Bioimaging and Biomedical Optics Commons^™

In Vivo Vascular Imaging With Photoacoustic Microscopy, Hsun-Chia Hsu

Engineering and Applied Science Theses & Dissertations

Photoacoustic (PA) tomography (PAT) has received extensive attention in the last decade for its capability to provide label-free structural and functional imaging in biological tissue with highly scalable spatial resolution and penetration depth. Compared to modern optical modalities, PAT offers speckle-free images and is more sensitive to optical absorption contrast (with 100% relative sensitivity). By implementing different regimes of optical wavelength, PAT can be used to image diverse light-absorbing biomolecules. For example, hemoglobin is of particular interest in the visible wavelength regime owing to its dominant absorption, and lipids and water are more commonly studied in the near-infrared regime.

In ...

Sbaigs18.Pdf, Sarfaraz Niaz Ali Baig

Sarfaraz Baig

No abstract provided.

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 ...

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 ...

Fluorescent Nanodiamonds: Past, Present, And Future, Masfer H. Alkahtani, Fahad Alghannam, Linkun Jiang, Abdulrahman Almethen, Arfaan A. Rampersaud, Robert Brick, Carmen L. Gomes, Marlan O. Scully, Philip R. Hemmer

Mechanical Engineering Publications

Multi-color fluorescent nanodiamonds (FNDs) containing a variety of color centers are promising fluorescent markers for biomedical applications. Compared to colloidal quantum dots and organic dyes, FNDs have the advantage of lower toxicity, exceptional chemical stability, and better photostability. They can be surface functionalized by techniques similar to those used for other nanoparticles. They exhibit a variety of emission wavelengths from visible to near infrared, with narrow or broad bandwidths depending on their color centers. In addition, some color centers can detect changes in magnetic fields, electric fields, and temperature. In this article review, we will discuss the current trends in ...

Developing Droplet Based 3d Cell Culture Methods To Enable Investigations Of The Chemical Tumor Microenvironment, Jacqueline A. De Lora

Biomedical Sciences ETDs

Adaptation of cancer cells to changes in the biochemical microenvironment in an expanding tumor mass is a crucial aspect of malignant progression, tumor metabolism, and drug efficacy. In vitro, it is challenging to mimic the evolution of biochemical gradients and the cellular heterogeneity that characterizes cancer tissues found in vivo. It is well accepted that more realistic and controllable in vitro 3D model systems are required to improve the overall cancer research paradigm and thus improve on the translation of results, but multidisciplinary approaches are needed for these advances. This work develops such approaches and demonstrates that new droplet-based cell-encapsulation ...

Super‐Resolution Imaging Of Amyloid Structures Over Extended Times By Using Transient Binding Of Single Thioflavin T Molecules, Kevin Spehar, Tianben Ding, Yuanzi Sun, Niraja Kedia, Jin Lu, George R. Nahass, Matthew D. Lew, Jan Bieschke

Electrical & Systems Engineering Publications and Presentations

Oligomeric amyloid structures are crucial therapeutic targets in Alzheimer's and other amyloid diseases. However, these oligomers are too small to be resolved by standard light microscopy. We have developed a simple and versatile tool to image amyloid structures by using thioflavin T without the need for covalent labeling or immunostaining. The dynamic binding of single dye molecules generates photon bursts that are used for fluorophore localization on a nanometer scale. Thus, photobleaching cannot degrade image quality, allowing for extended observation times. Super‐resolution transient amyloid binding microscopy promises to directly image native amyloid by using standard probes and record ...

New Algorithms For Compressed Sensing Of Mri: Wtwts, Dwts, Wdwts, Srivarna Settisara Janney

Master of Science in Computer Science Theses

Magnetic resonance imaging (MRI) is one of the most accurate imaging techniques that can be used to detect several diseases, where other imaging methodologies fail. MRI data takes a longer time to capture. This is a pain taking process for the patients to remain still while the data is being captured. This is also hard for the doctor as well because if the images are not captured correctly then it will lead to wrong diagnoses of illness that might put the patients lives in danger. Since long scanning time is one of most serious drawback of the MRI modality, reducing ...

Fluorescence Guided Tumor Imaging: Foundations For Translational Applications, Jessica P. Miller

Engineering and Applied Science Theses & Dissertations

Optical imaging for medical applications is a growing field, and it has the potential to improve medical outcomes through its increased sensitivity and specificity, lower cost, and small instrumentation footprint as compared to other imaging modalities. The method holds great promise, ranging from direct clinical use as a diagnostic or therapeutic tool, to pre-clinical applications for increased understanding of pathology. Additionally, optical imaging uses non-ionizing radiation which is safe for patients, so it can be used for repeated imaging procedures to monitor therapy, guide treatment, and provide real-time feedback. The versatile features of fluorescence-based optical imaging make it suited for ...

Developing Photoacoustic Tomography Devices For Translational Medicine And Basic Science Research, Tsz Wai Wong

Engineering and Applied Science Theses & Dissertations

Photoacoustic (PA) tomography (PAT) provides volumetric images of biological tissue with scalable spatial resolutions and imaging depths, while preserving the same imaging contrast—optical absorption. Taking the advantage of its 100% sensitivity to optical absorption, PAT has been widely applied in structural, functional, and molecular imaging, with both endogenous and exogenous contrasts, at superior depths than pure optical methods. Intuitively, hemoglobin has been the most commonly studied biomolecule in PAT due to its strong absorption in the visible wavelength regime.

One of the main focuses of this dissertation is to investigate an underexplored wavelength regime—ultraviolet (UV), which allows us ...

Modeling Eeg And Tdcs In Scirun Software Packages, Aiden Keene, Aiden Thomas Keene

Senior Honors Projects

Never before has there been a greater emphasis on improving the shortcomings of treating mental health conditions. Our generation has more knowledge about technological practices with the potential to monitor and treat mental health symptoms than that of any generation before us. A breakthrough in this field made by CREmedical is called Tripolar Concentric Ring Electrodes (TCRE’s), which can measure signals from the brain more accurately than conventional electrodes. At CREmedical, TCREs are being used to study differences in electrical activity in the brain so as to identify abnormalities, and monitor responses to stimulation therapies. This semester I had ...

Extraction And Analysis Of Vector Flow Imaging Data In A Pediatric Population, Bailey Stinnett

Biomedical Engineering Undergraduate Honors Theses

Vector flow imaging (VFI) is a new ultrasound technology that provides real time, angle-independent visualization of flow velocities in the heart and great vessels. Thus far, VFI has been used for superficial applications due to the limited penetration depth of available transducer probes; however, this depth in smaller pediatric patients enables adequate aortic views. In this project, VFI was used to study pediatric aortic stenosis (PAS)—a congenital heart defect that results in the narrowing of the aorta and/or aortic valve. The decision to refer PAS patients for surgical or catheter-based intervention is initially based on Doppler ultrasound. VFI ...

Optimization Of Microfluidic Chip Fabrication Via Femtosecond Laser Ablation, Kenneth Aycock

Senior Theses

Microfluidic devices have become staple tools in biomedical research and have a promising future as low cost, point-of-care (POC) diagnostic devices. Despite the advancements in microfluidic device technology, the manipulation and fabrication of these systems can be tedious and expensive. Repeatable techniques in which computer-aided designs are translated into microfluidic systems in a matter of minutes are highly desirable both for researchers and manufacturers. Laser ablation of tape substrates has shown promise in producing cost-effective, rapidly manipulable devices, but the work done thus far has utilized continuous wave lasers that perform suboptimally due to the relatively short wavelengths used and ...

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin ...

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 ...

Automatic Brain Tumor Segmentation By Deep Convolutional Networks And Graph Cuts, Zhenyi Wang

Electronic Thesis and Dissertation Repository

Brain tumor segmentation in magnetic resonance imaging (MRI) is helpful for diagnostics, growth rate prediction, tumor volume measurements and treatment planning of brain tumor. The difficulties for brain tumor segmentation are mainly due to high variation of brain tumors in size, shape, regularity, location, and their heterogeneous appearance (e.g., contrast, intensity and texture variation for different tumors). Due to recent advances in deep convolutional neural networks for semantic image segmentation, automatic brain tumor segmentation is a promising research direction.

This thesis investigates automatic brain tumor segmentation by combining deep convolutional neural network with regularization by a graph cut. We ...

Early Emerging Pathogen Detection, Mackenzie Wangenstein

Undergraduate Research & Mentoring Program

A supervised learning technique was employed to identify emerging pathogen species. Portland State University has partnered with the University of New Mexico to take encodings of unknown pathogen molecular structures to determine emerging species.

An Area Based Fan Beam Projection Model, Richard E. Steele, Jiehua Zhu

University Honors Program Theses

Area based projection models for computed tomography mitigate raw data errors by treating X-Rays as beams, whereas traditional line based projection models treat an X-Ray like a line, thus generating significant error. In an existing area based fan beam projection model, a rotation matrix, Q, simulates the rotation of the emitter detector pair to reduce computational load, but this introduces approximations by using an approximated rotation matrix. We eliminate approximations by deriving an exact formula for the entries of Q. Using a rotation of axes and by considering the neighboring cells' contributions to the area, the result has formulations for ...

Multimodal Noncontact Diffuse Optical Reflectance Imaging Of Blood Flow And Fluorescence Contrasts, Daniel Irwin

Theses and Dissertations--Biomedical Engineering

In this study we design a succession of three increasingly adept diffuse optical devices towards the simultaneous 3D imaging of blood flow and fluorescence contrasts in relatively deep tissues. These metrics together can provide future insights into the relationship between blood flow distributions and fluorescent or fluorescently tagged agents. A noncontact diffuse correlation tomography (ncDCT) device was firstly developed to recover flow by mechanically scanning a lens-based apparatus across the sample. The novel flow reconstruction technique and measuring boundary curvature were advanced in tandem. The establishment of CCD camera detection with a high sampling density and flow recovery by speckle ...