Farid Atry

Graphene-based carbon-layered electrode array technology for neural imaging and optogenetic applications

Neural micro-electrode arrays that are transparent over a broad wavelength spectrum from ultraviolet to infrared could allow for simultaneous electrophysiology and optical imaging, as well as optogenetic modulation of the underlying brain tissue. The long-term biocompatibility and reliability of neural micro-electrodes also require their mechanical flexibility and compliance with soft tissues. Here we present a graphene-based, carbon-layered electrode array (CLEAR) device, which can be implanted on the brain surface in rodents for high-resolution neurophysiological recording. We characterize optical transparency of the device at >90% transmission over the ultraviolet to infrared spectrum and demonstrate its utility through optical interface experiments that use this broad spectrum transparency. These include optogenetic activation of focal cortical areas directly beneath electrodes, in vivo imaging of the cortical vasculature via fluorescence microscopy and 3D optical coherence tomography. This study demonstrates an array of interfacing abilities of the CLEAR device and its utility for neural applications.

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.

The effect of micro-ECoG substrate footprint on the meningeal tissue response

OBJECTIVE There is great interest in designing implantable neural electrode arrays that maximize function while minimizing tissue effects and damage. Although it has been shown that substrate geometry plays a key role in the tissue response to intracortically implanted, penetrating neural interfaces, there has been minimal investigation into the effect of substrate footprint on the tissue response to surface electrode arrays. This study investigates the effect of micro-electrocorticography (micro-ECoG) device geometry on the longitudinal tissue response. APPROACH The meningeal tissue response to two micro-ECoG devices with differing geometries was evaluated. The first device had each electrode site and trace individually insulated, with open regions in between, while the second device had a solid substrate, in which all 16 electrode sites were embedded in a continuous insulating sheet. These devices were implanted bilaterally in rats, beneath cranial windows, through which the meningeal tissue response was monitored for one month after implantation. Electrode site impedance spectra were also monitored during the implantation period. MAIN RESULTS It was observed that collagenous scar tissue formed around both types of devices. However, the distribution of the tissue growth was different between the two array designs. The mesh devices experienced thick tissue growth between the device and the cranial window, and minimal tissue growth between the device and the brain, while the solid device showed the opposite effect, with thick tissue forming between the brain and the electrode sites. SIGNIFICANCE These data suggest that an open architecture device would be more ideal for neural recording applications, in which a low impedance path from the brain to the electrode sites is critical for maximum recording quality.

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.

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 Parkinsons 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.

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.

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.

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.

Axial Scaling Is Independent of Ocular Magnification in OCT Images

We read with great interest the article by Röck et al., as it is a well-known physical principle of optical coherence tomography (OCT) and its basis, low-coherence interferometry, that magnification of the image of the sample using an objective lens or eyes with varying refractive power applies only in the transverse dimension, not the axial dimension. In this article, the authors collected OCT scans of a subretinal implant of known thickness, but found a significant correlation between observed thickness of the implant and the subjects’ axial length. Regrettably, the authors made no mention of the surprising nature of their findings in the context of the physics of OCT. Since this violates the known physical properties of low-coherence interferometry, we attempted to determine possible sources of the reported effect. First, it is important to recall the proofs of the principle that axial measurements do not scale with ocular magnification. Maximum imaging depth (zmax) with spectral-domain (SD)OCT is dependent on a few hardware components, that is, the light source (center wavelength: k0 and bandwidth: Dk), spectrometer, and camera resolution (N), as well as the group refractive index (n) of the sample: