Biology subjects

Fogarty, M.

Publications and source records attributed to Fogarty, M..

7 recordsLinked to original sources

bioRxiv2026

Unconstrained naturalistic human brain imaging and decoding with a fully wearable high-density optical system

Understanding how the brain supports complex cognition in real-world environments requires neuroimaging systems that impose minimal constraints on natural behavior. Existing high-fidelity modalities, such as functional magnetic resonance imaging (fMRI), confine participants to the scanner, while wearable alternatives sacrifice spatial resolution or cortical coverage. Here, we developed a fully untethered whole-head optical neuroimaging system that achieves high-fidelity tomographic reconstruction through dense spatial sampling, configurable source multiplexing, and high dynamic range detection. This wearable high-density diffuse optical tomography (WHD-DOT) system achieves 151 dB effective dynamic range and nearly 3000 source-detector measurements, comparable to the highest-performing fiber-based DOT systems, while maintaining wireless, battery-powered mobility. We validate WHD-DOT across three paradigms of increasing ecological complexity, ranging from standard functional localizers to naturalistic movie viewing and live piano performance. Across all paradigms, WHD-DOT produces robust, well-localized encoding, repeatable single-trial responses, and above-chance decoding of stimulus-specific dynamics. Piano performance, which requires continuous bimanual movement and an unconstrained posture, is a rigorous real-world test for a wearable neuroimaging system. By decoding song-segment identity of free piano performance at 71.1% accuracy (chance 12.5%), WHD-DOT shows that brain activity from unconstrained, real-world behavior, previously beyond reach of high-fidelity imaging, is now both measurable and decodable.

neuroscience↗

bioRxiv2025

Visual Semantic Encoding and Identification of Naturalistic Movies via High-Density Diffuse Optical Tomography

Understanding how the brain represents meaning in real-world contexts is essential for both fundamental neuroscience and clinical applications. Brain encoding and decoding models from naturalistic stimuli provide a powerful window into semantic representations. Yet, existing approaches rely on a constrained scanning environment, or on conventional fNIRS, which has been limited to sparse sampling and/or block-design paradigms. Here, we tested whether high-density diffuse optical tomography (HD-DOT), an advanced high-density tomographic optical imaging method, can support semantic encoding and decoding using naturalistic movies. We collected 3.5 hours of naturalistic movie viewing data from six participants using stimuli labeled with 1,708 categories. Encoding models robustly predicted voxel-level responses, yielding single semantic category maps consistent with prior fMRI studies. In complementary decoding analyses, we showed that DOT responses captured sufficient semantic content to identify which clips participants viewed. To assess organization across individuals, we identified a shared low-dimensional semantic space that captures common semantic dimensions. Finally, clustering analyses revealed interpretable higher-order semantic dimensions like social and animate agents, objects vs natural organisms, and textural scenes, consistently mapped across the cortex. These findings demonstrate that DOT can recover distributed, high-dimensional semantic representations from naturalistic movies, bridging fMRI-level semantic mapping with the accessibility of optical imaging.

neuroscience↗

bioRxiv2021

Characterization of Reactive Oxygen Species Signaling changes in a cell culture model of skeletal muscle ageing, and its application to screening pharmacokinetically-relevant exposures of dietary polyphenols for bioactivity.

Age-related frailty is a significant health and social care burden, however treatment options are limited. There is currently a lack of suitable cell culture model for screening large numbers of test compounds to identifying those which can potentially promote healthy skeletal muscle function. This paper describes the characterization of reactive oxygen and nitrogen species (RONS) signalling changes in young and aged myoblasts and myotubes using the C2C12 cell line, and the application of aged myoblast and myotube cultures to assess the effect of dietary polyphenols on RONS signalling. Aged myoblasts and myotubes were observed to have significantly increased reactive oxygen species levels (p<0.01 and p<0.001 respectively), increases in nitric oxide levels (p<0.05 for myoblasts and myotubes), and lipid peroxidation markers (p<0.05 for myoblasts and myotubes). A panel of nine polyphenols were assessed in aged myoblasts and myotubes using concentrations and incubation times consistent with known pharmacokinetic parameters for these compounds. Of these, although several polyphenols were seen to reduce single markers of RONS signalling, only kaempferol and resveratrol consistently reduced multiple markers of RONS signalling with statistical significance in both cell models. Modulation of cellular enzymatic antioxidant activities (superoxide and catalase) was assessed as a possible mechanism of action for these polyphenols, and although both superoxide and catalase activities were significantly reduced in aged (versus young) myotubes (p<0.01 and p<0.05 respectively), no effect of polyphenol treatment on these enzyme activities were observed. Overall, this research has shown the utility of the C2C12 model, as both myoblasts and myotubes, as a suitable cell model for screening compounds for modulating RONS signalling in aged muscle, and that resveratrol and kaempferol (using pharmacokinetically-informed exposures) can modulate RONS signalling in skeletal muscle cells after an acute exposure.

pharmacology and toxicology↗

bioRxiv2021

A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex

Cells are not uniformly distributed in the human cerebral cortex. Rather, they are arranged in a regional and laminar fashion that span a range of scales. Here we demonstrate an innovative imaging and analysis pipeline to construct a reliable cell census across the human cerebral cortex. Magnetic resonance imaging (MRI) is used to establish a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with both traditional immunohistochemistry, to provide a stereological gold-standard, and with a custom-made inverted confocal light-sheet fluorescence microscope (LSFM) for 3D imaging at cellular resolution. Finally, mesoscale optical coherence tomography (OCT) enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system.

neuroscience↗

bioRxiv2021

Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution

The surface of the human cerebellar cortex is much more tightly folded than the cerebral cortex. Volumetric analysis of cerebellar morphometry in magnetic resonance imaging studies suffers from insufficient resolution, and therefore has had limited impact on disease assessment. Automatic serial polarization-sensitive optical coherence tomography (as-PSOCT) is an emerging technique that offers the advantages of microscopic resolution and volumetric reconstruction of large-scale samples. In this study, we reconstructed multiple cubic centimeters of ex vivo human cerebellum tissue using as-PSOCT. The morphometric and optical properties of the cerebellar cortex across five subjects were quantified. While the molecular and granular layers exhibited similar mean thickness in the five subjects, the thickness varied greatly between the crown of the folium and the depth of the fissure in the granular layer within subjects. Layer-specific optical property remained homogenous within individual subjects but showed higher cross-subject variability than layer thickness. High-resolution volumetric morphometry and optical property maps of human cerebellar cortex revealed by as-PSOCT have great potential to advance our understanding of cerebellar function and diseases. HighlightsWe reconstructed cubic centimeters of human cerebellar samples at micrometer resolution in five subjects. Thickness of the granular layer varies greatly between the crowns and depths of cerebellar fissures. Cross-subject variability is higher in optical property than cortical morphology. Our results suggest homogenous cell and myelin density in the cortical layers of human cerebellum despite the highly convoluted folding patterns.

neuroscience↗

bioRxiv2020

A novel algorithm to optimize generalized gamma distributed multiplicative noise with implications on speckle removal from OCT images

Optical coherence tomography (OCT) images are corrupted by multiplicative generalized gamma distributed speckle noise that significantly degrades the contrast to noise ratio (CNR) of microstructural compartments in biological applications. This work proposes a novel algorithm to optimize the negative log likelihood of the spatial distribution of speckle. Specifically, the proposed method formulates a penalized negative log likelihood (P-NLL) cost function and proposes a majorize-minimize-based optimization method that removes speckle from OCT images. The optimization reduces to solving an iterative gradient descent problem. We demonstrate the usefulness of the proposed method by removing speckle in OCT images of uniform phantoms with varying scattering coefficients and human brain tissue.

neuroscience↗

bioRxiv2018

Quantification of Structural Brain Connectivityvia a Conductance Model

Connectomics has proved promising in quantifying and understanding the effects of development, aging and an array of diseases on the brain. In this work, we propose a new structural connectivity measure that allows us to incorporate direct brain connections as well as indirect ones that would not be otherwise accounted for by standard techniques and that may be key for the better understanding of function from structure. From our experiments on the Human Connectome Project dataset, we find that our measure of structural connectivity better correlates with functional connectivity than streamline tractography does, meaning that it provides new structural information related to function. Through additional experiments on the ADNI-2 dataset, we demonstrate the ability of this new measure to better discriminate different stages of Alzheimers disease. Our findings suggest that this measure is useful in the study of the normal brain function and structure, and for quantifying the effects of disease on brain structure.

neuroscience↗