Biology subjects

Boas, D. A.

Publications and source records attributed to Boas, D. A..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Measuring human cerebral blood flow and brain function with fiber-based speckle contrast optical spectroscopy system

Cerebral blood flow (CBF) is an important indicator of brain health and function. Diffuse correlation spectroscopy (DCS) is an optical technique that enables non-invasive and continuous bedside monitoring of human CBF. However, traditional DCS consisting of a few channels has relatively low signal-to-noise ratio (SNR), preventing measurements at long source detector separations (SDS) with increased sensitivity to cerebral rather than extracerebral blood flow. Here we developed a fiber-based speckle contrast optical spectroscopy (SCOS) system and the corresponding data analysis pipeline to measure CBF variations. We show that SCOS outperforms traditional DCS by more than an order of magnitude in SNR with comparable financial cost. We also demonstrated human brain function measurements during a cognitive task at an SDS of 33 mm. This technology will establish the foundation for devices that use spatial speckle statistics to non-invasively monitor human CBF, leading to a new functional neuroimaging approach for cognitive neuroscience.

bioengineering↗

bioRxiv2022

High Throughput Detection of Capillary Stalling Events with Bessel Beam Two-Photon Microscopy

Disruptions in capillary flow have the potential to drive pathology across numerous diseases. But our understanding of the temporal and spatial dynamics of these events are hindered by slow volumetric imaging rates and the reliance on laborious manual analysis to process data. To address the challenges of increasing volumetric imaging speed, we use a custom-built Bessel beam two-photon microscope for efficient volumetric imaging of the capillary network. We demonstrate its ability to continuously monitor roughly 200 capillaries for capillary flow stoppages (i.e. stalling events) at a frame rate of approximately 0.5 Hz and develop a semi-automated correlation-based approach for identifying these stalling events. We applied our system and algorithm in a photothrombotic model of stroke and show elevated levels of stalling 1-week post-stroke in regions both within and outside of the stroke region, demonstrating that stalling may have impacts on stroke recovery that extend past the acute stage.

neuroscience↗

bioRxiv2022

High-throughput deep tissue two-photon microscopy at kilohertz frame rates

Strategies to image biological phenomena at millisecond time scales are generally technically challenging and suffer from compromises between imaging field-of-view, depth penetration and excitation efficiency in thick tissue. We present a simple and cost-effective solution that enables a conventional video-rate two-photon microscope (2PM) to perform 2D scanning at kilohertz frame rates, while preserving all the benefits of standard 2PM, which we demonstrate by imaging neurovascular dynamics in mouse brains.

bioengineering↗

bioRxiv2022

Measuring Capillary Flow Dynamics using Interlaced Two-Photon Volumetric Scanning

Two photon microscopy and optical coherence tomography (OCT) are two standard methods for measuring flow speeds of red blood cells in microvessels, particularly in animal models. However, traditional two photon microscopy lacks the depth of field to adequately capture the full volumetric complexity of the cerebral microvasculature and OCT lacks the specificity offered by fluorescent labeling. In addition, the traditional raster scanning technique utilized in both modalities requires a balance of image frame rate and field of view, which severely limits the study of RBC velocities in the microvascular network. Here, we overcome this by using a custom two photon system with an axicon based Bessel beam to obtain volumetric images of the microvascular network with fluorescent specificity. We combine this with a novel scan pattern that generates pairs of frames with short time delay sufficient for tracking red blood cell flow in capillaries. We track flow speed in 10 or more capillaries simultaneously at 1 Hz in a 237 m x 237m x 120 m volume and quantify both spatial and temporal variability in speed. We also demonstrate the ability to track flow speed changes around stalls in capillary flow.

bioengineering↗

bioRxiv2022

Decoding Attended Spatial Location during Complex Scene Analysis with fNIRS.

When analyzing complex scenes, humans often focus their attention on an object at a particular spatial location. The ability to decode the attended spatial location would facilitate brain computer interfaces for complex scene analysis. Here, we investigated functional near-infrared spectroscopys (fNIRS) capability to decode audio-visual spatial attention in the presence of competing stimuli from multiple locations. We targeted dorsal frontoparietal network including frontal eye field (FEF) and intra-parietal sulcus (IPS) as well as superior temporal gyrus/planum temporal (STG/PT). They all were shown in previous functional magnetic resonance imaging (fMRI) studies to be activated by auditory, visual, or audio-visual spatial tasks. We found that fNIRS provides robust decoding of attended spatial locations for most participants and correlates with behavioral performance. Moreover, we found that FEF makes a large contribution to decoding performance. Surprisingly, the performance was significantly above chance level 1s after cue onset, which is well before the peak of the fNIRS response. Our results demonstrate that fNIRS is a promising platform for a compact, wearable technology that could be applied to decode attended spatial location and reveal contributions of specific brain regions during complex scene analysis.

bioengineering↗

bioRxiv2022

Microcirculatory dysfunction associates with neurovascular uncoupling in peri-ischemic brain regions after ischemic stroke

BackgroundDespite recanalization after ischemic stroke, neurovascular coupling, i.e., the local hyperaemic response to neuronal activity, is impaired in peri-ischemic brain regions. Reduced neurovascular coupling may contribute to neurological deterioration over time. The mechanism underlying dysfunctional neurovascular coupling following stroke is largely unknown. MethodsMice implanted with chronic cranial windows were trained for awake head-fixation prior to experiments. One hour occlusion of the anterior middle cerebral artery branch was induced using single vessel photothrombosis. Cerebral perfusion and neurovascular coupling were assessed by optical coherence tomography and laser speckle contrast imaging. Capillaries and pericytes were studied in perfusion-fixed tissue by labelling lectin and platelet-derived growth factor receptor {beta}. ResultsArterial occlusion induced on average 11 spreading depressions over one hour associated with substantially reduced blood flow in the peri-ischemic cortex. Approximately half of the capillaries in the peri-ischemic area were no longer perfused 3 and 24 hours after reperfusion, which was associated with constriction of an equivalent proportion of peri-ischemic capillary pericytes. The capillaries in the peri-ischemic cortex that remained perfused showed increased prevalence of dynamic flow stalling. Whisker stimulation led to reduced neurovascular coupling responses in the sensory cortex corresponding to the peri-ischemic region 3 and 24 hours after reperfusion. ConclusionArterial occlusion led to constriction of pericytes in the peri-ischemic cortex associated with long-lasting microcirculatory failure. This reduced capillary capacity may, at least in part, underlie impaired neurovascular coupling in peri-ischemic brain regions after stroke and reperfusion.

physiology↗

bioRxiv2022

Targeted photothrombotic stroke leads to disruptions in neurovascular coupling

Functional neuroimaging, which measures hemodynamic responses to brain activity, has great potential for monitoring stroke patients. However, the neurophysiological interpretations of these hemodynamic signals remain a challenge as the stroke is likely to alter both neural activity and neurovascular coupling. To address this challenge, we simultaneously captured neural activity, through fluorescence calcium imaging, and hemodynamics, through intrinsic optical signal imaging, during longitudinal stroke recovery. We found that photothrombotic stroke to somatosensory forelimb region altered neurovascular coupling in the acute phase (2 days and 1 week post-stroke) within the affected forelimb and peri-infarct regions. Neurovascular coupling was reestablished in the chronic phase (4 weeks post-stroke), and acute recovery of neurovascular coupling predicted sensorimotor function. Stroke also resulted in increases in the power of global brain oscillations, which showed distinct patterns between calcium and hemodynamics. Increased calcium excitability in the contralesional hemisphere was associated with increased intrahemispheric connectivity. Additionally, acute increases in hemodynamic oscillations were associated with improved sensorimotor outcomes. TeaserAcute ischemic stroke leads to neurovascular uncoupling and the extent of early recoupling predicts sensorimotor recovery.

physiology↗

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

Microscopic Quantification of Oxygen Consumption across Cortical Layers

The cerebral cortex is organized in cortical layers that differ in their cellular density, composition, and wiring. Cortical laminar architecture is also readily revealed by staining for cytochrome oxidase - the last enzyme in the respiratory electron transport chain located in the inner mitochondrial membrane. It has been hypothesized that a high-density band of cytochrome oxidase in cortical layer IV reflects higher oxygen consumption under baseline (unstimulated) conditions. Here, we tested the above hypothesis using direct measurements of the partial pressure of O2 (pO2) in cortical tissue by means of 2-photon phosphorescence lifetime microscopy (2PLM). We revisited our previously developed method for extraction of the cerebral metabolic rate of O2 (CMRO2) based on 2-photon pO2 measurements around diving arterioles and applied this method to estimate baseline CMRO2 in awake mice across cortical layers. To our surprise, our results revealed a decrease in baseline CMRO2 from layer I to layer IV. This decrease of CMRO2 with cortical depth was paralleled by an increase in tissue oxygenation. Higher baseline oxygenation and cytochrome density in layer IV may serve as an O2 reserve during surges of neuronal activity or certain metabolically active brain states rather than baseline energy needs. Our study provides the first quantification of microscopically resolved CMRO2 across cortical layers as a step towards informed interpretation and modeling of cortical-layer-specific Blood Oxygen Level Dependent (BOLD) functional Magnetic Resonance Imaging (fMRI) signals.

neuroscience↗

bioRxiv2021

Refractive-index matching enhanced polarization-sensitive optical coherence tomography quantification in human brain tissue

The importance of polarization-sensitive optical coherence tomography (PS-OCT) has been increasingly recognized in human brain imaging. Despite the recent progress of PS-OCT in revealing white matter architecture and orientation, quantification of fine-scale fiber tracts in the human brain cortex has been a challenging problem, due to a low birefringence in the gray matter. In this study, we investigated the effect of refractive index matching by 2,2-thiodiethanol (TDE) immersion on the improvement of PS-OCT measurements in ex vivo human brain tissue. We obtain the cortical fiber orientation maps in the gray matter, which reveals the radial fibers in the gyrus, the U-fibers along the sulcus, as well as distinct layers of fiber axes exhibiting laminar organization. Further analysis shows that index matching reduces the noise in axis orientation measurements by 56% and 39%, in white and gray matter, respectively. Index matching also enables precise measurements of apparent birefringence, which was underestimated in the white matter by 82% but overestimated in the gray matter by 16% prior to TDE immersion. Mathematical simulations show that the improvements are primarily attributed to the reduction in the tissue scattering coefficient, leading to an enhanced signal-to-noise ratio in deeper tissue regions, which could not be achieved by conventional noise reduction methods.

bioengineering↗

bioRxiv2021

Exploring the human cerebral cortex using confocal microscopy

Cover-all mapping of the distribution of neurons in the human brain would have a significant impact on the deep understanding of brain function. Therefore, complete knowledge of the structural organization of different human brain regions at the cellular level would allow understanding their role in the functions of specific neural networks. Recent advances in tissue clearing techniques have allowed important advances towards this goal. These methods use specific chemicals capable of dissolving lipids, making the tissue completely transparent by homogenizing the refractive index. However, labeling and clearing human brain samples is still challenging. Here, we present an approach to perform the cellular mapping of the human cerebral cortex coupling immunostaining with SWITCH/TDE clearing and confocal microscopy. A specific evaluation of the contributions of the autofluorescence signals generated from the tissue fixation is provided as well as an assessment of lipofuscin pigments interference. Our evaluation demonstrates the possibility of obtaining an efficient clearing and labeling process of parts of adult human brain slices, making it an excellent method for morphological classification and antibody validation of neuronal and non-neuronal markers.

neuroscience↗

bioRxiv2021

Scalable mapping of myelin and neuron density in the human brain with micrometer resolution

Optical Coherence Tomography (OCT) is an emerging 3D imaging technique that allows quantification of intrinsic optical properties such as scattering coefficient and back-scattering coefficient, and has proved useful in distinguishing delicate microstructures in the human brain. The origins of scattering in brain tissues are contributed by the myelin content, neuron size and density primarily; however, no quantitative relationships between them have been reported, which hampers the use of OCT in fundamental studies of architectonic areas in the human brain and the pathological evaluations of diseases. To date, histology remains the golden standard, which is prone to errors and can only work on a small number of subjects. Here, we demonstrate a novel method that uses serial sectioning OCT to quantitatively measure myelin content and neuron density in the human brain. We found that the scattering coefficient possesses a strong linear relationship with the myelin content across different regions of the human brain, while the neuron density serves as a secondary contribution that only slightly modulates the overall tissue scattering.

neuroscience↗

bioRxiv2021

Guidelines for obtaining an absolute blood flow index with laser speckle contrast imaging

Laser speckle contrast imaging (LSCI) is a technique broadly applied in research and clinical settings for full-field characterization of tissue perfusion. It is based on the analysis of speckle pattern contrast, which can be theoretically related to the decorrelation time - a quantitative measure of dynamics. A direct contrast to decorrelation time conversion, however, requires prior knowledge of specific parameters of the optical system and scattering media and thus is often impractical. For this reason, and because of the nature of some of the most common applications, LSCI is historically used to measure relative blood flow change. Over time, the belief that the absolute blood flow index measured with LSCI is not a reliable metric and thus should not be used has become more widespread. This belief has resulted from the use of LSCI to compare perfusion in different animal models and to obtain longitudinal blood flow index observations without proper consideration given to the stability of the measurement. Here, we aim to clarify the issues that give rise to variability in the repeatability of the quantitative blood flow index and to present guidelines on how to make robust absolute blood flow index measurements with conventional single-exposure LSCI. We also explain how to calibrate contrast to compare measurements from different systems and show examples of applications that are enabled by high repeatability.

bioengineering↗

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↗

bioRxiv2020

Anatomical modeling of brain vasculature in two-photon microscopy by generalizable deep learning

Objective and Impact StatementSegmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. IntroductionVascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems, or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems, and is able to segment large-scale angiograms. MethodsWe employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and a total variation regularization on the networks output. Its effectiveness is demonstrated on experimentally acquired in-vivo angiograms from mouse brains of dimensions up to 808x808x702 m. ResultsTo demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope, and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10x faster computation in terms of voxels-segmented-per-second and 3x larger depth compared to the state-of-the-art. ConclusionOur work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.

neuroscience↗

bioRxiv2019

Rapid disruption of the cortical microcirculation after mild traumatic brain injury

Traumatic brain injury (TBI) is a major source of cognitive deficits affecting millions annually. The bulk of human injuries are mild, causing little or no macroscopic damage to neural tissue, yet can still lead to long-term neuropathology manifesting months or years later. Although the cellular stressors that ultimately lead to chronic pathology are poorly defined, one notable candidate is metabolic stress due to reduced cerebral blood flow (CBF), which is common to many forms of TBI. Here we used high-resolution in vivo intracranial imaging in a rodent injury model to characterize deficits in the cortical microcirculation during both acute and chronic phases after mild TBI. We found that CBF dropped precipitously during immediate post-injury periods, decreasing to less than half of baseline levels within minutes and remaining suppressed for 1.5-2 hours. Repeated time-lapse imaging of the cortical microvasculature revealed further striking flow deficits in the capillary network, where 18% of vessels were completely occluded for extended periods after injury, and an additional >50% showed substantial stoppages. Decreased CBF was paralleled by extensive vasoconstriction that is likely to contribute to loss of flow. Our data indicate a major role for vascular dysfunction in even mild forms of TBI, and suggest that acute post-injury periods may be key therapeutic windows for interventions that restore flow and mitigate metabolic stress.

neuroscience↗

bioRxiv2019

Functional ultrasound speckle decorrelation-based velocimetry of the brain

A high-speed, contrast free, quantitative ultrasound velocimetry (vUS) for blood flow velocity imaging throughout the rodent brain is developed based on the normalized first order temporal autocorrelation function of the ultrasound field signal. vUS is able to quantify blood flow velocity in both transverse and axial directions, and is validated with numerical simulation, phantom experiments, and in vivo measurements. The functional imaging ability of vUS is demonstrated by monitoring blood flow velocity changes during whisker stimulation in awake mice. Compared to existing power Doppler and color Doppler-based functional ultrasound imaging techniques, vUS shows quantitative accuracy in estimating both axial and transverse flow speeds and resistance to acoustic attenuation and high frequency noise.

bioengineering↗

bioRxiv2019

Dynamic Laser Speckle Imaging

Utilizing a high-speed camera and recording back-scattered laser light at more than 20,000 frames per second, we introduce the first wide-field dynamic laser speckle imaging (DLSI) in which we are able to quantify the laser speckleintensity temporal auto-correlation function g2({tau}) for every pixel individually to obtain a quantitative image of the dynamics of the light scattering particles in the sample. The ability to directly and quantitatively measure the intensity auto-correlation function allows us to solve the problem of how to quantitatively interpret data measured by laser speckle contrast imaging (LSCI), multi-exposure laser speckle imaging (MESI) and laser Doppler flowmetry (LDF). The intensity auto-correlation function is related to the field temporal auto-correlation function g1({tau}), which has been quantitatively related to the dynamics of the light scattering particles including flowing red blood cells. The form of g1({tau}) depends on the amount of light scattering (i.e. single or multiple scattering) and the type of particle motion (i.e. ordered or unordered). Although these forms of the field correlation functions have been established for over 30 years, there is no agreement nor experimental support on what scattering and motion regimes are relevant for the varied biomedical applications. We thus apply DLSI to image cerebral blood flow in mouse through a cranial window and show that the generally accepted form of g1({tau}), is applicable only to visible surface vessels of a specific size (20 - 200m). We demonstrate that for flow in smaller vessels and in parenchymal regions that the proper g1({tau}) form corresponds with multiple scattering light and unordered motion which was never considered to be relevant for these techniques. We show that the wrong assumption for the field auto-correlation model results in a severe underestimation of flow changes when measuring blood flow changes during ischemic stroke. Finally, we describe how DLSI can be integrated with other laser speckle methods to guide model selection, or how it can be used by itself as a quantitative blood flow imaging technique.

bioengineering↗