This PDF file contains the front matter associated with SPIE Proceedings Volume 11629, including the Title Page, Copyright information, and Table of Contents.

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. I 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 test the hypothesis using direct measurements of the partial pressure of O2 (pO2) in cortical tissue obtained with 2-photon phosphorescence lifetime microscopy (2PLM). We revisit our previously developed method for extraction of cerebral metabolic rate of O2 (CMRO2) based on 2-photon pO2 measurements around diving arterioles and apply this method to estimate baseline CMRO2 in awake mice across cortical layers. Our results show that, in contrary to the common notion, baseline CMRO2 in layer IV is not higher than that in upper layers. We speculate that the cytochrome oxidase band in layer IV may reflect higher metabolic demands during transient surges in neuronal activity. These findings are important for interpretation of cortical-layer-resolved Blood Oxygen Level Dependent (BOLD) functional Magnetic Resonance Imaging (fMRI) studies.

Life is dynamic and three-dimensional (3D). An ideal tool to study biological processes, particularly those involving large populations of functionally diverse cells and fast dynamics, such as brains, is to achieve volumetric imaging in vivo. Traditional imaging tools, such as point scanning confocal microscope, are too slow to catch rapid processes over large scales. Volumetric imaging techniques that completely parallelized the imaging collection start attracting increasingly more attentions recently. Here, we report several new types of light field microscopes that can do functional imaging of calcium activities over large populations of neurons at high speed. We demonstrated whole brain functional imaging in freely behaving larval zebrafish and captured activation of several functional neural ensembles during different phases of larval zebrafish prey capture behavior. We also recorded populations of neurons’ activity and track fast circulating blood cells in 3D vascular network in the mouse brain. We believe these volumetric high speed imaging techniques could open new windows to understand more dynamic biological processes in vivo.

Functional imaging in vivo has become a powerful tool for studying neuronal circuits during behavior. Here we use a microendoscopy system for deep-brain imaging from two distinct lateral hypothalamic neuron populations (i.e. LHPV and LHLEPR). By combining endomicroscopy, genetically encoded calcium indicators, optogenetics, and chemogenetics, we demonstrate that LHPV neurons modulate pain whereas LHLEPR neuronal activity encodes for appetitive behaviors in mice.

I will first show the latest advances in testing diffuse correlation spectroscopy (DCS) in neuro-monitoring applications and how new biomarkers of cerebral health are emerging through improved technology. This will be illustrated through clinical examples from several studies in clinics. Then I will describe next generation devices which are pushing the technology towards in both the direction of regulatory approvals and also in low-cost, wearable implementations.

Neuroscience research has focused largely on listening to the brain - on taking recordings, analyzing responses, and trying to extract meaning from them. But now we’re entering a new phase where we can go beyond listening and can start talking back to the brain, and we have developed the ability to do it in the brain’s own language. This opens the door to new technologies for treating disease. Here we present the development of one such technology: a new kind of optogenetic prosthetic for treating blindness.

Towards intraoperative THz diagnosis of brain gliomas

Welcome and Introduction to SPIE Photonics West BiOS conference 11629: Neural Imaging and Sensing 2021

Protoporphyrin IX (PpIX) fluorescence-guided surgery has established as a standard for resecting malign glioma. However, low-grade glioma or sparsely infiltrated brain often emit weak PpIX fluorescence and are hard to distinguish from non-pathological tissue. Furthermore, spectrally overlapping autofluorescence inherently limits the sensitivity of fluorescence-intensity based PpIX detection. We therefore integrated frequency-domain fluorescence lifetime imaging together with a spectrometer in a surgical microscope. When analyzing human glioma samples ex vivo, weak PpIX fluorescence could be differentiated from the autofluorescence background through increased lifetimes. Characteristic peaks in the spectral measurements (635, 705nm) confirmed low concentrations of PpIX in the tissue.

Real-time noninvasive cerebral blood flow monitoring during cardiac surgery could decrease rates of neurologic injury associated with hypothermic circulatory arrests (HCA). We used combined frequency domain near-infrared spectroscopy and diffuse correlation spectroscopy (FDNIRS-DCS) to measure cerebral oxygen saturation and an index of blood flow (CBFi) in 12 adults undergoing HCA. Our measurements revealed negligible CBFi during retrograde cerebral perfusion (RCP: CBFi 91.2%±3.3% drop; HCA-only: 95.5%±1.8% drop). There was a significant difference during antegrade cerebral perfusion (p = 0.003). We conclude that FDNIRS-DCS can be a powerful tool to optimize cerebral perfusion and that RCP’s efficacy needs to be further examined.

Evaluation of the brain’s resting-state is an important window into neuronal function, connectivity, and health. Resting-state brain activity is reflected via neurovascular coupling in low frequency (0.01-0.1 Hz) hemodynamics, and low frequency power (LFP) can be a proxy for regional neuronal activity. In this exploratory study, we measured LFP in cerebral blood flow using diffuse correlation spectroscopy (LFP-DCS) during the course of an asphyxial cardiac arrest model in pediatric swine. The data demonstrate that LFP-DCS has distinct temporal information to blood flow index and may provide an additional biomarker to predict successful recovery after neurologic insults.

We describe the development of a perturbation-free technique to measure tissue blood flow and metabolic rate of oxygen (MRO2) using LSI and SFDI. Analytical (diffusion) and computational (Monte Carlo) models are employed to characterize the contributions of diffuse and directed flow to the measured speckle contrast. Measured flow data is combined with the deoxygenated hemoglobin concentration and a path-length factor (both obtained from SFDI) to model tissue oxygen consumption in units of M O2/min. The results of this model were comparable with values of MRO2 measured with other imaging methods (PET, MRI/MRS).

Photodynamic therapy is a cancer treatment modality with great potential but moderate clinical success. One reason for the sub-optimal clinical success is the limited knowledge about light distribution in tissues and lack of ways to monitor treatment real-time. Modulight has developed a laser platform for glioblastoma which will utilize real-time treatment monitoring based on spectral properties of the tissue and the drug. This therapy modality is based on photodynamic therapy with 5-aminolevulinic acid (5-ALA) primarily because the approved use of 5-ALA in fluorescence guided resections for glioblastoma and because of the known photobleaching properties of 5-ALA metabolite Protoporphyrin-IX (PPIX). Photobleaching means the photochemical alteration of a dye or a fluorophore in a way that it becomes permanently unable to fluoresce, and the real-time spectral monitoring is based on monitoring the intensity of PPIX fluorescence emission at 703 nm upon excitation with treatment wavelength 635 nm. Modulight glioblastoma platform enables monitoring PPIX fluorescence throughout the treatment to inspect the decline in fluorescence intensity. This photobleaching phenomenon represents the time region where the maximal therapeutic effect occurs so the ability to monitor this would ultimately enable optimizing the treatment time individually for each patient. Novel Modulight lasers are internet connected so that the treatment monitoring data can be immediately uploaded to cloud improving data management and review and possible future machine learning and AI based medicine.

In this work, we demonstrate the application of Rose Bengal as a photo-thrombotic agent using 2-photon and 3-photon excitation by measuring the response to multiphotonic excitation. We also demonstrate, in the case of 2-photon excitation, that the mechanism used is different from laser injury alone with a control group of FitC injected mice. Preliminary results show that a capillary photo-thrombosis could be performed up to 200 μm and OCT imaging could confirm blockage.

We combined a home-built two photon microscope with a Bessel focus capable of volumetric imaging with a custom scan pattern that allowed us to generate image pairs with a time delay of ~12 ms. This approach allows us to track red blood cell (RBC) flow along individual capillaries and therefore calculate RBC speed. We demonstrate the ability to measure flow speeds in capillaries across a 475x475x150 µm volume which will enable us to monitor network wide changes in capillary flow.

Understanding the structure and function of vasculature in the brain is important for both the interpretation of medical functional imaging data and the mechanistic understanding of neurovascular disorders. Currently, there lacks a volumetric vasculature imaging method able to uncover distributed hemodynamics at sub-capillary resolution and blood flow-resolving speed. Here, we applied two-photon microscopy with an axially extended Bessel focus to fast volumetric imaging of vasculature in the awake brain. We measured vessel dilation, constriction, and 3-dimensional blood flow at unprecedentedly high throughput and capillary resolution. We expect our method to make broad impacts on studying neurovasculature in vivo.

Block face imaging is widely used in three-dimensional large biological samples imaging. However, high throughput and excellent optical sectioning cannot be achieved at the same time for imaging such large area. Here, we propose a line-scanning virtual structured modulation method to combine the advantages of optical sectioning and imaging speed in structured modulation microscopy and line-scanning microscopy. We significantly improve signal to noise ratio and throughput compared to wild-filed structured illumination microscopy. Our results also have no residual modulation artifacts. It indicates our method enables to achieve imaging 3D large biological sample with excellent optical sectioning and high throughput.

Calcium imaging is a widely-used technique for recording neuronal activity. For deep-brain imaging, light scattering degrades image acquisition. To avoid imaging through thick tissue, one common approach is to implant a small lens system (a microendoscope) into the brain. But there is no technique to achieve fast volumetric imaging through such lenses, and this lack forces a choice between abandoning optical sectioning or sampling with risk of confusion from overlaps (when labeling is dense) or being limited to modest neural population size (when labeling is sparse). To address these limitations, we designed a novel imaging technique, RE-imaging Axial Light-sheet Microscopy (REALM), suitable for fast three-dimensional imaging through a microendoscope. REALM images via a tilted light-sheet, illuminating and collecting fluorescence emission with single objective. The first-stage “Maxwell theorem” microscope employs a matching pair of objectives to reimage sample volume onto a sawtooth mirror, which consists of a series of sub-micrometer scale angled surfaces. The sawtooth mirror redirects the light horizontally into the second-stage microscope, forming a crisp image of the illuminated near-axial plane. The whole second microscope system collects over 40% of light reflected by the sawtooth mirror, compared to previous studies 28% of light collection efficiency at numerical apertures that are unavailable for microendoscopy. This microscope will combine the speed and resolution advantages of light-sheet microscopy with the capabilities of microendoscopes for deep-brain imaging, providing the ability to perform fast threedimensional imaging in deep tissue.

Optogenetics combined with microelectrode array electrophysiology is a valuable tool set for the investigation of structure-function relations e.g. for understanding of human neurodegenerative diseases at microscale levels. We conducted long-term electrophysiology, full field and holographic single-neuron stimulation experiments using a fast ferroelectric modulator on in-vitro networks of iNGN cells derived from human fibroblasts expressing wild-type Channelrhodopsin2-EYFP. Functional maturation and successful ChR2-expression are observed in significant rises in action potential frequencies. Single neuron stimulation allows the extraction of functional connectivity maps, signal origins and post- or presynaptic signal characteristics as well as other modalities we will discuss in our presentation.

Schwann cells are the most abundant glial cell in the peripheral nervous system. Apart from their important role on axonal myelination they exert a key role on the regulation of axonal excitability and metabolism, nerve repair, immunological response and pain sensation. However, we still need to fully understand their complete role in the peripheral nervous system. Infrared pulsed stimulation is a label-free technique that proved useful to stimulate neural cells. We present for the first time the use of this method to modulate Schwann cells physiology and the versatility of the method to induce different responses with different stimulation parameters.

Recent developments in optogenetics allow for quick and minimally-invasive methods of studying functional brain organization in animal models. DeepLabCut (DLC), a toolbox for markerless pose estimation, offers the ability to track user-defined features in 3-dimensions with human level accuracy. We demonstrate a hybrid method utilizing DLC and optogenetic motor mapping to localize the movements of multiple modalities to the mouse cortex. We outline a pipeline to map and characterize multiple motor representations in anesthetized and awake mice. Furthermore, we identify behaviorally-relevant motor movements of multiple limbs reside in overlapping cortical representations of the respective limbs.

Towards non-genetic, precise neural stimulation, we develop a photoacoustic neural stimulation technology. It employs a fiber-based optoacoustic process, in which pulsed light is delivered through an optical fiber into an absorbing layer coated at the tip, resulting in transient heating and generating a localized acoustic wave. We report photoacoustic stimulation in vitro and in vivo through a lab-built fiber based optoacoustic emitter (FOE). Single neuron optoacoustic neural modulation is achieved through a tapered FOE (TFOE) developed with negligible thermal deposition. TFOE single neuron stimulation is shown to be compatible with patch and provides insights towards mechanical modulation of neural systems.

This study analyzes the light emission pattern of tapered optical fibers (TFs) across different numerical apertures (NA), core diameters, laser input powers, cone angles, and light injection angles. The results will be used to tailor optical fibers for optimal light delivery to photosensitive neuronal actuators in the non-human primate (NHP) brain.

We present a small rotational fiber probe capable of endoscopically imaging the optic axis of white matter fiber bundles, deep in the brain, using a state-of-the-art polarization-sensitive optical coherence tomography system. The probe is easily modifiable to be housed by, or attached to, clinical instruments routinely descended into the brain (i.e. cannulas for deep brain stimulation electrodes or biopsy needles.) The optic axis contrast, stemming from the birefringent myelinated axons, informs about the location and orientation of white matter fiber bundles. This information can provide surgical guidance to neurosurgeons through its comparison with preoperative magnetic resonance imaging and diffusion tensor imaging.

We provide herein a simulation study of the effects of modulation frequency on the image quality obtainable with frequency domain high density diffuse optical tomography. Using an anatomical head model, we simulated point spread functions with modulation frequencies spanning 0-1,000 MHz throughout the optically accessible field of view. We assessed image quality using metrics of the full width at half maximum, the localization error, and the 50% success rate. Our results show higher modulation frequency improves image quality and provides access to deeper brain tissue.

Intraventricular hemorrhage (IVH) is the most common neurological complication of prematurity. IVH is a bleeding inside or around ventricles, spaces in the brain containing the cerebrospinal fluid, which occurs as a result of the fragility and immaturity of blood vessels in premature brains. Severe IVH disrupts development of structural and functional connectivity networks, leading to impairments of cerebral development and neurologic deficits. Preterm infants with IVH are prone to alterations in cerebral blood flow (CBF) and associated spontaneous low-frequency fluctuations. However, there are no established noninvasive imaging methods for continuous monitoring of CBF alterations at the bedside in neonatal intensive care units. An innovative CCD/CMOS based speckle contrast diffuse correlation tomography (scDCT) technology has been recently developed in our laboratory, which enables noncontact, noninvasive, and high-density 3D imaging of CBF distributions in deep brain cortex. In the present study, the capability of scDCT technique for noncontact 3D imaging of CBF distributions in a neonatal piglet model of IVH was demonstrated. Moreover, power spectral density analyses of scDCT data were performed to assess alterations in spontaneous low frequency fluctuations in the resting brain, before and after inducing IVH. IVH resulted in a CBF decrease in deep brain cortex. Resting-state spontaneous low-frequency fluctuations after IVH showed attenuations in all frequencies (0.009– 0.08 Hz) compared to the baseline before IVH. In conclusion, scDCT is capable of detecting brain hemodynamic disruptions (reduction in CBF and attenuation in spontaneous low-frequency fluctuations) after IVH, which might be useful for instant management of IVH and associated complications.

Cross-polarization (CP) OCT is a so-called functional extension of OCT that seems to have benefits in visualization of myelin. During surgery it may be quite useful receiving information concerning myelination rate in white matter surrounding tumor mass. It this study it was shown that the quantification of peritumoral white matter using pseudocolor en-face OCT maps based on three optical coefficients (the rate of attenuation in the co- and cross-channel, and the interchannel attenuation difference) correlated well with histological data. Therefore, accurate quantitative CP OCT assessment of peritumoral white matter condition supports the developing the intraoperative implementation of this method.

High-density speckle contrast optical tomography (HD-SCOT) is attractive for imaging cerebral blood flow (CBF), with desirable cost and signal-to-noise ratio (SNR). Previous studies showed feasibility of HD-SCOT in rodent models using lab instruments. To investigate potential performance for a dedicated HD-SCOT instrument, we simulated HD-SCOT imaging for an anatomical head model. We evaluated potential imaging performance versus depth for varying exposure times and measurement availability. Results showed that an HD-SCOT system could have image resolution of 13 mm full-width-half-maximum at 12 mm depth, with instrument parameters affecting localization error and SNR. These results will guide design of future research instruments

The signal of optical coherence tomography (OCT) decays exponentially in depth due to tissue scattering, resulting in indistinct tissue features in three-dimension. Moreover, due to limited light penetration depth, extensive volumetric investigation is usually constrained for large-scale biological samples. By integrating serial sectioning technology with block-face imaging, we establish a volumetric OCT acquisition and reconstruction pipeline that incorporates depth-resolved attenuation coefficient estimation, volumetric stitching and filtering, and feature enhancement visualization. We demonstrate this pipeline on ex vivo human brain volumes of several cubic centimeters with 5 um isotropic resolution.

We present a framework to coregister a large set of blood flow measurements from the cortical microvascular segments obtained by DLS-OCT with the microvascular angiogram obtained using TPM. By using this framework, we estimated the distributions of the mean RBC velocities in arterioles, venules, and capillaries, and as a function of the branching order from over 1,000 microvascular segments. The developed tools will help with more quantitative analysis of the large data sets obtained by OCT and TPM in the studies involving normal brain functioning, progression of various diseases, and numerical modeling of the oxygen transport in the microvascular networks.

Neuroimaging techniques aim to image deep, with high resolution and minimal invasiveness. Here, we present a label-free optical microscopy approach that achieves a unique balance between these competing goals. Specifically, we design a high numerical aperture optical coherence microscope centered near 1700 nm, where ballistic attenuation in the mouse brain is minimized. Dynamic focusing and image fusion are employed to balance speckle reduction against multiple scattered light reduction. Imaging through the thinned skull to preserve intracranial pressure and minimize inflammation, we present volumetric imaging of cytoarchitecture and myeloarchitecture across the entire mouse neocortex and some sub-cortical regions.

Optical Coherence Tomography (OCT) is a promising research tool for neuroimaging. However, persistent challenges remain in following a large population of neurons and axonal tracts over time and across the entire depth due to system limitations. Here we introduce a label-free highly stable OCT system configuration and a novel segmentation algorithm that enable a longitudinal study of white matter axonal tracts and neuron cell bodies in a mouse brain, across 0.7 mm depth, in vivo. The system configuration enabled the acquisition of high-resolution images, which reveals thousands of neuron cell bodies across the entire volume and their interactions with multiple white matter axon tracts.

Despite impressive strides in light-enabled stimulation, approaches to silence targeted unmodified neurons subsets are yet to be devised. We will present a novel method to silence unmodified neurons via photothermal-mediated targeted drug delivery. Our approach uses laser-stimulation of antibody-coated gold nanoparticles to heat-activate TRPV1 (a noxious heat-sensing channel), turning this channel into a cell-specific drug-entry port. We will show that photothermal silencing blocks neuronal calcium currents and peptide release, resulting in targeted silencing of nociceptors. This approach can help to elucidate the contribution of nociceptor subpopulations to autoimmune pathologies and with further efforts can be translated into novel treatments in neuroscience.

Infrared neural modulation is an optical technique to stimulate or inhibit neural activity with pulsed infrared light (IR). This study focuses on effects of IR and heat on microglial calcium signaling, a main indicator of physiological changes within the immune-like cell. Widefield fluorescence microscopy quantified the intracellular calcium fluxes, cell death, and early apoptosis fluorescent indicators in BV2 immortalized microglia cell culture after irradiation. We have found that unique cellular responses are highly associated with different temperature increases, and the irradiance thresholds for these responses do not drive cells to Caspase-3 apoptosis nor necrotic cellular death.

Here, we report development of AAV-carried therapeutic gene construct consisting of cell-specific promoter driven Multi-Characteristic Opsin (MCO-II) to target inhibitory cells of ACC. MCO-II is highly sensitive to light and can be activated at low intensity, thus requiring a very low power budget. This along with red-light sensitiveness of MCO allows deep penetration with a minimally invasive implant. We developed a wireless Bluetooth Optogenetic Pain Modulator device for control of the dose of optogenetic stimulation. We demonstrated that red light stimulation of inhibitory neurons in ACC expressing MCO-II leads to significant reduction in pain response in fully awake animals.

We combine the real-time structural imaging capability of OCT with laser microirradiation for causing layer-specific dystrophies to mimic Retinitis Pigmentosa and dry-AMD model. In addition, we integrated an ERG-module for functional characterization after laser-injury to monitor the disease progression as well as to evaluate therapeutic efficacy. Here, we show creation of local atrophies with our combined OCT-Laser-ERG system in animal models and measurement of different cone and rod responses to focal stimulation light of different wavelengths. By varying the different mode of laser microirradiation and focal adjustment to the targeted depth, we demonstrate layer specific primary RPE injury.

We hypothesized that PEDF gene transduction in retina can provide single-dose treatment to prevent ganglion cell damage. Here, we present OCT guided ultrafast laser based non-viral targeted delivery PEDF-encoding genes to retina for neuroprotection. The ultrafast laser gene delivery showed layer-specific reliable expression of PEDF gene in retina without any detectable damage. Monitoring of IOP and electroretinogram after ultrafast laser transfection showed no adverse changes. The ultrafast laser transfection of large PEDF genes in retina exhibited significant therapeutic benefit in an injury model. Absence of any immune response in retina subsequent to ultrafast-laser transfection provides unique opportunity for repeated dosing.

We examine the correlation of non-invasive, frequency-domain diffuse optical spectroscopy (FD-DOS) and diffuse correlation spectroscopy (DCS) measurements of cerebral tissue oxygen extraction fraction (OEF) and relative cerebral blood flow (rCBF) with invasive cerebral microdialysis measurement of the cerebral lactate-pyruvate ratio (LPR), a biomarker of metabolic stress, during extracorporeal membrane oxygenation (ECMO) in a pediatric swine model of ECMO assisted cardiopulmonary resuscitation (n=15). During 22-24 hours of ECMO, non-invasive FD-DOS/DCS neuromonitoring of OEF and rCBF demonstrated significant correlations with cerebral LPR. Non-invasive detection of critical neurometabolic stress at the bedside may facilitate brain-targeted ECMO management after cardiac arrest.

Carotid endarterectomy (CEA) is a prophylactic operation to remove plaques inside carotid arteries, during which the patients are at high risk of embolic stroke. CEA is performed at carotid bifurcation, where carotid arteries are cross-clamping in order to isolate from circulation. However, there has been no gold standard for monitoring blood flow during CEA. Here, we aimed to investigate changes in the blood flow index (CBFi) and hemoglobin oxygenation with a combined frequency-domain near-infrared spectroscopy (FDNIRS) and diffuse correlation spectroscopy (DCS) system in patients who underwent CEA. Our results revealed that CBFi and total hemoglobin concentration (HbT) dropped substantially (58±14% and 18±10%, respectively) when the carotid arteries were cross-clamped. We also found that overshoot in CBFi and HbT was noticeably higher respect to the baseline before clamping (22±43% and 38±23%, respectively). Oxygen saturation at carotid clamping dropped by an average of 8−5% with respect to the pre-clamp baseline. At unclamping, oxygen saturation had an average overshoot of 2±9% with respect to the baseline level. According to our results, FDNIRS-DCS could be a robust tool for observing vascular physiology changes during CEA. Furthermore, as an indicator of cerebral hemodynamic and a proper perioperative blood flow monitoring, FDNIRS-DCS could help mitigate some of the risks and complications that follow CEA procedures.

Cerebrovascular reactivity (CVR) refers to the ability of cerebral vasculature to dilate or constrict during vasoactive stimuli. CVR has been shown to be a biomarker for vascular health in a range of disease states. Herein, we use Diffuse Correlation Spectroscopy to quantify cerebrovascular reactivity in 10 healthy adults using 3 different experimental paradigms for CVR assessment: hypercapnia, breath holding, and resting-state. We compare CVR estimations across these 3 paradigms, and we find poor agreement between the methods, underscoring the need for improved understanding of the different mechanisms of action of each intervention on the vasculature.

Effects of extracorporeal membrane oxygenation (ECMO) treatment is a life saving treatment for patients that undergo cardiac or pulmonary arrest and is increasingly being used in adults. However, some adults develop brain injuries during treatment. Current neuroimaging techniques such as CT and MRI are inaccessible for these patients due to the high risk in moving them. In this study, we use diffuse correlation spectroscopy to non-invasively monitor cerebral blood flow in patients at the bedside during ECMO treatment. Using this data alongside physiological data, indices of cerebral autoregulation are calculated to observe how ECMO affects neurological health.

Subarachnoid hemorrhage (SAH) is a neurosurgical emergency that results from the rupture of an aneurysm in the subarachnoid space. One common complication of SAH is cerebral vasospasm, which can lead to a secondary stroke. Intrathecal (IT) Nicardipine holds promise in treating cerebral vasospasm through its direct vasodilatory effect on the cerebral vasculature. Here, we used diffuse correlation spectroscopy to continuously monitor microvascular cerebral blood flow changes in medium-high grade subarachnoid hemorrhage patients in response to the first dose of IT Nicardipine. To date, we have recruited 9 patients, 3 of whom developed a secondary stroke.

Blood transfusion therapy is the current standard of care to reduce elevated risk of primary and recurrent strokes in children with sickle cell disease. Despite great success, chronic transfusion is not without significant risks and comes with a substantial burden. Individualized cerebral monitoring for goal-oriented therapy may better ensure optimal response to treatment and further mitigate risk of infarctions. In this study, we demonstrate diffuse optical spectroscopies (Diffuse Correlation Spectroscopy and Frequency-Domain Near-infrared Spectroscopy) as a simple and low-cost means for bedside assessments of changes in cerebral blood flow, oxygen extraction, and metabolic rate of oxygen in response to transfusion.

Non-invasive monitoring of cerebral blood flow at the bedside using diffuse correlation spectroscopy is being investigated as a potential tool to improve brain health outcomes after surgery. In this work we characterize the performance of diffuse correlation spectroscopy measurements in assessing cerebral blood flow in the presence of systemic physiology interference through measurements on several healthy volunteers during CO2 inhalation. We report group averaged responses and the role of multi-layer models in increasing the accuracy of CBF estimates. We compare optical blood flow recordings with transcranial Doppler ultrasound and MRI ASL data.

The vascular network in the human brain is universally involved in physiology and neural activity and the alteration is commonly associated with neurological disorders such as traumatic brain injury, stroke, multiple sclerosis, and Alzheimer’s disease. However, small arterioles, venules, and the capillary networks are beyond the resolution of in vivo MRI and optical microscopy only reveals the vasculature of cortex in small animals. We reported a vascular network reconstruction with an automatic serial sectioning polarization sensitive optical coherence tomography at 3.5 micrometer resolution in ex vivo human brain tissue. Pathological patterns surrounding the vessel walls were revealed as well.

This study suggests a new approach to examine mirror neuron network (MNN) using Near-Infrared Spectroscopy (NIRS). Instead of looking at the averaged cerebral hemodynamic change during the action-observation and action-execution, we correlated the connectivity during the tasks across all subjects. We found 8 within region connections and 7 between regions connections in the precentral, postcentral, angular, and parietal lobes, which can be part of the MNN. These connections satisfy conditions of having a strong connectivity in both action-observation and action-execution task and a significant correlation between the connectivity during both tasks. This study results are consistent with previous studies.

Serial Sectioning Optical Coherence Tomography(serial sectioning OCT) has been widely used to investigate the structural and pathological features of brain samples. OCT is an optical imaging technique that provides both the 3D structure of the tissue as well as the optical properties including the scattering coefficient (μ_s) and back-scattering coefficient (μ_b). Serial sectioning OCT allows the reconstruction of distortion-free volumetric images at high contrast and high resolution, which has proven to be useful for the detection of cancerous tissue boundaries, visualizing 3D vascular structures and measuring neuron density. The tissue optical properties extracted from the OCT depth profile has been shown to be related to myelin content and neuron density. However, no quantitative correlation of the tissue optical properties with myelin content and neuron density has been reported. Establishing a quantitative relationship will potentially benefit the segmentation of anatomical layers and the characterization of demyelination and neuron loss, which are related to neurological diseases such as Alzheimer’s and Chronic Traumatic Encephalopathy(CTE). Here, we demonstrate using block-face imaging with optical coherence tomography (OCT) to quantitatively measure myelin content and neuron density in the human brain. By correlating the OCT measurements of tissue optical properties with the ground truth of myelin content and neuron density provided by histology, we found that the scattering coefficient possesses a linear relationship with the myelin content across different regions of the human brain, while the neuron density only slightly modulate the overall tissue scattering properties

Functional magnetic resonance imaging has decoded complex information about naturalistic stimuli using brain responses, but other non-invasive technologies have not achieved similar decoding capabilities. To evaluate feasibility of naturalistic visual decoding with diffuse optical tomography (DOT), a 6.5-mm-spaced optode grid was employed to decode which of four naturalistic, 90-second, audio-free movie clips was viewed by human subjects. Over 85% average decoding accuracy was achieved using a simple template-matching decoder, and this exceeded the accuracy from a sparser optode grid with 13-mm spacing. High-density DOT is therefore promising for more-complex neural decoding tasks in the future.

We report optical coherence tomography (OCT) imaging of localized fast optical signals (FOS) arising from whisker stimulation in awake mice. The activated voxels were identified by fitting the OCT intensity signal time course with a response function over a time scale of a few hundred milliseconds after the whisker stimulation. The significantly activated voxels were shown to be localized to the expected brain region for whisker stimulation. The ability to detect functional stimulation-evoked, depth resolved FOS with intrinsic contrast from the cortex provides a new tool for neural activity studies.

Monitoring brain activity associated with natural physiological behavior is at the core of many neuroscience studies, yet many labs utilize imaging modalities that require anesthesia or immobilization of animals that cause unnatural stress and perturbed behavior. Instead, we separated the physiological system from the optical one using a fiber-optic tether, which allows the use of larger, optimized optical components while allowing mice to move freely thereby minimizing interference to their behavior. In vivo astrocyte activity, both spontaneous and stimulus-evoked was observed. The developed dual-color fluorescence system extended functionality to study multiple cell types concurrently.

In recent years, advanced optical methods combined with genetically encoded indicators has gradually become a helpful solution for monitoring neural activities in behaving animals. Among various optical methods, fiber-based ones have become increasingly versatile as they have declined in size but gained in functionality. We developed a nonlinear optical fiber-based endoscope with single-cell resolution, which enables investigating neural activities within single nucleus in freely behaving mice. To further understand how neural activities are coordinated in the complex circuits over different brain regions, we implemented two multichannel fiber photometry systems for multi-site population neural activity recording in head-restrained mice.

Frequency-domain (FD) fNIRS is attractive for non-invasive brain imaging because phase-sensitive detection leads to increased resolution and may exhibit improved robustness to motion artifacts. We present an FD-fNIRS system with silicon photomultiplier (SiPM) receivers, where the sensitivity and dynamic range approach those of a first-class continuous-wave (CW-) fNIRS system. This represents a significant step toward fully exploiting the phase degree of freedom provided by FD-fNIRS. The transmitter subsystem includes 32 channels and each supplies 12.5 mW of coherent light at both 690 and 852 nm. A dedicated radio circuit intensity-modulates each laser, and they are independently configured to operate at frequencies up to 400 MHz. The transmitters are on-off-keyed according to a user-specified pattern to mitigate shot noise and maximize dynamic range. The receiver subsystem also includes 32 channels. Each consists of a large-area (2.16-mm diameter), high-NA (0.66) fiber bundle, which carries light to a custom photo-receiver. A three-lens assembly enhances coupling between the fiber-bundle and the SiPM, and the SiPM (ON Semiconductor MICRORB-10020) converts the signal to the electrical domain. The electrical signal is amplified and down-converted to the audio spectrum, and a transformer balances the signal and provides galvanic isolation. Each of the 32 audio waveforms is digitized at 192 kS/s in a bank of commercial audio digitizers. Using a modulation frequency of 211 MHz, swept-power measurements demonstrate that the average noise-equivalent power of the SiPM photo-receivers is 20.5 fW per square root Hz, with about 6 decades of optical dynamic range. This work was funded by a research contract under Facebook’s Sponsored Academic Research Agreement.

Diffuse correlation spectroscopy (DCS) is an established diffuse optical technique that uses the analysis of temporal speckle intensity fluctuations to measure blood flow in tissue. DCS cerebral blood flow measurements in clinical applications have shown promise, but measurements contain contamination of the signal from changes in superficial blood flow. Recent studies have shown that moving to wavelengths beyond the water absorption peak at 970 nm when making DCS measurements improves SNR and reduced influence of superficial flow. Here, we present a DCS system operating at 1064 nm utilizing two InGaAs SPADs to calculate the cross correlation to address detector non-idealities.

We introduce a new wearable HD-DOT system that allows neuroimaging in naturalistic environments. Test results with visual paradigms show comparable performance to larger fiber-based systems.

Diffusing wave spectroscopy (DWS) is a well-known set of methods to measure the temporal dynamics of dynamic samples. In DWS, dynamic samples scatter the incident coherent light, and the information of the temporal dynamics is encoded in the scattered light. To record and analyze the light signal, there exist two types of methods – temporal sampling methods and speckle ensemble methods. Temporal sampling methods, including diffuse correlation spectroscopy (DCS), use one or multiple large bandwidth detectors to well sample and analyze the temporal light signal to infer the sample temporal dynamics. Speckle ensemble methods, including speckle visibility spectroscopy (SVS), use a high-pixel-count camera sensor to capture a speckle pattern and use the speckle contrast to infer sample temporal dynamics. In this paper, we theoretically and experimentally demonstrate that the decorrelation time (τ ) measurement accuracy or SNR of the two types of methods has a unified and similar fundamental expression based on the number of independent observables (NIO) and the photon flux. Given a time measurement duration, NIO in temporal sampling methods is constrained by the measurement duration, while speckle ensemble methods can outperform by using simultaneous sampling channels to scale up NIO significantly. In the case of optical brain monitoring, the interplay of these factors favors speckle ensemble methods. We illustrate that this important engineering consideration is consistent with the previous research on blood pulsatile flow measurements, where a speckle ensemble method operating at 100-fold lower photon flux than a conventional temporal sampling system can achieve a comparable SNR.

We developed a wearable HD-DOT instrument (WHD-DOT) that provides a safe and portable neuroimaging modality with enhanced image resolution and brain specificity. Our design replaces bulky fibers with smart electronic cylindrical source and detector modules that brush through hair and maintain stable optode-scalp coupling. Our current prototype has four independent WHD patches to create a system with 32 sources and 32 detectors at 13 mm optode spacing. Light level vs. distance curves confirm dynamic range and cross-talk specifications match fiber-based HD-DOT. We tested feasibility using retinotopic mapping of visual cortex. Optode location error between photometric measurements and MRI-based fiducials is <5mm.

Most reports on oblique plane microscopy (OPM) have a limited microscopic field of view (FOV), typically within 1x1 mm2. We implemented an optical design of mesoscopic scanning oblique plane microscopy (OPM) to allow using low numerical aperture (NA) objective lens. The angle of the intermediate image before the remote focusing system was increased by a demagnification under Scheimpflug condition such that the light collecting efficiency in the remote focusing system was significantly improved. We demonstrate a mesoscopic FOV up to ~6× 5×0.6 mm3 volumetric imaging, the largest reported FOV by OPM so far.

By paying careful attention to optical and mechanical design, a two-photon microscope (TPM) can image a large field of view (FOV) with high spatial and temporal resolution. Successfully applying such a TPM for functional neuroimaging requires careful consideration of the signal properties, physiological limitations, and image processing techniques. We present our thermal imaging results as well as functional imaging results in awake mice using a fast, large FOV TPM, and discuss how the system expands the spatial bandwidth available for studying functional connectivity.

We present a novel method for real-time measurement of the oxygen (pO2) gradients between intra- and extra-vascular compartments in rat brain cortex during functional activation. This information, obtained in parallel with measurements of cerebral blood flow (CBF), permits determination of absolute cerebral metabolic rate of oxygen (CMRO2). The timing of pO2, CBF, and CMRO2 responses is captured with high temporal resolution (~7 Hz). We discuss these results in the context of physiological models that connect oxidative metabolism to neuronal activation.

Understanding how different diseases of the central nervous system affect neurovascular coupling will allow for linking changes in neural or metabolic dysfunction to changes in hemodynamic signaling upon which blood-based imaging methods rely. We developed a dual fluorophore imaging system for simultaneous, high-speed mapping of neural, metabolic, and hemodynamic activity. Proof-of-concept measurements of spontaneous and stimulus-evoked dynamics are presented in awake and anesthetized mice. This flexible hardware platform allows for integrating optogenetic stimulation for all optical neural circuit interrogation and readout, and for examining the interaction between multiple cell populations.

Vinculin is a known key regulator of focal adhesions; it undergoes tension in the locations of attachment to the extracellular matrix. In this study, we explore the use of a vinculin tension FRET probe to investigate vinculin tension within neurons. A critical component of neuronal growth is migration, which is dependent on the mechanical cues between the cells and the extracellular matrix. An understanding of tension variation within the neuron may help us understand mechanisms of neurogenesis. To study these forces, we use a previously developed molecular tension sensor, which consists of an elastic linker, TSMod, a 40-amino-acid-long peptide inserted between teal fluorescent protein (mTFP1) and mVenus. The vinculin tension sensor, VinTS, consists of TSMod embedded between the Vinculin head and tail. When under tension, VinTS will exhibit a lower fluorescence resonance energy transfer (FRET) efficiency between mTFP1 and mVenus. Cortical neurons were isolated from embryonic rat brains and cultured on glass coverslips coated with poly-D-lysine and laminin. The neurons were transfected with TSMod (the unloaded tension sensor) or VinTS. Neurons expressing TSMod are used as the experiment’s control group since TSMod on its own is not affected by vinculin tension. The mean FRET efficiency of 171 TSMod and 127 VinTS expressing neurons was 27.08 ± 4.98%, and 22.86 ± 3.98%, respectively. The FRET efficiency of VinTS was significantly lower than that of TSMod (p = 6.6e15 by Welch’s t-test). These results support the feasibility of using the VinTS probe in neurons and provide a first assessment of VinTS FRET efficiency in neurons. The lower FRET efficiency of VinTS compared with TSMod suggests that VinTS may be under tension in neurons. However, additional studies are required to further characterize these results.

In a study on one patient during hemodialysis, we used near-infrared spectroscopy (NIRS) to measure coherent oscillations of cerebral concentrations of oxyhemoglobin ([HbO₂]), deoxyhemoglobin ([Hb]), and total-hemoglobin ([HbT]) induced by systemic oscillations in mean arterial pressure (MAP) at a frequency of 0.07 Hz. During hemodialysis, we observed that the phase of [Hb] versus [HbO₂] becomes less negative, whereas the phase of [HbT] versus MAP becomes more negative. By applying a quantitative hemodynamic model, we assign these phase changes to an increase in venous blood transit time and a less effective cerebral autoregulation during the hemodialysis process.

We present the use of intrinsic optical signal imaging to monitor the progression of ischemic stroke in the acute and chronic phases of recovery. An optimized mouse photothrombosis stroke model is used to induce stroke in the sensory forelimb area and longitudinal recovery is assessed using resting state functional connectivity as well as forelimb stimulation. These functional measures are then correlated with behavioral outcome assessed with a forelimb asymmetry test. Obtaining measures in both the acute and chronic phases of recovery will enable better interpretation of human functional neuroimaging stroke studies and allow their use in understanding acute stroke.

Recent advances in pluripotent stem cell technology have enabled generation of neuronal cell lines and cerebral organoids from human induced pluripotent stem cells (hiPSCs). These organoids are self-assembled, 3D cellular structures that resemble early developmental stages of the human brain. However, the lack of the natural brain microenvironment in cultured organoids can influence the phenotype and maturation of the reprogrammed neurons. To mitigate this limitation, cerebral organoids are transplanted into the mouse brain where their activity can be monitored using 2-photon imaging through cranial “windows.” Here, we will replace these windows with optically transparent graphene electrode microgrids to enable multimodal longitudinal monitoring and interrogation of neuronal activity in the graft and the surrounding host neuronal circuits. We envision that this technology can helpful for modeling of disease, examination of candidate treatments, and replacement therapy.

Maximal safe resection is key to prolonging overall survival during intracranial surgery. Capabilities of optical coherence tomography (OCT) to discriminate tissue types have been previously reported. We utilized an OCT-based microscope (OCM) to acquire reflectivity data of resected brain tumor samples and perform textural analyses. Twelve features showed statistically significant differences between different tissue types. Three of those – contrast, energy and entropy – are described in detail in this work. Contrast and entropy increased with tissue malignancy, and energy decreased. These results suggest that OCM data-based textural analyses are capable of differentiating different tissue types based on their intrinsic structures.

Cellular layering is a hallmark of the mammalian neocortex. A key challenge in studying circuit function within the neocortex is to understand the spatial and temporal patterns of information flow between different columns and layers. In the paper, a mesoscopic functional imaging method for neural activities in mouse cortex in vivo was developed and demonstrated. We demonstrated the depth-resolved capability of 3D mesoscopic imaging by photostimulating the layer 5 neurons in Thy1-ChR2-YFP transgenic mice and further recorded the layer-specific functional projections between primary somatosensory cortex and primary motor cortex in vivo, following single whisker deflection.

To obtain an accurate representation of a brain structural connectivity, diffusion MRI and fiber tracking depend on a good understanding of white matter fiber structures. Although the tracking methods work well when performed in single orientation fiber bundles, most methods are limited in more complex cases, especially to take into account crossing, fanning, and kissing fibers. A recent international fiber tracking challenge concluded that most tracking algorithms generated 4–5 times more false positive tracks than true tracks on average. This was attributed in large part to a lack of knowledge about the fiber crossing geometry. There is thus a dire need to study more complex fiber geometries to improve the tractography algorithms, for example by classifying those geometries into characteristic crossing topologies (e.g., fanning, curving, bottleneck, pure crossing, ...). Here, we propose a multimodal neuroimaging pipeline to identify and acquire fiber crossing areas in whole mouse brains. Our method uses the Allen Mouse Brain connectivity atlas and tractogram analysis using diffusion MRI techniques to identify candidate regions of interests containing fiber crossings based on two predetermined retrograde viral injection site locations. Based on serial OCT acquisitions, we confirmed the location of crossings. Further experiments will validate in detail the structural nature of crossings using retrograde injections of fluorescent tracers and whole mouse brain serial blockface histology. We believe that this new methodological approach will provide indispensable data for the development of a new generation of tractography algorithms that better resolve complex fiber geometries.

Obtaining fine structures in the whole brain is necessary for understanding brain function. Simple and effective methods for large-scale 3D imaging at optical resolution are still lacking. Here, we proposed a deep-learning-based fluorescence micro-optical sectioning tomography (DL-fMOST) method for fast, high-resolution whole-brain imaging. We utilized a wide-field microscope and a convolutional neural network for optical sectioning imaging, replacing traditional optical method. A 3D dataset of a mouse brain with a voxel size of 0.32 × 0.32 × 2 µm was acquired in 1.5 days. We demonstrated the robustness of DL-fMOST for mouse brains with labeling of different types of neurons.

An ongoing effort in many neuroscience laboratories is to perform chronic optical imaging and multiplexed electrophysiological recordings in awake behaving mice. We have adapted the use of conformal thin parylene C in conjunction with conductive polymer PEDOT:PSS coating on the electrode sites to realize wearable microelectrode array devices with sufficient optical transparency to allow simultaneous multiphoton imaging and optogenetic manipulation. These devices replace the current cranial glass windows providing broadband measurements of the extracellular potential as well as a see-through optical access. We have developed a mechanical solution for installation, connectorization and protection of the device and circuit board aiming for lifetime of several months while worn by a mouse. Our design allows access for high numerical aperture microscope objectives and does not obstruct the mouse face and whiskers enabling meaningful behaviors.

We propose a new sensitive diffuse correlation spectroscopy(DCS) method that can probe and identify different decorrelation events happens in sub-second, by acquiring parallelized measurements from 12 fiber detectors placed at different positions on the tissue-phantom surface with a 32 ×32 SPAD array, and process the data with deep learning methods. Both experimental and simulation phantom studies are conducted to evaluate the performance of our system in classifying and imaging decorrelation patterns presented under a 5mm thick tissue phantom made with rapidly decorrelating scattering media.

Scattering in the skull limits spatial resolution in optical neuroimaging experiments in mice, so it is necessary to excise a portion of the skull. Such craniotomy procedures have traditionally been done manually, but automating the process provides greater control of the cutting path and depth. A computer numerical controlled (CNC) milling machine can perform craniotomies of arbitrary shape and position with high precision. Automating the procedure improves repeatability and consistency, poses fewer risks for damaging the brain, and makes the procedure easier to learn. We have developed an automated craniotomy procedure which utilizes a CNC machine to obtain a curvature profile of the skull with an impedance-sensitive probing circuit and to interpolate a cut path along this profile to remove a portion of a mouse’s skull. This procedure does not damage the underlying brain tissue and can be performed in under two hours.

Despite the growing use of transcranial focused ultrasound (TUS) methods in pre-clinical research, noninvasive real-time monitoring of the TUS procedures remains an open challenge. Here we devised a wide-angle spherical array bidirectional interface for high-resolution parallelized optoacoustic imaging and transcranial ultrasound delivery (POTUS). The system is capable of generating and steering tightly focused ultrasound spots across a field of view covering the entire mouse brain, while the same array is used to capture 3D optoacoustic data in real time. We showcase the system’s versatile beam-forming capacities as well as volumetric optoacoustic imaging capabilities.

The inability to directly visualize large-scale neural dynamics across the entire mammalian brain in the millisecond temporal resolution regime is among the main limitations of existing neuroimaging methods. Recent advances in optoacoustic imaging systems have led to the establishment of this technology as an alternative method for real-time deep-tissue observations. Particularly, functional optoacoustic neurotomography (FONT) has recently been suggested for three-dimensional imaging of both direct calcium activity and cerebral hemodynamic parameters in rodents. However, the lack of suitable calcium indicators featuring optical absorption peaks within the so-called near-infrared window has hampered the applicability of FONT for imaging neuronal activity deep within the mammalian brain. To surmount this challenge, we developed and validated an intracardially perfused murine brain model labelled with genetically encoded calcium indicator GCaMP6f that closely simulates in vivo conditions. Penetration of light through skull and skin is greatly facilitated after blood is substituted by artificial cerebrospinal fluid (ACSF). The new preparation enabled here the observation of stimulus-evoked calcium dynamics within the mouse brain at penetration depths and spatio-temporal resolution scales not attainable with other neuroimaging techniques.

Current functional imaging techniques, such as functional magnetic resonance imaging, rely upon activity-induced blood flood changes to neurons. This indirect measurement of neuronal activity inherently limits image resolution and specificity, however, advances in transgenic technology and Photoacoustic (PA) methodology have offered new solutions. We previously demonstrated using PA imaging in conjunction with a Fos-LacZ rat model to map activated neurons through selective formation of PA-active X-gal product within Fos-expressing neurons. While we have previously used intracranial injections for successful delivery of X-gal to detect neurons that are highly-active after classical fear conditioning using PA imaging, now, we have further advanced this technique by using an intrathecal route of administration of X-gal combined with in vivo imaging to improve the translatability of this approach and whole-brain imaging capabilities. We subjected Fos/LacZ rats to fear conditioning, or control conditions. Ninety minutes post stimulus presentation, X-gal was delivered via intrathecal or intravenous injection. After 24 hours, a cranial window was made in animals and they were PA imaged in vivo. PA intensity within the medial prefrontal cortex (mPFC) of acquired images was quantified using ImageJ software. We presently report quantification of PA images of rat brains stained with X-gal product generated in vivo within activated neurons. Detailed PA signal differences are reported between mPFC subregions. We discuss the feasibility and translatability of this reporter method for neuronal activity based on our acquired images. With this technique, we propose a method of longitudinally monitoring activated neurons in vivo with high resolution and specificity.

Recently, we developed a time-domain diffuse correlation spectroscopy (TD-DCS) method for neurovascular sensing with higher brain sensitivity. In this paper, laser pulse shaping was designed and demonstrated for TD-DCS at 1064 nm. A quantum superconducting nanowire single-photon detector (SNSPD) with high photon detection efficiency (PDE) and low jitter collects the back-scattered light from the brain. The presented approach is the first step towards scaling up a full fiber optic cap with 96 source channels and 192 custom-made single-photon detectors which will cover most of an adult head.

Maintenance of cerebral blood flow (CBF) is required for normal brain function. Yet, measuring CBF in adult humans requires high-end medical instrumentation. Here, leveraging two-dimensional (2D) complementary metal-oxide-semiconductor (CMOS) technology, we present and validate an optical approach, called multi-exposure interferometric Diffusing Wave Spectroscopy (MiDWS), to monitor blood flow index (BFI), a proxy for CBF, via the adult human forehead. MiDWS employs interferometry to detect low light levels, and probes the optical field autocorrelation by varying the sensor exposure time. This approach may enable human brain optical BFI monitoring with 2D CMOS sensors, with associated economies of scale.

We present a 32-transmitter, 32-receiver dual-wavelength frequency-domain (FD) fNIRS system comprised of commercially available avalanche photodiodes, laser drivers and laser mounts. The custom frequency domain (FD) fNIRS system is used to interrogate cerebral tissue with optodes positioned at the posterior occipital region of the head. Data are collected from human subjects watching movie scenes with no sound. We applied cross-validated PCA to identify the number of dimensions retained in the neural signal recorded using FD-fNIRS for the magnitude, phase, and FD (magnitude and phase combined) components of the recorded signal. Importantly, a comparison of the cross-validation error for each signal allows us quantify the dimensionality of the linear subspace spanned by each data type. The number of principal components producing the minimum cross-validation error for the held-out test runs represents the number of orthogonal signal dimensions preserved across training and held-out test data runs. We find that the FD signal captures a higher dimensional space compared to the magnitude or phase signals in isolation. Previous theoretical and empirical work suggest that signals extracted using FD-fNIRS contain higher fidelity neural information than CW-fNIRS in isolation. The findings reported here further support this hypothesis and extend beyond the findings reported in the literature, demonstrating that a higher dimension linear subspace is covered by FD-fNIRS above and beyond the baseline signal captured using traditional CW-fNIRS, assuming other optical performance metrics such as optical dynamic range, noiseequivalent power and cross-talk are comparable. This work was funded by a research contract under Facebook’s Sponsored Academic Research Agreement.

Polarization-sensitive optical coherence tomography (PS-OCT) provides volumetric tissue imaging based on inherent scattering and polarization properties. In fibrous structures such as white matter tissue, PS-OCT enables quantitative mapping of birefringence. For single-input PS-OCT layouts, the accuracy of birefringence measurements strongly depends on the signal-to-noise ratio (SNR) and is prone to mapping artifacts in case of low SNR. Here we present a simple yet effective approach for improving the accuracy of phase retardation and birefringence measurements by performing a noise bias correction of the detected signal amplitudes. We present simulation data to illustrate the influence of the noise bias correction on phase retardation measurements and support our analysis with real-world PS-OCT image data.

Functional near-infrared spectroscopy (fNIRS) is an optical brain imaging technique that maps brain function in terms of changes in oxygenated and deoxygenated hemoglobin concentration (hemodynamic response) on the cortical surface of the brain. Wireless wearable fNIRS imaging is always preferable to study a brain in an unconstrained environment. However, an LED and photodetector based miniaturized fNIRS system suffers from several technical challenges to provide high fidelity fNIRS signal. This paper reports the design and development of an internet-of-things (IoT)-based wireless fNIRS headband to image hemodynamic response of the prefrontal cortex of the brain in naturalistic settings. The headband has four dual-wavelength LEDs and four silicon photodiode detectors arranged to provide 10 usable fNIRS channels. The designed IoT-based controller has dedicated digital and analog circuit and is operated by an embedded computing algorithm to facilitate source modulation, lock-in detection, onboard calibration, and basic signal processing to improve SNR of the optical measurements at 9 Hz. A graphical user interface (GUI) software on the host computer helps the users to visualize and record the fNIRS signal wirelessly. The experimental validation of the system was performed by imaging prefrontal cortex of the brain while the participants (n=16) performed cognitive tasks that induced four different levels of mental workload. The experimental results demonstrated that the fNIRS headband was capable of imaging hemodynamic activity of the brain. The experimental results also showed on average, four different stimulus-evoked hemodynamic responses due to the four difficulty levels of the tasks

Functional near-infrared spectroscopy (fNIRS) is a brain imaging methodology that is appertaining to imaging the hemodynamic responses or blood oxygenation level-dependency of the brain. Machine learning (ML) has the potential to classify different mental states from the fNIRS signal to build a brain-computer interface (BCI) system. In this work, we have used a portable fNIRS system, WearLight, to image the prefrontal cortex of the brain of 12 participants while performing n-back working memory (WM) tasks. We converted the time-series raw data to the hemodynamic response by implementing a processing pipeline. A simple method based on checking the hemodynamic signal level of all the channels during task blocks with respect to the rest periods was used to identify the thee most dominant channels. We extracted eight important features from the hemodynamic brain signals to construct the feature matrix and trained six different k-nearest neighbors (k-NN) ML classifiers. The performance of the six k-NN classifiers was evaluated with the new experimental data sets. The results have shown that Weighted and Fine k-NN performed best (75%) in classifying the 4 different WM loads. The method is encouraging for real-time classification of the mental workload using a portable fNIRS system augmented by advanced machine learning techniques.

Functional near-infrared spectroscopy (fNIRS) images the changes in oxygenated and deoxygenated hemoglobin blood concentration on the cortical surface of the brain. This technology has been widely used to assess human perceptual and cognitive functions, with many studies showing a positive correlation between working memory (WM) task difficulty and the hemodynamic response measured in frontal regions of the brain. In this work, an unsupervised machine learning (ML) method, k-means clustering, was used to study the relationship between WM task difficulty, user performance, and hemodynamic brain response. We used an fNIRS data set derived from 25 healthy participants performing a WM task with four difficulty levels, with data collected using a portable fNIRS device. For each participant, the raw fNIRS time-series data were processed and block-averaged to find hemodynamic responses in the four WM task conditions. A k-means clustering ML algorithm was used to identify clusters of participants based on hemodynamic responses across the four conditions. The elbow method suggested three optimal clusters (groups). We studied the task-induced hemodynamic response variation in the three groups as well as task performance (accuracy and reaction time). Clusters were related to WM task performance. At increasing task difficulty levels (1-back, 2-back), cluster membership predicted changes in task performance. Specifically, higher hemodynamic responses in the 2-back condition predicted poorer performance outcomes in the 1-back and 2-back conditions. At higher task difficulty levels, the hemodynamic response signals greater metabolic costs associated with diminishing performance, suggesting future directions for closed-loop systems for monitoring and predicting performance outcomes.

Functional near infrared spectroscopy (fNIRS) is a non-invasive technique for quantifying functional changes in cortical blood volume and oxygenation. Regression techniques are used in cognitive research to separate the neural component from strong physiological and motion artifacts. In this work, we used single stimulus Kalman filter regression to estimate the hemodynamic response function (HRF) produced by subjects performing one of four different tasks (left vs. right finger tapping either overt or covert). We train a linear discriminant analysis (LDA) classifier with a subset of the data and perform cross-validation to estimate mean classification accuracy. The HRF regressed signal displays decreased noise and a modest increase in classification accuracy compared to classification performed on the raw chromophore concentration signal.