Illumination pattern optimization in tomography based on the Kalman estimation filter and optimal experiment design.

Tomography is widely used in medical imaging or industrial non-destructive testing applications. One costly and time consuming operation in any form of tomography is the process of data acquisition where a large number of measurements are made and collected data is used for image reconstruction. Data acquisition can slow down tomography to the point that the scanner cannot catch up with the speed of changes in the medium under test. By optimizing the information content of each measurement, we can reduce the number of measurements needed to achieve the target precision. Development of algorithms to optimize the information content of tomography measurements is the main goal of this article. Here, the dynamics of the medium and tomography measurements are formulated in the form of a Kalman estimation filter. A mathematical algorithm is developed to compute the optimal measurement matrix which minimizes the uncertainty left in the estimation of the distribution the tomography scanner is reconstructing. Results, as presented in the paper, show noticeable improvement is the quality of generated images when the medium is scanned by optimal measurements instead of traditional raster or random scanning protocols.

Optimal data acquisition in tomography.

In tomography, three-dimensional images of a medium are reconstructed from a set of two-dimensional projections. Each projection is the result of a measurement made by the scanner via radiating some form of energy and collecting the scattered field after interacting with the medium. The information content of these measurements is not equal, and one projection can be more informative than others. By choosing the most informative measurement at every step of scanning, an optimal tomography system can maximize the speed of data acquisition and temporal resolution of acquired images, reducing the operation cost and exposure to possible harmful radiations. The aim of this paper is to introduce mathematical algorithms that can be used to design measurements with optimal information content when imaging static or dynamically evolving objects.

Analysis of intermediary scan-lens and tube-lens mechanisms for optical coherence tomography.

Combining an optical coherence tomography (OCT) scanner with other techniques such as optogenetic neurostimulation or fluorescence imaging requires integrating auxiliary components into the optical path of the setup. Due to the short scanning distance of most OCT objectives, adding scan and tube lenses in the device is essential to open space between the back-focal-plane of the objective and center of mass of the mirrors in the galvanometer. The effect of the scan and tube lenses on the focal spot size of the scanner using off-the-shelf components are theoretically explored for three different designs in this paper. Two lens mechanisms were implemented and tested in a custom-built OCT scanner to experimentally measure point-spread functions. Based on our analysis, proper form of a four-element semi-Plössl lens provides a superior performance compared with an achromatic doublet when used as a scan/tube lens. The former lens design provides close to diffraction-limited resolution for scan angles up to 6.4°; however, due to aberrations in an achromatic doublet, the later design offers diffraction-limited resolution confined to 2° scan angles.

Calibration of digital optical phase conjugation setups based on orthonormal rectangular polynomials.

Digital optical phase conjugation (DOPC) has proven to be a promising technique in deep tissue fluorescence imaging. Nonetheless, DOPC optical setups require precise alignment of all optical components to accurately read the wavefront of scattered light in a turbid medium and playback the conjugated beam toward the sample. Minor misalignments and possible imperfections in the arrangement or the structure of the optical components significantly reduce the performance of the method. In this paper, a calibration procedure based on orthogonal rectangular polynomials is introduced to compensate major imperfections including the optical aberration in the wavefront of the reference beam and the substrate curvature of the spatial light modulator without adding extra optical components to the original setup. The proposed algorithm also provides a systematic calibration procedure for mechanical fine tuning of DOPC systems. It is shown experimentally that the proposed calibration process improves the peak-to-background ratio when focusing light after passing through a highly scattering medium.

Effect of blood vessels on light distribution in optogenetic stimulation of cortex.

In this Letter, the impact of blood vessels on light distribution during photostimulation of cortical tissue in small rodents is investigated. Brain optical properties were extracted using a double-integrating sphere setup, and optical coherence tomography was used to image cortical vessels and capillaries to generate a three-dimensional angiogram of the cortex. By combining these two datasets, a complete volumetric structure of the cortical tissue was developed and linked to a Monte Carlo code which simulates light propagation in this inhomogeneous structure and illustrates the effect of blood vessels on the penetration depth and pattern preservation in optogenetic stimulation.

Nonlinear optical signal processing on multiwavelength sensitive materials.

Exploiting salient features in the photodynamics of specific types of light sensitive materials, a new approach is presented for realization of parallel nonlinear operations with optics. We briefly review the quantum structure and mathematical models offered for the photodynamics of two multiwavelength sensitive materials, doped crystals of lithium niobate and thick layers of bacteriorhodopsin. Next, a special mode of these dynamics in each material is investigated and a graphical design procedure is offered to produce highly nonlinear optical responses that can be dynamically reshaped via applying minimum changes in the optical setup.

Optimization of data acquisition operation in optical tomography based on estimation theory.

The data acquisition process is occasionally the most time consuming and costly operation in tomography. Currently, raster scanning is still the common practice in making sequential measurements in most tomography scanners. Raster scanning is known to be slow and such scanners usually cannot catch up with the speed of changes when imaging dynamically evolving objects. In this research, we studied the possibility of using estimation theory and our prior knowledge about the sample under test to reduce the number of measurements required to achieve a given image quality. This systematic approach for optimization of the data acquisition process also provides a vision toward improving the geometry of the scanner and reducing the effect of noise, including the common state-dependent noise of detectors. The theory is developed in the article and simulations are provided to better display discussed concepts.

Optimal Scanning Protocol for Optical Tomography.

Tomography is a two step process in which the sample under test is first scanned by the hardware of the system to acquire data and then the operating software reconstruct images from the gathered information. The main objective of this work is to optimize the scanning process to acquire maximum amount of information in each measurement when the system is scanning the sample. By exploiting our prior information about the sample and using estimation theory, we developed a systematic approach to implement the optimal scanning protocol. Results of this study provide strong evidence that the developed algorithms can speed up data acquisition. Also it is shown that the proposed method can reduce the impact of noise as well as improving the reconstruction error while performing less number of measurements.Clinical relevance- The proposed method can enhance data acquisition time, exposure dosage and cost of operation in medical applications of tomography.

Optical Coherence Tomography Angiography in the Thirteen-Lined Ground Squirrel.

Purpose: To assess the performance of two spectral-domain optical coherence tomography-angiography systems in a natural model of hypoperfusion: the hibernating thirteen-lined ground squirrel (13-LGS). Methods: Using a high-speed (130 kHz) OCT-A system (HS-OCT-A) and a commercial OCT (36 kHz; Bioptigen Envisu; BE-OCT-A), we imaged the 13-LGS retina throughout its hibernation cycle. Custom software was used to extract the superior, middle, and deep capillary plexus (SCP, MCP, and DCP, respectively). The retinal vasculature was also imaged with adaptive optics scanning light ophthalmoscopy (AOSLO) during torpor to visualize individual blood cells. Finally, correlative histology with immunolabeled or DiI-stained vasculature was performed. Results: During euthermia, vessel density was similar between devices for the SCP and MCP (P = 0.88, 0.72, respectively), with a small difference in the DCP (-1.63 ± 1.54%, P = 0.036). Apparent capillary dropout was observed during torpor, but recovered after forced arousal, and this effect was exaggerated in high-speed OCT-A imaging. Based on cell flux measurements with AOSLO, increasing OCT-A scan duration by ∼1000× would avoid the apparent capillary dropout artifact. High correspondence between OCT-A (during euthermia) and histology enabled lateral scale calibration. Conclusions: While the HS-OCT-A system provides a more efficient workflow, the shorter interscan interval may render it more susceptible to the apparent capillary dropout artifact. Disambiguation between capillary dropout and transient ischemia can have important implications in the management of retinal disease and warrants additional diagnostics. Translational Relevance: The 13-LGS provides a natural model of hypoperfusion that may prove valuable in modeling the utility of OCT-A in human pathologies associated with altered blood flow.

A system identification analysis of optogenetically evoked electrocorticography and cerebral blood flow responses.

OBJECTIVE: The main objective of this research was to study the coupling between neural circuits and the vascular network in the cortex of small rodents from system engineering point of view and generate a mathematical model for the dynamics of neurovascular coupling. The model was adopted to implement closed-loop blood flow control algorithms. APPROACH: We used a combination of advanced technologies including optogenetics, electrocorticography, and optical coherence tomography to stimulate selected populations of neurons and simultaneously record induced electrocorticography and hemodynamic signals. We adopted system identification methods to analyze the acquired data and investigate the relation between optogenetic neural activation and consequential electrophysiology and blood flow responses. MAIN RESULTS: We showed that the developed model, once trained by the acquired data, could successfully regenerate subtle spatio-temporal features of evoked electrocorticography and cerebral blood flow responses following an onset of optogenetic stimulation. SIGNIFICANCE: The long term goal of this research is to open a new line for computational analysis of neurovascular coupling particularly in pathologies where the normal process of blood flow regulation in the central nervous system is disrupted including Alzheimer's disease.

Wheel running for 26 weeks is associated with sustained vascular plasticity in the rat motor cortex.

Vascular pathologies represent the leading causes of mortality worldwide. The nervous system has evolved mechanisms to compensate for the cerebral hypoxia caused by many of these conditions. Vessel dilation and growth of new vessels are two prominent responses to hypoxia, both of which play a critical role in maintaining cerebral homeostasis. One way to facilitate cerebrovascular plasticity, and develop neuroprotection against vascular pathologies, is through aerobic exercise. The present study explored the long-term consequences of aerobic exercise on vascular structure and function in the motor cortex. Rats were assigned to a sedentary condition or were provided access to running wheels for 26 weeks. Rats were then anesthetized, and angiograms were captured using spectral domain optical coherence tomography (SD-OCT) to explore cerebrovascular reactivity in response to altered oxygen and carbon dioxide status. Following this procedure, all rats were euthanized, and unbiased stereological quantification of blood vessel density was collected from sections of the primary motor cortex infused with India ink. Results demonstrated that chronic exercise increased capillary and arteriole surface area densities and enhanced arteriole reactivity in response to hypercapnia-hypoxia, as displayed by increased vasodilation within the motor cortex of exercised animals.

Optogenetic interrogation of neurovascular coupling in the cerebral cortex of transgenic mice.

OBJECTIVE: We introduce an engineering approach to study spatiotemporal correlations between vasodynamics and the nearby neural activity in open-loop and closed-loop paradigms. APPROACH: We integrated optogenetic technology with optical coherence tomography to apply spatiotemporal patterns of optical neurostimulation to the cortex of transgenic optogenetic mice and measure blood flow-rate, velocity, and diameter changes of selected middle cerebral artery branches. MAIN RESULTS: The spatiotemporal characteristics of blood flow-rate, velocity, and vessel diameter responses to localized neurostimulation light pulses were measured. It was observed that the location of stimulation relative to the surrounding vascular topology had notable effects on temporal patterns of vasodynamic responses. This effect was studied by creating velocity, flow-rate, and diameter sensitivity maps for selected arteries. Generally, neural stimulation in the vicinity of downstream capillaries of an artery evoked a fast transient increase in the blood flow-rate, velocity, and vessel diameter which was followed by a long-lasting secondary peak-response. The temporal span of the flow-rate response was quasi-linearly proportional to the length of stimulation. When neural stimulation was delivered to the area in the vicinity of one daughter branch of an artery, in other branches, we observed some drop in blood velocity and/or flow-rate and concurring increase of the vessel diameter. To examine the reliability of the coupling between neural activity and regional blood flow, a closed-loop feedback controller was implemented which is capable of maintaining blood flow-rate at any desired level for relatively longer periods by continuously adjusting the width of stimulation pulses. SIGNIFICANCE: The proposed approach opens new lines of research with potential applications in understanding the role of different cell types in the cerebrovascular regulatory mechanisms and the study of the adaptive process of angiogenesis in the cerebral cortex. The observation of incoherent responses of vessel diameter, blood flow-rate, and velocity suggests that such detailed information is necessary to obtain an accurate interpretation of the data acquired via hemodynamic based functional imaging techniques.

Electrical Neural Stimulation and Simultaneous in Vivo Monitoring with Transparent Graphene Electrode Arrays Implanted in GCaMP6f Mice.

Electrical stimulation using implantable electrodes is widely used to treat various neuronal disorders such as Parkinson's disease and epilepsy and is a widely used research tool in neuroscience studies. However, to date, devices that help better understand the mechanisms of electrical stimulation in neural tissues have been limited to opaque neural electrodes. Imaging spatiotemporal neural responses to electrical stimulation with minimal artifact could allow for various studies that are impossible with existing opaque electrodes. Here, we demonstrate electrical brain stimulation and simultaneous optical monitoring of the underlying neural tissues using carbon-based, fully transparent graphene electrodes implanted in GCaMP6f mice. Fluorescence imaging of neural activity for varying electrical stimulation parameters was conducted with minimal image artifact through transparent graphene electrodes. In addition, full-field imaging of electrical stimulation verified more efficient neural activation with cathode leading stimulation compared to anode leading stimulation. We have characterized the charge density limitation of capacitive four-layer graphene electrodes as 116.07-174.10 µC/cm2 based on electrochemical impedance spectroscopy, cyclic voltammetry, failure bench testing, and in vivo testing. This study demonstrates the transparent ability of graphene neural electrodes and provides a method to further increase understanding and potentially improve therapeutic electrical stimulation in the central and peripheral nervous systems.

Fluorescence laminar optical tomography for brain imaging: system implementation and performance evaluation.

We present our effort in implementing a fluorescence laminar optical tomography scanner which is specifically designed for noninvasive three-dimensional imaging of fluorescence proteins in the brains of small rodents. A laser beam, after passing through a cylindrical lens, scans the brain tissue from the surface while the emission signal is captured by the epi-fluorescence optics and is recorded using an electron multiplication CCD sensor. Image reconstruction algorithms are developed based on Monte Carlo simulation to model light­tissue interaction and generate the sensitivity matrices. To solve the inverse problem, we used the iterative simultaneous algebraic reconstruction technique. The performance of the developed system was evaluated by imaging microfabricated silicon microchannels embedded inside a substrate with optical properties close to the brain as a tissue phantom and ultimately by scanning brain tissue in vivo. Details of the hardware design and reconstruction algorithms are discussed and several experimental results are presented. The developed system can specifically facilitate neuroscience experiments where fluorescence imaging and molecular genetic methods are used to study the dynamics of the brain circuitries.

Intracranial Injection of an Optogenetics Viral Vector Followed by Optical Cannula Implantation for Neural Stimulation in Rat Brain Cortex.

Optogenetics is rapidly gaining acceptance as a preferred method to study specific neuronal cell types using light. Optogenetic neuromodulation requires the introduction of a cell-specific viral vector encoding for a light activating ion channel or ion pump and the utilization of a system to deliver light stimulation to brain. Here, we describe a two-part methodology starting with a procedure to inject an optogenetic AAV virus into rat cortex followed by a second procedure to surgically implant an optical cannula for light delivery to the deeper cortical layers.

Fabrication and utility of a transparent graphene neural electrode array for electrophysiology, in vivo imaging, and optogenetics.

Transparent graphene-based neural electrode arrays provide unique opportunities for simultaneous investigation of electrophysiology, various neural imaging modalities, and optogenetics. Graphene electrodes have previously demonstrated greater broad-wavelength transmittance (∼90%) than other transparent materials such as indium tin oxide (∼80%) and ultrathin metals (∼60%). This protocol describes how to fabricate and implant a graphene-based microelectrocorticography (µECoG) electrode array and subsequently use this alongside electrophysiology, fluorescence microscopy, optical coherence tomography (OCT), and optogenetics. Further applications, such as transparent penetrating electrode arrays, multi-electrode electroretinography, and electromyography, are also viable with this technology. The procedures described herein, from the material characterization methods to the optogenetic experiments, can be completed within 3-4 weeks by an experienced graduate student. These protocols should help to expand the boundaries of neurophysiological experimentation, enabling analytical methods that were previously unachievable using opaque metal-based electrode arrays.

OptogenSIM: a 3D Monte Carlo simulation platform for light delivery design in optogenetics.

Optimizing light delivery for optogenetics is critical in order to accurately stimulate the neurons of interest while reducing nonspecific effects such as tissue heating or photodamage. Light distribution is typically predicted using the assumption of tissue homogeneity, which oversimplifies light transport in heterogeneous brain. Here, we present an open-source 3D simulation platform, OptogenSIM, which eliminates this assumption. This platform integrates a voxel-based 3D Monte Carlo model, generic optical property models of brain tissues, and a well-defined 3D mouse brain tissue atlas. The application of this platform in brain data models demonstrates that brain heterogeneity has moderate to significant impact depending on application conditions. Estimated light density contours can show the region of any specified power density in the 3D brain space and thus can help optimize the light delivery settings, such as the optical fiber position, fiber diameter, fiber numerical aperture, light wavelength and power. OptogenSIM is freely available and can be easily adapted to incorporate additional brain atlases.

Monitoring cerebral hemodynamics following optogenetic stimulation via optical coherence tomography.

In this article, spectral domain optical coherence tomography is used to measure the hemodynamic response induced by optogenetic stimulation in the somatosensory cortex of transgenic mice. By analyzing the 3-D angiograms and Doppler measurements produced by coherence tomography, we observed significant increase in blood flow as a result of increased vessel diameter and blood velocity following optical stimulation of cortical neurons. Such distinct responses were not observed in control experiments where the brain of wild-type mice were exposed to the same light pulses.

Patterned optogenetic modulation of neurovascular and metabolic signals.

The hemodynamic and metabolic response of the cortex depends spatially and temporally on the activity of multiple cell types. Optogenetics enables specific cell types to be modulated with high temporal precision and is therefore an emerging method for studying neurovascular and neurometabolic coupling. Going beyond temporal investigations, we developed a microprojection system to apply spatial photostimulus patterns in vivo. We monitored vascular and metabolic fluorescence signals after photostimulation in Thy1-channelrhodopsin-2 mice. Cerebral arteries increased in diameter rapidly after photostimulation, while nearby veins showed a slower smaller response. The amplitude of the arterial response was depended on the area of cortex stimulated. The fluorescence signal emitted at 450/100 nm and excited with ultraviolet is indicative of reduced nicotinamide adenine dinucleotide, an endogenous fluorescent enzyme involved in glycolysis and the citric acid cycle. This fluorescence signal decreased quickly and transiently after optogenetic stimulation, suggesting that glucose metabolism is tightly locked to optogenetic stimulation. To verify optogenetic stimulation of the cortex, we used a transparent substrate microelectrode array to map cortical potentials resulting from optogenetic stimulation. Spatial optogenetic stimulation is a new tool for studying neurovascular and neurometabolic coupling.

Closed-Loop Optogenetic Brain Interface.

This paper presents a new approach for implementation of closed-loop brain-machine interface algorithms by combining optogenetic neural stimulation with electrocorticography and fluorescence microscopy. We used a new generation of microfabricated electrocorticography (micro-ECoG) devices in which electrode arrays are embedded within an optically transparent biocompatible substrate that provides optical access to the brain tissue during electrophysiology recording. An optical setup was designed capable of projecting arbitrary patterns of light for optogenetic stimulation and performing fluorescence microscopy through the implant. For realization of a closed-loop system using this platform, the feedback can be taken from electrophysiology data or fluorescence imaging. In the closed-loop systems discussed in this paper, the feedback signal was taken from the micro-ECoG. In these algorithms, the electrophysiology data are continuously transferred to a computer and compared with some predefined spatial-temporal patterns of neural activity. The computer which processes the data also readjusts the duration and distribution of optogenetic stimulating pulses to minimize the difference between the recorded activity and the predefined set points so that after a limited period of transient response the recorded activity follows the set points. Details of the system design and implementation of typical closed-loop paradigms are discussed in this paper.