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Automated Beam Stitching and Segmentation Procedure for Space Division Multiplexing Optical Coherence Tomography Angiography
Full text linkOptical Coherence Tomography Angiography (OCTA) has revolutionized ophthalmic imaging and its capability to produce high-resolution 3D maps of the retinal microvasculature is instrumental in diagnosing retinovascular diseases such as diabetic retinopathy and age-related macular degeneration; However, the existing OCTA devices often suffer from slow acquisition speed limiting the field-of-view (FOV) in the clinic. Space Division Multiplexing OCTA (SDM-OCTA) address these limitations by acquiring multiple beams simultaneously, achieving manyfold faster acquisition speeds than single beam OCTA systems. But as each beam contains only part of the image, SDM-OCTA requires additional processing steps to produce coherent wide-field images. Though manual stitching and segmentation was previously used, it is time-consuming and prone to human error. The need for an automated solution is clear, especially in clinical settings where rapid and accurate imaging is essential for timely diagnosis and treatment of retinal diseases. Stitching and segmenting the multiple beams is a non-trivial task due to the misalignment that can occur during acquisition, and the large data sizes making it computationally expensive to process using traditional segmentation methods. This thesis presents an automated beam stitching and segmentation procedure for SDM-OCTA imaging, which offers benefits in the clinical setting by producing wide-field projections of retinal microvasculature quickly and accurately. This procedure utilizes a combination of custom graph-theoretic algorithms and deep learning techniques to integrate beam cropping, registration, stitching, flattening, and segmentation steps. Written in Rust, the implementation is designed to be fast and efficient, allowing for the processing of large SDM-OCTA volumes in a few seconds. We evaluate the performance of our method using public and private datasets, and demonstrate its utility in clinical settings
Computational Dead Time Correction in Fluorescence Lifetime Imaging Microscopy (FLIM)
No full textFluorescence Lifetime Imaging Microscopy (FLIM) is a crucial tool in biomedical research. It can visualize and measure molecular interactions and cellular processes by analyzing the fluorescence decay of molecules in biological samples. Unlike traditional imaging methods based on fluorescence intensity, FLIM uses fluorescence lifetime - the time delay between excitation and emission in the fluorescence process - to provide detailed information about the biochemical environment and molecular activity.
In photon-counting systems, dead time is the short period after detecting a photon when the detection system cannot record new photons. The effect of dead time on the measured fluorescence intensity and lifetime is highly dependent on the photon rate (the number of incident photons per laser period). Dead time causes photon counts to be underestimated, especially at high photon rates, leading to errors in both fluorescence intensity and lifetime measurements. To address this issue, the Cross-Cycle computational correction method, inspired by techniques from Light Detection and Ranging (LiDAR) systems, has been developed to correct for dead time effects. The Cross-Cycle method statistically models the loss of photons within and across laser cycles, estimates the probability of photon detection, and reconstructs fluorescence intensity and lifetime. Here, we demonstrate that the Cross-Cycle method improves the accuracy of fluorescence intensity and lifetime in simulated data.
This correction allows more accurate fluorescence intensity and lifetime estimation at high photon rates, enabling faster imaging and more reliable results in FLIM
Counter-Environments and the Myth of Progress: A Practice of Participatory Disruption
No full textThis thesis explores the potential of archival and participatory practices to illuminate and disrupt societal barriers to genuine human connection, particularly those arising from productivity, routine, and capitalist notions of progress. Rooted in an extensive personal archive—over 70,000 photographs, hundreds of journal entries, and fragmented sensory experiences—my artistic process involves meticulously collecting, rearranging, and interpreting patterns within everyday consumption. Through iterative methods akin to artists such as Wolfgang Tillmans, I juxtapose images, texts, and found materials, embedding personal narratives and subjective insights to uncover deeper connections and overlooked truths.
Central to my practice is the critique of contemporary societal norms, inspired by philosophers like Brian O’Connor, who questions the destructive impacts of relentless productivity and advancement. In response, my work intentionally creates counter-environments that encourage idleness, collective play, and reflection. Projects like a large-scale Capture the Flag event at Washington University and communal installations challenge institutional expectations by fostering spaces that prioritize presence and interpersonal engagement over efficiency and output.
By employing humor, myth-making, and participatory disruptions, my practice not only highlights societal hindrances to connection but also proposes alternative ways of being together. The result is a transformative dialogue that resonates beyond the immediate experience, persisting through collective memory and storytelling, and ultimately redefining our understanding of communal interaction and resistance
Lines of Thought: The Cartoon as a Phenomenological Object and a Philosophical Tool
Full text linkCartooning’s greatest strength is its simplicity. This essay argues that the cartoon’s inherent modesty and accessibility are central to its philosophical utility, and that its spare visual language conveys more than meets the eye. Drawing on phenomenology, it considers cartooning as a process grounded in the body, and it investigates the bodily encounter between the viewer and the cartoon. Through an analysis of cartooning work by Saul Steinberg, R.O. Blechman, and Liana Finck - a “family of cartoonists” - it demonstrates how a line-drawn, representational cartooning language can transform the act of looking into a participatory experience that interrogates issues of self, meaning, and mortality. Ultimately, it positions cartooning as a uniquely embodied form of thinking and communicating with a significant and often overlooked role in American visual culture
What is Lost When Time is Saved: Drawing in Collaboration with the Urban Periphery
Full text linkI pay attention to the overlooked spaces where land and industry meet, prompting me to wonder what can be gleaned in the oily and cracked urban periphery. With a focus on my hometown St. Louis, this industrial city is my subject matter. And so, I draw in a neighborhood bisected by a highway. I animate with sand near the river confluence on land preserved after a historic flood. I make my own bricks in this Brick City, setting up in locations of former terra cotta clay mines. I sit in the tension of what author Michael Martone calls the “midwestern paradox,” in which “I [feel], simultaneously, my isolation on one of the margins of the world and my connection to what is essential in the scheme of all things.”
In this paper, I use four recent artworks to describe my relationship with drawing, time, and site. I expand my methods for image-making by using sand, clay, and metal as drawing materials. Committed to working observationally, I use drawing to slow down and observe what would normally flash through my car window. I work on site to be in collaboration with the landscape and meet passersby who share their stories. I emphasize time’s relationship to the industrialized landscape by inefficiently rebuilding common forms, producing sequenced analog works and making display systems which suggest movement. By emphasizing time in the work, I ask what is lost when efficiency is prioritized
Delivering Financial Guidance: Institutional Assessment and Directions for Inclusion
Full text linkFor low-income and minoritized groups, sound guidance on financial matters has become increasingly vital. The financial sector has reached deeper into daily life, contributing to racial and economic inequality. Institutions must change, and households must be more fully included. However, little research has assessed the institutional availability and quality of formal financial guidance. This paper examines key systems delivering financial guidance to such households. With the concept of financial capability as a theoretical starting point, the paper uses six constructs to assess delivery capacity: inclusivity, appropriateness, comprehensiveness, safety and reliability, scalability, and equity. The analysis identifies gaps in outreach and service, and opportunities for strengthening financial guidance especially to financially vulnerable populations. Critically, the authors highlight the role of the social welfare sector and social workers in improving financial well-being, along with future directions for research
Investigating the Dietary, Demographic, and Environmental Correlates of Gut Microbial Community Composition in Emperor (Tamarinus imperator) and Saddleback (Leontocebus weddelli) Tamarins
No full textUnderstanding how dietary and microbial adaptations shape species coexistence is fundamental to ecological and evolutionary research. This dissertation investigates the diet and gut microbiome composition of two sympatric callitrichids, emperor tamarins (Tamarinus imperator) and saddleback tamarins (Leontocebus weddelli), to understand the environmental and dietary drivers of gut microbiome composition, assess mechanisms of niche differentiation and the potential for microbial-mediated resource partitioning. Chapter two investigates the dietary ecology of T. imperator and L. weddelli using fecal DNA metabarcoding to identify the plant, arthropod, and vertebrate taxa in their diets. A key challenge in metabarcoding studies is the reliance on comprehensive barcode reference libraries, which remain incomplete for many Neotropical species. To address this, we generated novel DNA barcode sequences for plant species commonly consumed by primates, improving taxonomic resolution and expanding reference datasets. Using a combination of newly generated DNA barcodes and published reference data, comprehensively characterized the omnivorous diet of these two primate species. This multi-marker approach identified 264 plant genera, 34 arthropod families, and several frog taxa, revealing both substantial dietary overlap and notable interspecific differences. Although both species relied heavily on Cecropia, particularly in the dry season, L. weddelli exhibited a broader dietary range, consuming a greater diversity of plant genera than T. imperator. Seasonal variation in the diet of L. weddelli also showed significant shifts in dominant plant taxa from Cecropia and Philodendron during wet season to Annona, Inga, and Tapirira during the dry season. Arthropod consumption included both actively hunted prey such as Geometridae (geometer moths) and Staphylinidae (rove beetles), as well as small-bodied prey likely consumed incidentally, such as Diptera (flies) and Aphidae (aphids). Vertebrate DNA, primarily from amphibians, was detected in a small subset of samples, suggesting opportunistic predation. These findings highlight the utility of fecal metabarcoding in clarifying dietary diversity and identifying cryptic food sources that are often overlooked in observational studies. In chapter three, we analyzed the gut microbiome composition and its relationship to dietary intake and habitat use. Firmicutes dominated the gut microbiota of both species, indicating a strong reliance on microbes for carbohydrate metabolism. We found that despite their overlapping home ranges, L. weddelli and T. imperator exhibit species-specific differences in their gut microbial communities, however species identity only accounted for a small proportion of microbiome variation (3.37%). Microbial diversity varied across primary, secondary, flooded, and bamboo forests, and home range overlap significantly influenced microbiome similarity between individuals, even when controlling for species identity. Notably, tamarins in secondary forests exhibited increased abundances of Helicobacter, Mycoplasma, and Streptococcus, taxa associated with gastrointestinal dysbiosis in both humans and non-human primates. While previous research indicated that T. imperator is highly adapted to disturbed habitats, our findings suggest that this adaptability may come at a physiological cost, with potential implications for long-term health and survival in fragmented landscapes. We found significant associations between dietary taxa and microbes, indicating that host microbiomes are enriched with taxa that may facilitate the metabolism of specific dietary substrates, or may be transmitted from specific dietary items. These findings highlight the role of gut microbiota in facilitating dietary flexibility, which may be crucial for species persistence in dynamic and disturbed environments, ultimately reducing direct competition and promoting coexistence. In chapter four, demographic factors such as age, sex, and reproductive status were examined as drivers of gut microbiome variation within each species. We observed varying trends between the two species. Juveniles exhibited distinct microbial communities from adults in both species. In L. weddelli, non-breeding females harbored microbial communities enriched with taxa associated with lactate metabolism, while reproductive females had microbiomes enriched with taxa associated with short-chain fatty acid (SCFA) production. In T. imperator, non-breeding individuals had increased Escherichia abundances. Additionally, social group membership emerged as a key determinant of microbiome composition, with network analyses also showing that juveniles shared more microbial taxa with primary breeding males, reinforcing the role of alloparental care in horizontal microbial transmission through close social interaction, such as infant carrying, in these species. Together, these findings demonstrate that dietary specialization, environmental exposure, and social structure shape gut microbiome composition in T. imperator and L. weddelli, reinforcing microbial-mediated niche differentiation. This research underscores the gut microbiome’s role in facilitating dietary adaptability and species coexistence in complex ecosystems. Future work incorporating functional metagenomics could provide deeper insights into the evolutionary and ecological consequences of microbiome variation in wild primates
The Gene Regulatory Landscape of Proximal Tubule Sub-populations in Kidney Disease
No full textChronic kidney disease exacts an enormous and inequitable toll on the health of the population. Improvements to the existing therapeutic armamentarium are critically needed. Single cell sequencing is a powerful research technique that has yielded exciting advancements in the understanding of kidney physiology and disease. In this dissertation, I review how single cell sequencing has facilitated the use of kidney organoid systems in modeling kidney diseases, revealed key disease-associated cell types and states, and enabled mechanistic annotation of kidney disease-associated genetic variants. I focus on a profibrotic, proinflammatory proximal tubule state that is implicated in maladaptive repair following acute kidney injury and may promote fibrotic processes in chronic kidney disease. I hypothesize that changes in gene regulatory mechanisms drive the formation of this distinct cell state and that single cell multiomic sequencing, in which simultaneous gene expression and chromatin accessibility profiles are generated for each individual cell, offers an unprecedented opportunity to computationally predict the involved gene regulatory networks. I explore how to apply a regularized regression approach to a single cell multiomic dataset generated from human adult kidney samples to predict cell type-specific cis-regulatory elements and transcription factors for all major kidney cell types. Applying this model to study the formation of the maladaptive, disease-associated proximal tubule cell state identifies key cis-regulatory elements and transcription factors predicted to regulate the healthy-maladaptive proximal tubule transition. I show that gene regulatory networks driving maladaptive proximal tubule gene expression are strongly enriched for chronic kidney disease heritability, implicating the cell state in disease pathogenesis. Transcription factors predicted to promote or inhibit the formation of the maladaptive proximal tubule state include novel therapeutic candidates, such as NFAT5, and previously implicated regulators, including ESRRG and PPARA. I validate the model predictions through a combination of computational and experimental approaches. I also detail a computational framework to analyze a single cell multiome dataset of kidney organoid differentiation, characterizing maturation and computationally predicting developmentally important transcription factors. This dissertation concludes with a discussion of future directions in modeling gene regulation with single cell datasets and possible applications to studying mechanisms of disease
Computational Dissection of Innate Immune Cell States: Tissue-Driven Heterogeneity Across Human Development
No full textThis dissertation investigates the diversity and function of dendritic cells (DCs) and innate lymphoid cells (ILCs) across different human tissues and developmental stages. Using single-cell RNA sequencing and other high-dimensional computational immunology techniques, we identified a novel subset of an antigen-presenting cell expressing the transcription factor RORγt, characterized tissue-specific states of plasmacytoid DCs in children and adults, and uncovered a spectrum of group 1 ILC subtypes. Key findings include the discovery of human RORγt+ DC-like cells with proliferative potential, age- and tissue-dependent dynamics of plasmacytoid DC function and development, and the identification of tissue-imprinted NK cells phenotypically resembling ILC1s. This research provides critical insights into the heterogeneity and plasticity of innate immune cell populations, with implications for understanding immune homeostasis, inflammation, and potential therapeutic targets in autoimmune diseases and cancer
Non-Violent Mobilization in Violent Conflict: Explaining Civilian Assistance to Armed Groups
No full textDespite the prevalent notion that armed groups must win the “hearts and minds” of civil- ians, there has been insufficient systematic investigation into the determinants of civilian willingness to assist armed groups and such support’s effects on the conflict. This disser- tation rigorously analyzes the mechanisms driving civilians to provide material, logistical, medical, and financial support to state forces, and assesses how this assistance can mitigate the duration of violent episodes. To offer a comprehensive examination of civilian wartime assistance, and conceptualize civilians as pivotal actors in conflict scenarios, I develop a series of papers that employ both quantitative and qualitative methodologies to assess the underly- ing motivations and consequent behaviors of civilians during armed conflicts. Together, my dissertation advances our understanding of the microdynamics of conflict by addressing three key questions in the literature: 1) why civilians participate in high-risk activities during war, 2) how violence can unintentionally result in more resilient communities, and 3) why armed groups prioritize civilian support. My research proposes that civilians’ emotional responses to violence play a critical role in their decisions to provide assistance, and thereby progresses our burgeoning understanding of the intersection between political psychology and conflict dynamics