEMO particles were produced by synthesizing manganese oxide …

Multimodal Ultrasound Imaging For Improved Metastatic Lymph Node Detection, Sidhartha Jandhyala

Dartmouth College Ph.D Dissertations

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and is complex in nature due to the variety of organs located in the head and neck region. Knowing the metastatic state of the lymph nodes is paramount in accurately staging and treating HNSCC patients. Currently, metastatic lymph node detection involves the use of magnetic resonance imaging and/or x-ray computed tomography, followed by biopsies for histological confirmation. The main diagnostic criteria is the size of the nodes; however, current imaging methods are not 100% accurate due natural lymph node variability. Ultrasound imaging is able to provide …

Deep Learning Approach To Improved Image Quality For Medical Diagnostics, Olivia Loesch, Katie Leyba, Halyley Chan, Craig Goergen

Discovery Undergraduate Interdisciplinary Research Internship

The United Nation’s health-related Sustainable Development Goals are difficult to achieve in low- and middle-income countries due to workforce shortages and inadequate health surveillance systems. However, with the growth of artificial intelligence (AI) and computer algorithms, it is possible to apply AI to healthcare technologies to improve progress towards these UN standards. This project aims at using and improving computer algorithms and deep learning to aid in the extraction of important structural and functional information from murine carotid artery ultrasound and photoacoustic images. First, we created a large database of simulated photoacoustic images to optimize the algorithms. These images were …

Inter-Subject Correlation While Listening To Minimalist Music: A Study Of Electrophysiological And Behavioral Responses To Steve Reich’S Piano Phase, Tysen Dauer, Duc T. Nguyen, Nick Gang, Jacek P. Dmochowski, Jonathan Berger, Blair Kaneshiro

Publications and Research

Musical minimalism utilizes the temporal manipulation of restricted collections of rhythmic, melodic, and/or harmonic materials. One example, Steve Reich’s Piano Phase, offers listeners readily audible formal structure with unpredictable events at the local level. For example, pattern recurrences may generate strong expectations which are violated by small temporal and pitch deviations. A hyper-detailed listening strategy prompted by these minute deviations stands in contrast to the type of listening engagement typically cultivated around functional tonal Western music. Recent research has suggested that the inter-subject correlation (ISC) of electroencephalographic (EEG) responses to natural audio-visual stimuli objectively indexes a state of “engagement,” demonstrating …

Design Of Miniaturized Antipodal Vivaldi Antennas And A Microwave Head Imaging System For The Detection Of Blood Clots In The Brain, Farhana Parveen

Electronic Theses and Dissertations, 2020-2023

Traditional brain imaging modalities, for example, MRI, CT scan, X-ray, etc. can provide precise and high-resolution images of the brain for diagnosing lesions, tumors or clots inside the brain. However, these modalities require bulky and expensive test setups accessible only at specialized diagnostic centers, and hence may not be suitable or affordable to many patients. Furthermore, the inherent health risks limit the usability of these modalities for frequent monitoring. Microwave imaging is deemed a promising alternative due to its being cost-effective, portable, non-ionizing, non-intrusive. Therefore, this work aims to design an effective microwave head imaging system for the detection of …

Generation, Analysis, And Evaluation Of Patient-Specific, Osteoligamentous, Spine Meshes, Austin R. Tapp

Biomedical Engineering Theses & Dissertations

Scoliosis, an abnormal curvature of the spine, is traditionally corrected with bracing treatments or by a highly invasive posterior spinal fusion (PSF) operation. These correction strategies are constrained by current imaging modalities, which fail to elucidate the soft tissue anatomy that is known to play a critical role in spinal stiffness and overall structure. Osteoligamentous segmentations of the spinal column offer a foundation for downstream finite element (FE) studies seeking to optimize bracing treatments or determine ideal surgical approaches.

This thesis presents methods for automatically and semi-automatically segmenting vertebrae and surrounding soft tissues of the spinal column using X-ray computed …

Time-Lapse Observation Of Sarcomeric Addition In Hypertrophic Models Based On A Tissue Like Cardiomyocyte Culture, Ailin Wei

All Dissertations

Cardiac hypertrophy is the response of the heart to increased mechanical stress exerted on the heart. In a hypertrophic heart, the muscles elongate or/and thicken with cardiomyocytes growing sizes. It is assumed that cardiomyocytes elongate by adding sarcomeres in series; the cardiomyocytes thicken with the addition of sarcomeres in the parallel position.

In this study, a tissue-like culture model was achieved with step-like ICDs. Uniaxial static stretch has been applied to our unique culture model for studying mechanical-load-induced cardiac hypertrophy. Hypertrophic responses of these cardiomyocytes have been confirmed on transcriptional and translational levels in our tissue-like model. The two-photon excitation …

Single-Molecule Localization Microscopy Of 3d Orientation And Anisotropic Wobble Using A Polarized Vortex Point Spread Function, Tianben Ding, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Within condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecule’s wobble, simultaneously from a single image. Even when imaging dim emitters (∼500 photons detected), the polarized vortex PSF can obtain 12 nm localization precision, 4°–8° orientation precision, and 26° wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics …

Dataset Of Concurrent Eeg, Ecg, And Behavior With Multiple Doses Of Transcranial Electrical Stimulation, Nigel Gebodh, Zeinab Esmaeilpour, Abhishek Datta, Marom Bikson

Publications and Research

We present a dataset combining human-participant high-density electroencephalography (EEG) with physiological and continuous behavioral metrics during transcranial electrical stimulation (tES). Data include within participant application of nine High-Definition tES (HD-tES) types, targeting three cortical regions (frontal, motor, parietal) with three stimulation waveforms (DC, 5 Hz, 30 Hz); more than 783 total stimulation trials over 62 sessions with EEG, physiological (ECG, EOG), and continuous behavioral vigilance/alertness metrics. Experiment 1 and 2 consisted of participants performing a continuous vigilance/alertness task over three 70-minute and two 70.5-minute sessions, respectively. Demographic data were collected, as well as self-reported wellness questionnaires before and after each …