Optogenetic brain interfaces

Large-scale multimodal surface neural interfaces for primates

Deciphering the function of neural circuits can help with the understanding of brain function and treating neurological disorders. Progress toward this goal relies on the development of chronically stable neural interfaces capable of recording and modulating neural circuits with high spatial and temporal precision across large areas of the brain. Advanced innovations in designing high-density neural interfaces for small animal models have enabled breakthrough discoveries in neuroscience research. Developing similar neurotechnology for larger animal models such as nonhuman primates (NHPs) is critical to gain significant insights for translation to humans, yet still it remains elusive due to the challenges in design, fabrication, and system-level integration of such devices. This review focuses on implantable surface neural interfaces with electrical and optical functionalities with emphasis on the required technological features to realize scalable multimodal and chronically stable implants to address the unique challenges associated with nonhuman primate studies.

Recent Advances in Encapsulation of Flexible Bioelectronic Implants: Materials, Technologies, and Characterization Methods

Bioelectronic implantable systems (BIS) targeting biomedical and clinical research should combine long-term performance and biointegration in vivo. Here, recent advances in novel encapsulations to protect flexible versions of such systems from the surrounding biological environment are reviewed, focusing on material strategies and synthesis techniques. Considerable effort is put on thin-film encapsulation (TFE), and specifically organic-inorganic multilayer architectures as a flexible and conformal alternative to conventional rigid cans. TFE is in direct contact with the biological medium and thus must exhibit not only biocompatibility, inertness, and hermeticity but also mechanical robustness, conformability, and compatibility with the manufacturing of microfabricated devices. Quantitative characterization methods of the barrier and mechanical performance of the TFE are reviewed with a particular emphasis on water-vapor transmission rate through electrical, optical, or electrochemical principles. The integrability and functionalization of TFE into functional bioelectronic interfaces are also discussed. TFE represents a must-have component for the next-generation bioelectronic implants with diagnostic or therapeutic functions in human healthcare and precision medicine.

"Magnetism-Optogenetic" System for Wireless and Highly Sensitive Neuromodulation

Neuromodulation is becoming more and more important in studying brain function, disease treatment, and brain-computer interfaces. However, traditional regulation methods cannot effectively achieve both wireless regulation and highly sensitive response, which are essential factors in neuromodulation. In this paper, a "magnetism-optogenetic" system is constructed, which uses a magnetic field to drive mechanoluminescent materials (ZnS:Cu) to generate light, thus stimulating photogenetic proteins. This system effectively combines the wireless magnetic regulation with the high sensitivity of optogenetics. The results show that the luminous intensity of this system changes with the power of an external magnetic field. In addition, under the continuous stimulation of the wireless magnetic field, this system can activate hippocampal-related neural responses and induce the expression of C-fos. In the end, this system can further regulate the movement behavior of rats with C1V1 protein expression in the primary motor cortex. This new magnetism-optogenetic system will provide an excellent reference for wireless and highly sensitive neuromodulation.

Wireless multilateral devices for optogenetic studies of individual and social behaviors

Advanced technologies for controlled delivery of light to targeted locations in biological tissues are essential to neuroscience research that applies optogenetics in animal models. Fully implantable, miniaturized devices with wireless control and power-harvesting strategies offer an appealing set of attributes in this context, particularly for studies that are incompatible with conventional fiber-optic approaches or battery-powered head stages. Limited programmable control and narrow options in illumination profiles constrain the use of existing devices. The results reported here overcome these drawbacks via two platforms, both with real-time user programmability over multiple independent light sources, in head-mounted and back-mounted designs. Engineering studies of the optoelectronic and thermal properties of these systems define their capabilities and key design considerations. Neuroscience applications demonstrate that induction of interbrain neuronal synchrony in the medial prefrontal cortex shapes social interaction within groups of mice, highlighting the power of real-time subject-specific programmability of the wireless optogenetic platforms introduced here.

Implantable Optrode Array for Optogenetic Modulation and Electrical Neural Recording

During the last decade, optogenetics has become an essential tool for neuroscience research due to its unrivaled feature of cell-type-specific neuromodulation. There have been several technological advances in light delivery devices. Among them, the combination of optogenetics and electrophysiology provides an opportunity for facilitating optogenetic approaches. In this study, a novel design of an optrode array was proposed for realizing optical modulation and electrophysiological recording. A 4 × 4 optrode array and five-channel recording electrodes were assembled as a disposable part, while a reusable part comprised an LED (light-emitting diode) source and a power line. After the characterization of the intensity of the light delivered at the fiber tips, in vivo animal experiment was performed with transgenic mice expressing channelrhodopsin, showing the effectiveness of optical activation and neural recording.

A Survey on State-of-the-art Denoising Techniques for Brain Magnetic Resonance Images

The accuracy of the magnetic resonance (MR) image diagnosis depends on the quality of the image, which degrades mainly due to noise and artifacts. The noise is introduced because of erroneous imaging environment or distortion in the transmission system. Therefore, denoising methods play an important role in enhancing the image quality. However, a tradeoff between denoising and preserving the structural details is required. Most of the existing surveys are conducted on a specific MR image modality or on limited denoising schemes. In this context, a comprehensive review on different MR image denoising techniques is inevitable. This survey suggests a new direction in categorizing the MR image denoising techniques. The categorization of the different image models used in medical image processing serves as the basis of our classification. This study includes recent improvements on deep learning-based denoising methods alongwith important traditional MR image denoising methods. The major challenges and their scope of improvement are also discussed. Further, many more evaluation indices are considered for a fair comparison. An elaborate discussion on selecting appropriate method and evaluation metric as per the kind of data is presented. This study may encourage researchers for further work in this domain.

Development of optically controlled "living electrodes" with long-projecting axon tracts for a synaptic brain-machine interface

For implantable neural interfaces, functional/clinical outcomes are challenged by limitations in specificity and stability of inorganic microelectrodes. A biological intermediary between microelectrical devices and the brain may improve specificity and longevity through (i) natural synaptic integration with deep neural circuitry, (ii) accessibility on the brain surface, and (iii) optogenetic manipulation for targeted, light-based readout/control. Accordingly, we have developed implantable "living electrodes," living cortical neurons, and axonal tracts protected within soft hydrogel cylinders, for optobiological monitoring/modulation of brain activity. Here, we demonstrate fabrication, rapid axonal outgrowth, reproducible cytoarchitecture, and simultaneous optical stimulation and recording of these tissue engineered constructs in vitro. We also present their transplantation, survival, integration, and optical recording in rat cortex as an in vivo proof of concept for this neural interface paradigm. The creation and characterization of these functional, optically controllable living electrodes are critical steps in developing a new class of optobiological tools for neural interfacing.

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.

A wireless, implantable optoelectrochemical probe for optogenetic stimulation and dopamine detection

Physical and chemical technologies have been continuously progressing advances in neuroscience research. The development of research tools for closed-loop control and monitoring neural activities in behaving animals is highly desirable. In this paper, we introduce a wirelessly operated, miniaturized microprobe system for optical interrogation and neurochemical sensing in the deep brain. Via epitaxial liftoff and transfer printing, microscale light-emitting diodes (micro-LEDs) as light sources and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS)-coated diamond films as electrochemical sensors are vertically assembled to form implantable optoelectrochemical probes for real-time optogenetic stimulation and dopamine detection capabilities. A customized, lightweight circuit module is employed for untethered, remote signal control, and data acquisition. After the probe is injected into the ventral tegmental area (VTA) of freely behaving mice, in vivo experiments clearly demonstrate the utilities of the multifunctional optoelectrochemical microprobe system for optogenetic interference of place preferences and detection of dopamine release. The presented options for material and device integrations provide a practical route to simultaneous optical control and electrochemical sensing of complex nervous systems.

Toward Standardization of Electrophysiology and Computational Tissue Strain in Rodent Intracortical Microelectrode Models

Progress has been made in the field of neural interfacing using both mouse and rat models, yet standardization of these models' interchangeability has yet to be established. The mouse model allows for transgenic, optogenetic, and advanced imaging modalities which can be used to examine the biological impact and failure mechanisms associated with the neural implant itself. The ability to directly compare electrophysiological data between mouse and rat models is crucial for the development and assessment of neural interfaces. The most obvious difference in the two rodent models is size, which raises concern for the role of device-induced tissue strain. Strain exerted on brain tissue by implanted microelectrode arrays is hypothesized to affect long-term recording performance. Therefore, understanding any potential differences in tissue strain caused by differences in the implant to tissue size ratio is crucial for validating the interchangeability of rat and mouse models. Hence, this study is aimed at investigating the electrophysiological variances and predictive device-induced tissue strain. Rat and mouse electrophysiological recordings were collected from implanted animals for eight weeks. A finite element model was utilized to assess the tissue strain from implanted intracortical microelectrodes, taking into account the differences in the depth within the cortex, implantation depth, and electrode geometry between the two models. The rat model demonstrated a larger percentage of channels recording single unit activity and number of units recorded per channel at acute but not chronic time points, relative to the mouse model Additionally, the finite element models also revealed no predictive differences in tissue strain between the two rodent models. Collectively our results show that these two models are comparable after taking into consideration some recommendations to maintain uniform conditions for future studies where direct comparisons of electrophysiological and tissue strain data between the two animal models will be required.

Anisotropic light scattering from myelinated axons in the spinal cord

Optogenetics has become an integral tool for studying and dissecting the neural circuitries of the brain using optical control. Recently, it has also begun to be used in the investigation of the spinal cord and peripheral nervous system. However, information on these regions' optical properties is sparse. Moreover, there is a lack of data on the dependence of light propagation with respect to neural tissue organization and orientation. This information is important for effective simulations and optogenetic planning, particularly in the spinal cord where the myelinated axons are highly organized. To this end, we report experimental measurements for the scattering coefficient, validated with three different methods in both the longitudinal and radial directions of multiple mammalian spinal cords. In our analysis, we find that there is indeed a directional dependence of photon propagation when interacting with organized myelinated axons. Specifically, light propagating perpendicular to myelinated axons in the white matter of the spinal cord produced a measured reduced scattering coefficient ( μ s ' ) of 3.52 ± 0.1    mm - 1 , and light that was propagated along the myelinated axons in the white matter produced a measured μ s ' of 1.57 ± 0.03    mm - 1 , across the various species considered. This 50% decrease in scattering power along the myelinated axons is observed with three different measurement strategies (integrating spheres, observed transmittance, and punch-through method). Furthermore, this directional dependence in scattering power and overall light attenuation did not occur in the gray matter regions where the myelin organization is nearly random. The acquired information will be integral in preparing future light-transport simulations and in overall optogenetic planning in both the spinal cord and the brain.

Ultrasonic sculpting of virtual optical waveguides in tissue

Optical imaging and stimulation are widely used to study biological events. However, scattering processes limit the depth to which externally focused light can penetrate tissue. Optical fibers and waveguides are commonly inserted into tissue when delivering light deeper than a few millimeters. This approach, however, introduces complications arising from tissue damage. In addition, it makes it difficult to steer light. Here, we demonstrate that ultrasound can be used to define and steer the trajectory of light within scattering media by exploiting local pressure differences created by acoustic waves that result in refractive index contrasts. We show that virtual light pipes can be created deep into the tissue (>18 scattering mean free paths). We demonstrate the application of this technology in confining light through mouse brain tissue. This technology is likely extendable to form arbitrary light patterns within tissue, extending both the reach and the flexibility of light-based methods.

Advances in Penetrating Multichannel Microelectrodes Based on the Utah Array Platform

The Utah electrode array (UEA) and its many derivatives have become a gold standard for high-channel count bi-directional neural interfaces, in particular in human subject applications. The chapter provides a brief overview of leading electrode concepts and the context in which the UEA has to be understood. It goes on to discuss the key advances and developments of the UEA platform in the past 15 years, as well as novel wireless and system integration technologies that will merge into future generations of fully integrated devices. Aspects covered include novel device architectures that allow scaling of channel count and density of electrode contacts, material improvements to substrate, electrode contacts, and encapsulation. Further subjects are adaptations of the UEA platform to support IR and optogenetic simulation as well as an improved understanding of failure modes and methods to test and accelerate degradation in vitro such as to better predict device failure and lifetime in vivo.

Implantable Neural Probes for Brain-Machine Interfaces - Current Developments and Future Prospects

A Brain-Machine interface (BMI) allows for direct communication between the brain and machines. Neural probes for recording neural signals are among the essential components of a BMI system. In this report, we review research regarding implantable neural probes and their applications to BMIs. We first discuss conventional neural probes such as the tetrode, Utah array, Michigan probe, and electroencephalography (ECoG), following which we cover advancements in next-generation neural probes. These next-generation probes are associated with improvements in electrical properties, mechanical durability, biocompatibility, and offer a high degree of freedom in practical settings. Specifically, we focus on three key topics: (1) novel implantable neural probes that decrease the level of invasiveness without sacrificing performance, (2) multi-modal neural probes that measure both electrical and optical signals, (3) and neural probes developed using advanced materials. Because safety and precision are critical for practical applications of BMI systems, future studies should aim to enhance these properties when developing next-generation neural probes.

High-Density μLED-Based Optical Cochlear Implant With Improved Thermomechanical Behavior

This study reports the realization of an optical cochlear implant (oCI) with optimized thermomechanical properties for optogenetic experiments. The oCI probe comprises 144 miniaturized light-emitting diodes (μLEDs) distributed along a bendable, 1.5-cm-long, 350-μm-wide and 26-μm-thick probe shaft, individually controlled via a n × p matrix interconnection. In contrast to our earlier approach based on polyimide (PI) and epoxy resin with different thermal expansion coefficients, the μLEDs and interconnecting wires are now embedded into a triple-layer stack of a single, biocompatible, and highly transparent epoxy material. The new material combination results in a pronounced reduction of thermomechanical bending in comparison with the material pair of the earlier approach. We developed a spin-coating process enabling epoxy resin layers down to 5 μm at thickness variations of less than 7% across the entire carrier wafer. We observed that the cross-linking of epoxy resin layers strongly depends on the spin-coating parameters which were found to be correlated to a potential separation of epoxy resin components of different densities. Furthermore, various metallization layers and corresponding adhesion promoting layers were investigated. We identified the combination of silicon carbide with a titanium-based metallization to provide the highest peeling strength, achieving an adhesion to epoxy improved by a factor of two. In order to obtain a high process yield, we established a stress-free implant release using the electrochemical dissolution of a sacrificial aluminum layer. The direct comparison of oCI probe variants using a single epoxy material and the combination of PI and epoxy resin revealed that the epoxy-resin-only probe shows minimal thermomechanical probe bending with a negligible hysteresis. The thermal probe characterization demonstrated that the temperature increase is limited to 1 K at μLED DC currents of up to 10 mA depending on the stimulation duration and the medium surrounding the probe. The optical output power and peak wavelengths of the new oCI variant were extracted to be 0.82 mW and 462 nm when operating the μLEDs at 10 mA, 10 kHz, and a duty cycle of 10%. The optical power corresponds to a radiant emittance of 407 mW/mm2, sufficient for optogenetic experiments using channelrhodopsin-2.

Upconverting nanoparticle micro-lightbulbs designed for deep tissue optical stimulation and imaging

Optical methods for imaging and stimulation of biological events based on the use of visible light are limited to the superficial layers of tissue due to the significant absorption and scattering of light. Here, we demonstrate the design and implementation of passive micro-structured lightbulbs (MLBs) containing bright-emitting lanthanide-doped upconverting nanoparticles (UCNPs) for light delivery deep into the tissue. The MLBs are realized as cylindrical pillars made of Parylene C polymer that can be implanted deep into the tissue. The encapsulated UCNPs absorb near-infrared (NIR) light at λ = 980 nm, which undergoes much less absorption than the blue light in the brain tissue, and then locally emit blue light (¹G₄→³H₆ and ¹D₂→³F₄ transitions) that can be used for optogenetic excitation of neurons in the brain. The ³H₄→³H₆ transition will result in the emission of higher energy NIR photons at λ = 800 nm that can be used for imaging and tracking MLBs through thick tissue.

Design and manufacturing challenges of optogenetic neural interfaces: a review

Optogenetics is a relatively new technology to achieve cell-type specific neuromodulation with millisecond-scale temporal precision. Optogenetic tools are being developed to address neuroscience challenges, and to improve the knowledge about brain networks, with the ultimate aim of catalyzing new treatments for brain disorders and diseases. To reach this ambitious goal the implementation of mature and reliable engineered tools is required. The success of optogenetics relies on optical tools that can deliver light into the neural tissue. Objective/Approach: Here, the design and manufacturing approaches available to the scientific community are reviewed, and current challenges to accomplish appropriate scalable, multimodal and wireless optical devices are discussed.

SIGNIFICANCE

Overall, this review aims at presenting a helpful guidance to the engineering and design of optical microsystems for optogenetic applications.

Light-Guiding Biomaterials for Biomedical Applications

Optical techniques used in medical diagnosis, surgery, and therapy require efficient and flexible delivery of light from light sources to target tissues. While this need is currently fulfilled by glass and plastic optical fibers, recent emergence of biointegrated approaches, such as optogenetics and implanted devices, call for novel waveguides with certain biophysical and biocompatible properties and desirable shapes beyond what the conventional optical fibers can offer. To this end, exploratory efforts have begun to harness various transparent biomaterials to develop waveguides that can serve existing applications better and enable new applications in future photomedicine. Here, we review the recent progress in this new area of research for developing biomaterial-based optical waveguides. We begin with a survey of biological light-guiding structures found in plants and animals, a source of inspiration for biomaterial photonics engineering. We describe natural and synthetic polymers and hydrogels that offer appropriate optical properties, biocompatibility, biodegradability, and mechanical flexibility have been exploited for light-guiding applications. Finally, we briefly discuss perspectives on biomedical applications that may benefit from the unique properties and functionalities of light-guiding biomaterials.

Use of SU8 as a stable and biocompatible adhesion layer for gold bioelectrodes

Gold is the most widely used electrode material for bioelectronic applications due to its high electrical conductivity, good chemical stability and proven biocompatibility. However, it adheres only weakly to widely used substrate materials such as glass and silicon oxide, typically requiring the use of a thin layer of chromium between the substrate and the metal to achieve adequate adhesion. Unfortunately, this approach can reduce biocompatibility relative to pure gold films due to the risk of the underlying layer of chromium becoming exposed. Here we report on an alternative adhesion layer for gold and other metals formed from a thin layer of the negative-tone photoresist SU-8, which we find to be significantly less cytotoxic than chromium, being broadly comparable to bare glass in terms of its biocompatibility. Various treatment protocols for SU-8 were investigated, with a view to attaining high transparency and good mechanical and biochemical stability. Thermal annealing to induce partial cross-linking of the SU-8 film prior to gold deposition, with further annealing after deposition to complete cross-linking, was found to yield the best electrode properties. The optimized glass/SU8-Au electrodes were highly transparent, resilient to delamination, stable in biological culture medium, and exhibited similar biocompatibility to glass.

Towards miniaturized closed-loop optogenetic stimulation devices

OBJECTIVE

Electrical brain stimulation provides therapeutic benefits for patients with drug-resistant neurological disorders. It, however, has restricted access to cell-type selectivity which limits its treatment effectiveness. Optogenetics, in contrast, enables precise targeting of a specific cell type which can address the issue with electrical brain stimulation. It, nonetheless, disregards real-time brain responses in delivering optimized stimulation to target cells. Closed-loop optogenetics, on the other hand, senses the difference between normal and abnormal states of the brain, and modulates stimulation parameters to achieve the desired stimulation outcome. Current review articles on closed-loop optogenetics have focused on its theoretical aspects and potential benefits. A review of the recent progress in miniaturized closed-loop optogenetic stimulation devices is thus needed.

APPROACH

This paper presents a comprehensive study on the existing miniaturized closed-loop optogenetic stimulation devices and their internal components.

MAIN RESULTS

Hardware components of closed-loop optogenetic stimulation devices including electrode, light-guiding mechanism, optical source, neural recorder, and optical stimulator are discussed. Next, software modules of closed-loop optogenetic stimulation devices including feature extraction, classification, control, and stimulation parameter modulation are described. Then, the existing devices are categorized into open-loop and closed-loop groups, and the combined operation of their neural recorder, optical stimulator, and control approach is discussed. Finally, the challenges in the design and implementation of closed-loop optogenetic stimulation devices are presented, suggestions on how to tackle these challenges are given, and future directions for closed-loop optogenetics are stated.

SIGNIFICANCE

A generic architecture for closed-loop optogenetic stimulation devices involving both hardware and software perspectives is devised. A comprehensive investigation into the most current miniaturized and tetherless closed-loop optogenetic stimulation devices is given. A detailed comparison of the closed-loop optogenetic stimulation devices is presented.

Engineered Axonal Tracts as "Living Electrodes" for Synaptic-Based Modulation of Neural Circuitry

Brain-computer interface and neuromodulation strategies relying on penetrating non-organic electrodes/optrodes are limited by an inflammatory foreign body response that ultimately diminishes performance. A novel "biohybrid" strategy is advanced, whereby living neurons, biomaterials, and microelectrode/optical technology are used together to provide a biologically-based vehicle to probe and modulate nervous-system activity. Microtissue engineering techniques are employed to create axon-based "living electrodes", which are columnar microstructures comprised of neuronal population(s) projecting long axonal tracts within the lumen of a hydrogel designed to chaperone delivery into the brain. Upon microinjection, the axonal segment penetrates to prescribed depth for synaptic integration with local host neurons, with the perikaryal segment remaining externalized below conforming electrical-optical arrays. In this paradigm, only the biological component ultimately remains in the brain, potentially attenuating a chronic foreign-body response. Axon-based living electrodes are constructed using multiple neuronal subtypes, each with differential capacity to stimulate, inhibit, and/or modulate neural circuitry based on specificity uniquely afforded by synaptic integration, yet ultimately computer controlled by optical/electrical components on the brain surface. Current efforts are assessing the efficacy of this biohybrid interface for targeted, synaptic-based neuromodulation, and the specificity, spatial density and long-term fidelity versus conventional microelectronic or optical substrates alone.

An Embedded Real-Time Processing Platform for Optogenetic Neuroprosthetic Applications

Optogenetics offers a powerful new approach for controlling neural circuits. It has numerous applications in both basic and clinical science. These applications require stimulating devices with small processors that can perform real-time neural signal processing, deliver high-intensity light with high spatial and temporal resolution, and do not consume a lot of power. In this paper, we demonstrate the implementation of neuronal models in a platform consisting of an embedded system module and a portable digital light processing projector. As a replacement for damaged neural circuitry, the embedded module processes neural signals and then directs the projector to optogenetically activate a downstream neural pathway. We present a design in the context of stimulating circuits in the visual system, but the approach is feasible for a broad range of biomedical applications.

Recent Progress of Development of Optogenetic Implantable Neural Probes

As a cell type-specific neuromodulation method, optogenetic technique holds remarkable potential for the realisation of advanced neuroprostheses. By genetically expressing light-sensitive proteins such as channelrhodopsin-2 (ChR2) in cell membranes, targeted neurons could be controlled by light. This new neuromodulation technique could then be applied into extensive brain networks and be utilised to provide effective therapies for neurological disorders. However, the development of novel optogenetic implants is still a key challenge in the field. The major requirements include small device dimensions, suitable spatial resolution, high safety, and strong controllability. In this paper, I present a concise review of the significant progress that has been made towards achieving a miniaturised, multifunctional, intelligent optogenetic implant. I identify the key limitations of current technologies and discuss the possible opportunities for future development.

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 light–tissue 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.

Fabrication and analysis of microfiber array platform for optogenetics with cellular resolution

Optogenetics has emerged as a revolutionary technology especially for neuroscience and has advanced continuously over the past decade. Conventional approaches for patterned in vivo optical illumination have a limitation on the implanted device size and achievable spatio-temporal resolution. In this work, we developed a fabrication process for a microfiber array platform. Arrayed poly(methyl methacrylate) (PMMA) microfibers were drawn from a polymer solution and packaged with polydimethylsiloxane (PDMS). The exposed end face of a packaged microfiber was tuned to have a size corresponding to a single cell. To demonstrate its capability for single cell optogenetics, HEK293T cells expressing channelrhodopsin-2 (ChR2) were cultured on the platform and excited with UV laser. We could then observe an elevation in the intracellular Ca²⁺ concentrations due to the influx of Ca²⁺ through the activated ChR2 into the cytosol. The statistical and simulation results indicate that the proposed microfiber array platform can be used for single cell optogenetic applications.

Proceedings of the Eighth International Workshop on Advances in Electrocorticography

Excerpted proceedings of the Eighth International Workshop on Advances in Electrocorticography (ECoG), which convened October 15-16, 2015 in Chicago, IL, are presented. The workshop series has become the foremost gathering to present current basic and clinical research in subdural brain signal recording and analysis.

Bioelectric Medicine and Devices for the Treatment of Spinal Cord Injury

Recovery of motor control is paramount for patients living with paralysis following spinal cord injury (SCI). While a cure or regenerative intervention remains on the horizon for the treatment of SCI, a number of neuroprosthetic devices have been employed to treat and mitigate the symptoms of paralysis associated with injuries to the spinal column and associated comorbidities. The recent success of epidural stimulation to restore voluntary motor function in the lower limbs of a small cohort of patients has breathed new life into the promise of electric-based medicine. Recently, a number of new organic and inorganic electronic devices have been developed for brain-computer interfaces to bypass the injury, for neurorehabilitation, bladder and bowel control, and the restoration of motor or sensory control. Herein, we discuss the recent advances in neuroprosthetic devices for treating SCI and highlight future design needs for closed-loop device systems.

A User-Configurable Headstage for Multimodality Neuromonitoring in Freely Moving Rats

Multimodal monitoring of brain activity, physiology, and neurochemistry is an important approach to gain insight into brain function, modulation, and pathology. With recent progress in micro- and nanotechnology, micro-nano-implants have become important catalysts in advancing brain research. However, to date, only a limited number of brain parameters have been measured simultaneously in awake animals in spite of significant recent progress in sensor technology. Here we have provided a cost and time effective approach to designing a headstage to conduct a multimodality brain monitoring in freely moving animals. To demonstrate this method, we have designed a user-configurable headstage for our micromachined multimodal neural probe. The headstage can reliably record direct-current electrocorticography (DC-ECoG), brain oxygen tension (PbrO₂), cortical temperature, and regional cerebral blood flow (rCBF) simultaneously without significant signal crosstalk or movement artifacts for 72 h. Even in a noisy environment, it can record low-level neural signals with high quality. Moreover, it can easily interface with signal conditioning circuits that have high power consumption and are difficult to miniaturize. To the best of our knowledge, this is the first time where multiple physiological, biochemical, and electrophysiological cerebral variables have been simultaneously recorded from freely moving rats. We anticipate that the developed system will aid in gaining further insight into not only normal cerebral functioning but also pathophysiology of conditions such as epilepsy, stroke, and traumatic brain injury.

Optogenetic Functional MRI

The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional magnetic resonance imaging (ofMRI), which is a novel technique that combines the relatively high spatial resolution of high-field fMRI with the precision of optogenetic stimulation. Fiber optics that enable delivery of specific wavelengths of light deep into the brain in vivo are implanted into regions of interest in order to specifically stimulate targeted cell types that have been genetically induced to express light-sensitive trans-membrane conductance channels, called opsins. fMRI is used to provide a non-invasive method of determining the brain's global dynamic response to optogenetic stimulation of specific neural circuits through measurement of the blood-oxygen-level-dependent (BOLD) signal, which provides an indirect measurement of neuronal activity. This protocol describes the construction of fiber optic implants, the implantation surgeries, the imaging with photostimulation and the data analysis required to successfully perform ofMRI. In summary, the precise stimulation and whole-brain monitoring ability of ofMRI are crucial factors in making ofMRI a powerful tool for the study of the connectomics of the brain in both healthy and diseased states.

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.

Realistic Numerical and Analytical Modeling of Light Scattering in Brain Tissue for Optogenetic Applications(1,2,3)

In recent years, optogenetics has become a central tool in neuroscience research. Estimating the transmission of visible light through brain tissue is of crucial importance for controlling the activation levels of neurons in different depths, designing optical systems, and avoiding lesions from excessive power density. The Kubelka–Munk model and Monte Carlo simulations have previously been used to model light propagation through rodents' brain tissue, however, these prior attempts suffer from fundamental shortcomings. Here, we introduce and study two modified approaches for modeling the distributions of light emanating from a multimode fiber and scattering through tissue, using both realistic numerical Monte Carlo simulations and an analytical approach based on the beam-spread function approach. We demonstrate a good agreement of the new methods' predictions both with recently published data, and with new measurements in mouse brain cortical slices, where our results yield a new cortical scattering length estimate of ∼47 µm at λ = 473 nm, significantly shorter than ordinarily assumed in optogenetic applications.

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.

The Evolution of Neuroprosthetic Interfaces

The ideal neuroprosthetic interface permits high-quality neural recording and stimulation of the nervous system while reliably providing clinical benefits over chronic periods. Although current technologies have made notable strides in this direction, significant improvements must be made to better achieve these design goals and satisfy clinical needs. This article provides an overview of the state of neuroprosthetic interfaces, starting with the design and placement of these interfaces before exploring the stimulation and recording platforms yielded from contemporary research. Finally, we outline emerging research trends in an effort to explore the potential next generation of neuroprosthetic interfaces.

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.

Miniaturized optogenetic neural implants: a review

Optogenetics is an exciting new technology that allows targetable fast control and readout of specific neural populations in complex brain circuits. With the rapid development of light-sensitive microbial opsins, substantial gains in understanding the causal relationships between neural activity and behavior in both healthy and diseased brains have been achieved during the last decade. However, the intricate and complex interactions between different neural populations in mammalian brains require novel, implantable, neural interfaces that are capable of manipulating and probing targeted neurons at multiple sites and with high spatiotemporal resolution. Advanced microtechnology has offered the highest potential to meet these demands of optogenetic applications. In this paper, we review a variety of miniaturized optogenetic neural implants developed in recent years, based on different light sources, including lasers, laser diodes, and light-emitting diodes. We then summarize the specifications of these microimplants and their related microfabrication approaches and discuss the major challenges of current techniques and the vision for the future of the field.

Strategies for optical control and simultaneous electrical readout of extended cortical circuits

BACKGROUND

To dissect the intricate workings of neural circuits, it is essential to gain precise control over subsets of neurons while retaining the ability to monitor larger-scale circuit dynamics. This requires the ability to both evoke and record neural activity simultaneously with high spatial and temporal resolution.

NEW METHOD

In this paper we present approaches that address this need by combining micro-electrocorticography (μECoG) with optogenetics in ways that avoid photovoltaic artifacts.

RESULTS

We demonstrate that variations of this approach are broadly applicable across three commonly studied mammalian species - mouse, rat, and macaque monkey - and that the recorded μECoG signal shows complex spectral and spatio-temporal patterns in response to optical stimulation.

COMPARISON WITH EXISTING METHODS

While optogenetics provides the ability to excite or inhibit neural subpopulations in a targeted fashion, large-scale recording of resulting neural activity remains challenging. Recent advances in optical physiology, such as genetically encoded Ca(2+) indicators, are promising but currently do not allow simultaneous recordings from extended cortical areas due to limitations in optical imaging hardware.

CONCLUSIONS

We demonstrate techniques for the large-scale simultaneous interrogation of cortical circuits in three commonly used mammalian species.

Photoreceptor engineering

Sensory photoreceptors not only control diverse adaptive responses in Nature, but as light-regulated actuators they also provide the foundation for optogenetics, the non-invasive and spatiotemporally precise manipulation of cellular events by light. Novel photoreceptors have been engineered that establish control by light over manifold biological processes previously inaccessible to optogenetic intervention. Recently, photoreceptor engineering has witnessed a rapid development, and light-regulated actuators for the perturbation of a plethora of cellular events are now available. Here, we review fundamental principles of photoreceptors and light-regulated allostery. Photoreceptors dichotomize into associating receptors that alter their oligomeric state as part of light-regulated allostery and non-associating receptors that do not. A survey of engineered photoreceptors pinpoints light-regulated association reactions and order-disorder transitions as particularly powerful and versatile design principles. Photochromic photoreceptors that are bidirectionally toggled by two light colors augur enhanced spatiotemporal resolution and use as photoactivatable fluorophores. By identifying desirable traits in engineered photoreceptors, we provide pointers for the design of future, light-regulated actuators.

Closed-loop and activity-guided optogenetic control

Advances in optical manipulation and observation of neural activity have set the stage for widespread implementation of closed-loop and activity-guided optical control of neural circuit dynamics. Closing the loop optogenetically (i.e., basing optogenetic stimulation on simultaneously observed dynamics in a principled way) is a powerful strategy for causal investigation of neural circuitry. In particular, observing and feeding back the effects of circuit interventions on physiologically relevant timescales is valuable for directly testing whether inferred models of dynamics, connectivity, and causation are accurate in vivo. Here we highlight technical and theoretical foundations as well as recent advances and opportunities in this area, and we review in detail the known caveats and limitations of optogenetic experimentation in the context of addressing these challenges with closed-loop optogenetic control in behaving animals.

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.

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.

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.

Extraction of optical properties and prediction of light distribution in rat brain tissue

Predicting the distribution of light inside any turbid media, such as biological tissue, requires detailed information about the optical properties of the medium, including the absorption and scattering coefficients and the anisotropy factor. Particularly, in biophotonic applications where photons directly interact with the tissue, this information translates to system design optimization, precision in light delivery, and minimization of unintended consequences, such as phototoxicity or photobleaching. In recent years, optogenetics has opened up a new area in deep brain stimulation with light and the method is widely adapted by researchers for the study of the brain circuitries and the dynamics of neurological disorders. A key factor for a successful optogenetic stimulation is delivering an adequate amount of light to the targeted brain objects. The adequate amount of light needed to stimulate each brain object is identified by the tissue optical properties as well as the type of opsin expressed in the tissue, wavelength of the light, and the physical dimensions of the targeted area. Therefore, to implement a precise light delivery system for optogenetics, detailed information about the optical properties of the brain tissue and a mathematical model that incorporates all determining factors is needed to find a good estimation of light distribution in the brain. In general, three measurements are required to obtain the optical properties of any tissue, namely diffuse transmitted light, diffuse reflected light, and transmitted ballistic beam. In this report, these parameters were measured in vitro using intact rat brain slices of 500 μm thickness via a two-integrating spheres optical setup. Then, an inverse adding doubling method was used to extract the optical properties of the tissue from the collected data. These experiments were repeated to cover the whole brain tissue with high spatial resolution for the three different cuts (transverse, sagittal, and coronal) and three different wavelengths (405, 532, and 635 nm) in the visible range of the spectrum. A three-dimensional atlas of the rat brain optical properties was constructed based on the experimental measurements. This database was linked to a Monte Carlo toolbox to simulate light distribution in the tissue for different light source configurations.