Bioimaging and Biomedical Optics Commons^™

Noninvasively Monitoring Of Cerebral Blood Flow In Piglet Models Of Graded Hemorrhage And Hypoxic Ischemic Brain Injury Using Diffuse Correlation Spectroscopy And Near-Infrared Spectroscopy, Randolph Sinahon, Danielle Shoshany, Shadi Malaeb, Mert Deniz Polat, Meltem Izzetoglu, Kurtulus Izzetoglu

St. Chris Research Day

No abstract provided.

Cerebral Blood Flow Measured By Diffuse Correlation Spectroscopy For Monitoring Depth Of Anesthesia In Piglets, Mert Deniz Polat, Kurtulus Izzetoglu, Randolph Sinahon, Meltem Izzetoglu, Shadi Malaeb

St. Chris Research Day

No abstract provided.

Portable Diffuse Reflectance Spectroscopy For Non-Invasive And Quantitative Assessment Of The Parathyroid Glands Viability During Surgery, Mark Romine, Linh Luong, Alex Moazzen, Katie Cho, Paul Lee

Symposium of Student Scholars

Portable Diffuse Reflectance Spectroscopy for Non-invasive and Quantitative Assessment of the Parathyroid Glands Viability During Surgery

Mark Romine, Linh Luong, Alex Moazzen, Katie Cho and Paul Lee

The parathyroid glands (PTGs) are responsible for the regulation of calcium levels in the blood by secreting a parathyroid hormone. This parathyroid hormone then regulates the body’s absorption, storage, and secretion of calcium, which can directly affect the way muscles and nerves operate. PTGs are often at risk of damage, or accidental removal during thyroid surgeries, because it is challenging to identify PTGs and to determine their viability. Current methods of visual inspections …

Wireless, Handheld Diffuse Reflectance Spectroscopy To Quantify Tissue Microvascular Hemodynamics, Linh Luong, Alex Moazzen, Mark Romine, Katie Cho, Paul Lee

Symposium of Student Scholars

Diffuse Reflectance Spectroscopy (DRS) is a non-invasive optical method to characterize tissue optical properties for disease diagnosis and health monitoring. Two optical fibers are often used in a DRS system: one to deliver light to the tissue and the other to gather diffuse reflectance spectra, which provide quantitative details about the structure and composition of the tissue. The conventional DRS system, however, is expensive, bulky, and composed of fragile optical fibers and multiple electrical connections. Here we propose to build a wireless, handheld, and fiber-less diffuse optical spectroscopy system. Unfortunately, the diffusion approximation utilized for data analysis of the conventional …

Enhancement Of Deep Learning Protein Structure Prediction, Ruoming Shen

Modeling, Simulation and Visualization Student Capstone Conference

Protein modeling is a rapidly expanding field with valuable applications in the pharmaceutical industry. Accurate protein structure prediction facilitates drug design, as extensive knowledge about the atomic structure of a given protein enables scientists to target that protein in the human body. However, protein structure identification in certain types of protein images remains challenging, with medium resolution cryogenic electron microscopy (cryo-EM) protein density maps particularly difficult to analyze. Recent advancements in computational methods, namely deep learning, have improved protein modeling. To maximize its accuracy, a deep learning model requires copious amounts of up-to-date training data.

This project explores DeepSSETracer, a …

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 …

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 …

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 …

Quantifying Iron Overload Using Mri, Active Contours, And Convolutional Neural Networks, Andrea Sajewski, Stacey Levine

Undergraduate Research and Scholarship Symposium

Iron overload, a complication of repeated blood transfusions, can cause tissue damage and organ failure. The body has no regulatory mechanism to excrete excess iron, so iron overload must be closely monitored to guide therapy and measure treatment response. The concentration of iron in the liver is a reliable marker for total body iron content and is now measured noninvasively with magnetic resonance imaging (MRI). MRI produces a diagnostic image by measuring the signals emitted from the body in the presence of a constant magnetic field and radiofrequency pulses. At each pixel, the signal decay constant, T2*, can be calculated, …

Flow Chamber For Confocal Tracking Of Particles In Bone, Brennan Flannery, Russell Main, Xiaoyu Xu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Interstitial fluid flow in the lacunar-canalicular system (LCS) of bone is recognized as a potential regulator of bone remodeling. Movement of fluid across bone cells called osteocytes regulates gene expression that leads to either bone formation or resorption. Interstitial fluid moves in response to bone loading during daily activity, and bone growth occurs to compensate for these loads, affecting bone shape and strength. While interstitial fluid flow is thoroughly studied using computational models, there is a critical need to study flow in real bone samples with imaging techniques. Flow velocities determined from imaging will be more accurate than computational models …

Tissue Clearing As A Mechanism To Identify Changes In Fibronectin Structure During Breast Cancer Metastasis, Maryam Nuru, Kelsey Hopkins, Luis Solorio

The Summer Undergraduate Research Fellowship (SURF) Symposium

With metastasis accounting for approximately 90% of breast cancer deaths and an alarming number of over 300,000 new breast cancer cases to be diagnosed by the end of 2018, there is growing need to understand the process of breast cancer. Changes in the extracellular matrix (ECM) of the tumor microenvironment play an essential role in this deadly tumor progression. Specifically, the glycoprotein fibronectin (FN), has been identified to be up-regulated in patients with worse clinical outcomes. During tumor progression fibronectin undergoes conformational changes that aid in metastatic dissemination. In order to analyze the dynamic changes in FN expression and evaluate …

Method Validation Of Functional Magnetic Resonance Imaging And Electrophysiological Recording To Investigate Mechanisms Of Vagus Nerve, Christina L. Hendren, Jiayue Cao, Zhongming Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Vagus nerve stimulation (VNS) is used clinically to treat epilepsy and depression, but its mechanism of action is unknown. Useful techniques to study this are functional magnetic resonance imaging (fMRI) and the local field potential (LFP). fMRI relies on oxygen use in the brain to show areas where neurons are active. The LFP is an electrical signal created by neuron action potentials and other current moving across cell membranes. The most information can be gained when the two methods are used simultaneously, however, this is difficult to do. This study seeks to validate the technique of fMRI-LFP as applied to …

P-42 Using The Raspberry Pi For Ecl Reaction Analysis, Jonathan Swerdlow

Honors Scholars & Undergraduate Research Poster Symposium Programs

Using a Raspberry Pi and its camera module, we developed an affordable and easily available system for photographing and analyzing electrochemiluminescent (ECL) reactions. These reactions can be represented as a function of average light intensity over time, allowing for a future program to determine the concentration of certain reactants. Such ECL reactions will be useful in the diagnosis of medical conditions such as cancer without the need for expensive equipment or laboratories. The proposed system will make certain diagnoses easy and available to people across the globe and will likely require only a small blood sample. It will also be …

Dual-Tuned Removable Common-Mode Current Trap For Mri, Angel G. Enriquez, Joseph V. Rispoli

The Summer Undergraduate Research Fellowship (SURF) Symposium

Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) are preferred methods of gathering information from the body due to their non-invasive approach of obtaining a diagnosis. MRI can obtain spatial mappings from a region of interest, while MRS can obtain metabolic information from different elements. Dual-tuned radiofrequency (RF) coils are able to capture signals produced by both hydrogen atoms and a second atom of interest. Unwanted shield currents occur in these scans, which can cause image distortion, while the high energy dissipated can create harmful heat, which can injure the patient. These shield currents, also known as common-mode currents, …

Multi-Color Ultra-High Resolution Imaging, David A. Miller, Michael Mlodzianoski, Sheng Liu, Fang Huang

The Summer Undergraduate Research Fellowship (SURF) Symposium

Fluorescence microscopy, which allows multiple-color imaging, plays an important role in observing structures inside cells with high specificity. The advent of super-resolution fluorescence microscopy, or nanoscopy techniques such as single-molecule switching nanoscopy (SMSN), has extended the application range of fluorescence microscopy beyond the diffraction limit, achieving up to 10-fold improvement in spatial resolution. At the same time, the recent development of expansion microscopy (ExM) allows samples to be physically expanded by 4-fold in the lateral dimensions providing another independent method to resolve structures beyond the diffraction limit. When combined, ExM-SMSN makes it possible to achieve another significant leap in resolution …

Gui For Mri-Compatible Neural Stimulator And Recorder, Soo Han Soon, Nishant Babaria, Ranajay Mandal, Zhongming Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) are useful tools to analyze brain activities given active stimulation. However, the electromagnetic noise from the MRI distorts the brain signal recording and damages the subject with excessive heat generated on the electrodes attached to the skin. MRI-compatible recording and stimulation systems previously developed at LIBI lab were capable of removing the electromagnetic noise during the imaging process. Previously, the hardware systems had required the integrative software that could control both circuits simultaneously and enable users to easily change recording and stimulation parameters. Graphical user interface (GUI) programmed with computer language informed …

A Novel Hybrid Imaging System To Aid In Surgical Decision Making, Lawrence Yip, Madeleine Van De Kleut, Ivan Kosik, Astrid Chamson-Reig, Jeffrey Jl Carson

Western Research Forum

Background:

Breast cancer accounts for 25% of all cancer cases among women. In breast-conserving surgery, a common treatment, the tumour is excised with a healthy tissue margin. However, detection of the margin can be difficult. Current techniques to guide excision are often insufficient, and re-excision can occur up to 25% of the time.

Methods:

Photoacoustic imaging is a hybrid imaging modality that combines the advantages of optical imaging and ultrasound while using safe non-ionizing light. This project involves the development of a novel imaging system with a new scanner design to overcome common limitations and provide images to aid in …

Ex Vivo Bio-Orthogonal Mri Imaging – A Novel Method Proposed For Metastatic Cancer Detection, Tanner Ravsten, William G. Pitt, Neal K. Bangerter, Randy Hartley, Forrest Howell, Jessica Doud

Biomedical Engineering Western Regional Conference

Bio-orthogonal detection of metastatic cancer using MRI, Gd Iron-oxide contrast agents using T1 T2* scans

Mri Field Mapping Using Bssfp Elliptical Signal Model, Joseph Valentine, Meredith Taylor, Steven Whitaker, Michael Hoff, Neal Bangerter

Biomedical Engineering Western Regional Conference

MRI, Field Mapping, bSSFP, ssfp, Elliptical Signal model, ellipse, phase unwrapping

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.

Lipid Detection In Pig Arteries Using Intravascular Photoacoustic Imaging, Jieying Mai, Yingchun Cao, Ayeeshik Kole, Michael Sturek, Ji-Xin Cheng

The Summer Undergraduate Research Fellowship (SURF) Symposium

Heart disease is the leading cause of death in the United States and worldwide. Each year over 370,000 people died from coronary artery disease in America. As the primary form of coronary artery disease, atherosclerosis behaves as lipid-rich plaque development inside an artery wall. Vulnerable plaques are those prone to rupture, which may result in thrombus or even death. Typical hallmarks of a vulnerable plaque include thin fibrous cap, a large lipid-rich necrotic core and inflammatory infiltrate. The identification and accurate detection of these lipid depositions in the arterial wall is crucial in the diagnosis of atherosclerosis. However, none of …

3d Modeling Of Murine Abdominal Aortic Aneurysms: Quantification Of Segmentation And Volumetric Reconstruction, Paula A. Sarmiento, Amelia R. Adelsperger, Craig J. Goergen Ph.D.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal Aortic Aneurysms (AAA) cause 5,900 deaths in the United States each year. Surgical intervention is clinically studied by non-invasive techniques such as computed tomography and magnetic resonance imaging. However, three-dimensional (3D) ultrasound imaging has become an inexpensive alternative and useful tool to characterize aneurysms, allowing for reconstruction of the vessel, quantification of hemodynamics through computational fluid dynamics (CFD) simulation, and possible prediction of aortic expansion and rupture. However, current analysis techniques for these images require the use of multiple software platforms for either modeling or simulation, prompting the need for alternatives to improve data processing. This study monitors the …

Initial Validation Of A Novel Method Of Presurgical Language Localization Through Functional Connectivity (Fcmri), Stephanie M. Noble, Dustin Scheinost, Susan Y. Bookheimer, Patricia Walshaw, R Todd Constable, Christopher F. Benjamin

Yale Day of Data

OBJECTIVE: Neurosurgery is potentially curative in chronic epilepsy but can only be offered to patients if the surgical risk to language is known. Clinical functional magnetic resonance imaging (fMRI) is an ideal, noninvasive method for localizing language cortex yet remains to be validated for this purpose. We have recently presented a novel method for localizing language cortex. Here we present a preliminary evaluation of this method’s validity. We hypothesized language regions identified using this novel method would demonstrate stronger functional connectivity than randomly generated set of proximal networks. METHOD: fMRI data were collected from sixteen temporal lobe patients …

Angiotensin Ii-Induced Hypertension In Apolipoprotein E-Deficient Rats, Sydney N. Gorman, Craig J. Goergen, A Nicole Blaize

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysms (AAAs) are characterized by a weakened vessel wall and a diameter 50% greater than normal. AAA are usually asymptomatic until they are near rupturing, which can be fatal if not treated immediately. Apolipoprotein E-deficient (ApoE) mice are commonly used as a model to study aneurysm growth. Our lab has created a similar model using rats, which are more similar to humans. This study focuses on the analysis of blood pressures collected from ApoE rats for comparison with a known mouse model. Five ApoE rats (1 female, 4 males) received subcutaneous implants of osmotic mini pumps that released …

Changes In Vessel Properties During Early Progression Of Murine Abdominal Aortic Aneurysms From In Vivo Ultrasound, Luis R. Avila Murati, Evan H. Phillips, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysms (AAA) are a common and frequently fatal disease characterized by the weakening and dilation of the aorta. The larger the aneurysm, the higher the chances are of rupturing and life-threatening hemorrhage. The aim of this study is to apply the angiotensin II (AngII) model of AAAs in male apolipoprotein-E-deficient mice (apoE^-/- C57Bl/6J), in order to analyze, quantify, and understand the pathologies and characteristics associated with early AAA development. To date, many studies focusing on the evaluation of AAA characteristics have been performed ex vivo. Therefore, we focused on in vivo assessment, through the use of …

Optimization Of Imaging Parameters To Determine Flow Velocity Using Nanoparticles, Sabrina M. Scalf, Haisheng Yang, Russell P. Main

The Summer Undergraduate Research Fellowship (SURF) Symposium

Microfluidic flow chambers have been developed and used to measure flow at the microscopic level. Nanoparticles can be used to track the fluid flow within the chamber and this allows for accurate velocity measures. Microscope parameters used for experimentation differ across various projects and resources; therefore, there is a need to determine the best combination of settings for the equipment at hand. Once appropriate settings are selected, images of the flow are captured with a confocal microscope and can be analyzed using custom written MATLAB code. A pair cross-correlation function is used to determine where the particles have traveled in …

Three Dimensional Quantification Of Angiotensin Ii-Induced Murine Abdominal Aortic Aneurysms Using High Frequency Ultrasound, Amelia R. Adelsperger, Alexa A. Yrineo, Hilary D. Schroeder, Ashley Nicole Blaize, Katherine E. Wilson, Evan H. Phillips, Frederick W. Damen, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysms (AAAs), a localized dilation of the vessel wall of 50% or more above normal, claims approximately 14,000 U.S. lives yearly due to aortic rupture. This commonly asymptomatic disease can only be treated by endovascular stent grafts or invasive surgery, usually after the AAA diameter reaches 5 cm. Because these treatment methods carry serious risk, stem cell therapy is being explored in order to provide a low risk option for managing smaller AAAs. To determine if stem cell therapy, once administered, could stabilize or reduce AAA growth, baseline 3D ultrasound measurements in a control group were first needed. …

Nonlinear Optical Microscopy Of Murine Abdominal Aortic Aneurysm, Katherine E. Wilson, Alexa A. Yrineo, Amelia J. Adelsperger, Hilary D. Schroeder, Delong Zhang, Jesse Zhang, Chien-Sheng Liao, Frederick W. Damen, Ji-Xin Cheng, Evan H. Phillips, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysm (AAA) is a cardiovascular disease characterized by dilation and weakening of the vessel wall. AAA rupture is responsible for approximately 14,000 deaths annually in the United States [1]. Nonlinear optical (NLO) microscopy presents new possibilities for analyzing AAA tissue samples from murine models. Common NLO techniques are two-photon excitation fluorescence (TPEF), which detects the intrinsic autofluorescent properties of elastin, and second-harmonic generation (SHG), which is specific for collagen fibrils. Elastin and collagen, two major extracellular matrix components, help the aortic wall withstand internal pressure. Murine AAAs were created through 1) subcutaneous continuous systemic infusion of angiotensin II …

In Vivo Flow Measurements Of Murine Renal Arteries And Veins With High Frequency Ultrasound, Amy E. Bogucki, Hilary D. Schroeder, Alexa A. Yrineo, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

The number of glomeruli in the kidneys has been shown to have an effect on the decline in renal function over time (Brenner, Garcia, Anderson 1988). Furthermore, flow in the renal arteries and veins may depend on the number of glomeruli in the kidney. Consistent in vivo measurements of volumetric flow in the renal arteries and veins are difficult to obtain. Thus, the purpose of this study was to develop non-invasive imaging techniques capable of estimating arterial and venous flow to kidneys. A high-frequency small animal ultrasound system was chosen based upon its excellent spatial and temporal resolution when imaging …