Closed-Loop Optogenetic Brain Interface

Wireless and battery-free technologies for neuroengineering

Tethered and battery-powered devices that interface with neural tissues can restrict natural motions and prevent social interactions in animal models, thereby limiting the utility of these devices in behavioural neuroscience research. In this Review Article, we discuss recent progress in the development of miniaturized and ultralightweight devices as neuroengineering platforms that are wireless, battery-free and fully implantable, with capabilities that match or exceed those of wired or battery-powered alternatives. Such classes of advanced neural interfaces with optical, electrical or fluidic functionality can also combine recording and stimulation modalities for closed-loop applications in basic studies or in the practical treatment of abnormal physiological processes.

Auxiliary controller design and performance comparative analysis in closed-loop brain-machine interface system

Brain-machine interface (BMI) can realize information interaction between the brain and external devices, and yet the control accuracy is limited by the change of electroencephalogram signals. The introduction of auxiliary controller can overcome the above problems, but the performance of different auxiliary controllers is quite different. Hence, in this paper, we comprehensively compare and analyze the performance of different auxiliary controllers to provide a theoretical basis for designing BMI system. The main work includes: (1) designing four kinds of auxiliary controllers based on simultaneous perturbation stochastic approximation-function approximator (SPSA-FA), iterative feedback tuning-PID (IFT-PID), model predictive control (MPC) and model-free control (MFC); (2) based on the model of improved single-joint information transmission, constructing the closed-loop BMI systems with the decoder-based Wiener filter; and (3) comparing their performance in the constructed closed-loop BMI systems for dynamic motion restoration. The results show that the order of tracking accuracy is MPC, IFT-PID, SPSA-FA, MFC, and the order of time consumed is opposite. A good control effectiveness is achieved at the expense of time, so a suitable auxiliary controller should be selected according to the actual requirements.

Closed-loop Modulation of the Self-regulating Brain: A Review on Approaches, Emerging Paradigms, and Experimental Designs

Closed-loop approaches, setups, and experimental designs have been applied within the field of neuroscience to enhance the understanding of basic neurophysiology principles (closed-loop neuroscience; CLNS) and to develop improved procedures for modulating brain circuits and networks for clinical purposes (closed-loop neuromodulation; CLNM). The contents of this review are thus arranged into the following sections. First, we describe basic research findings that have been made using CLNS. Next, we provide an overview of the application, rationale, and therapeutic aspects of CLNM for clinical purposes. Finally, we summarize methodological concerns and critics in clinical practice of neurofeedback and novel applications of closed-loop perspective and techniques to improve and optimize its experiments. Moreover, we outline the theoretical explanations and experimental ideas to test animal models of neurofeedback and discuss technical issues and challenges associated with implementing closed-loop systems. We hope this review is helpful for both basic neuroscientists and clinical/ translationally-oriented scientists interested in applying closed-loop methods to improve mental health and well-being.

Online Decoding System with Calcium Image From Mice Primary Motor Cortex

With the development of calcium imaging, neuroscientists have been able to study neural activity with a higher spatial resolution. However, the real-time processing of calcium imaging is still a big challenge for future experiments and applications. Most neuroscientists have to process their imaging data offline due to the time-consuming of most existing calcium imaging analysis methods. We proposed a novel online neural signal processing framework for calcium imaging and established an Optical Brain-Computer Interface System (OBCIs) for decoding neural signals in real-time. We tested and evaluated this system by classifying the calcium signals obtained from the primary motor cortex of mice when the mice were performing a lever-pressing task. The performance of our online system could achieve above 80% in the average decoding accuracy. Our preliminary results show that the online neural processing framework could be applied to future closed-loop OBCIs studies.

A Closed-Loop Optogenetic Platform

Neuromodulation is an established treatment for numerous neurological conditions, but to expand the therapeutic scope there is a need to improve the spatial, temporal and cell-type specificity of stimulation. Optogenetics is a promising area of current research, enabling optical stimulation of genetically-defined cell types without interfering with concurrent electrical recording for closed-loop control of neural activity. We are developing an open-source system to provide a platform for closed-loop optogenetic neuromodulation, incorporating custom integrated circuitry for recording and stimulation, real-time closed-loop algorithms running on a microcontroller and experimental control via a PC interface. We include commercial components to validate performance, with the ultimate aim of translating this approach to humans. In the meantime our system is flexible and expandable for use in a variety of preclinical neuroscientific applications. The platform consists of a Controlling Abnormal Network Dynamics using Optogenetics (CANDO) Control System (CS) that interfaces with up to four CANDO headstages responsible for electrical recording and optical stimulation through custom CANDO LED optrodes. Control of the hardware, inbuilt algorithms and data acquisition is enabled via the CANDO GUI (Graphical User Interface). Here we describe the design and implementation of this system, and demonstrate how it can be used to modulate neuronal oscillations in vitro and in vivo.

Light Modulation of Brain and Development of Relevant Equipment

Light modulation plays an important role in understanding the pathology of brain disorders and improving brain function. Optogenetic techniques can activate or silence targeted neurons with high temporal and spatial accuracy and provide precise control, and have recently become a method for quick manipulation of genetically identified types of neurons. Photobiomodulation (PBM) is light therapy that utilizes non-ionizing light sources, including lasers, light emitting diodes, or broadband light. It provides a safe means of modulating brain activity without any irreversible damage and has established optimal treatment parameters in clinical practice. This manuscript reviews 1) how optogenetic approaches have been used to dissect neural circuits in animal models of Alzheimer's disease, Parkinson's disease, and depression, and 2) how low level transcranial lasers and LED stimulation in humans improves brain activity patterns in these diseases. State-of-the-art brain machine interfaces that can record neural activity and stimulate neurons with light have good prospects in the future.

Living Things Are Not (20th Century) Machines: Updating Mechanism Metaphors in Light of the Modern Science of Machine Behavior

One of the most useful metaphors for driving scientific and engineering progress has been that of the “machine.” Much controversy exists about the applicability of this concept in the life sciences. Advances in molecular biology have revealed numerous design principles that can be harnessed to understand cells from an engineering perspective, and build novel devices to rationally exploit the laws of chemistry, physics, and computation. At the same time, organicists point to the many unique features of life, especially at larger scales of organization, which have resisted decomposition analysis and artificial implementation. Here, we argue that much of this debate has focused on inessential aspects of machines – classical properties which have been surpassed by advances in modern Machine Behavior and no longer apply. This emerging multidisciplinary field, at the interface of artificial life, machine learning, and synthetic bioengineering, is highlighting the inadequacy of existing definitions. Key terms such as machine, robot, program, software, evolved, designed, etc., need to be revised in light of technological and theoretical advances that have moved past the dated philosophical conceptions that have limited our understanding of both evolved and designed systems. Moving beyond contingent aspects of historical and current machines will enable conceptual tools that embrace inevitable advances in synthetic and hybrid bioengineering and computer science, toward a framework that identifies essential distinctions between fundamental concepts of devices and living agents. Progress in both theory and practical applications requires the establishment of a novel conception of “machines as they could be,” based on the profound lessons of biology at all scales. We sketch a perspective that acknowledges the remarkable, unique aspects of life to help re-define key terms, and identify deep, essential features of concepts for a future in which sharp boundaries between evolved and designed systems will not exist.

Decoding with Calcium Signals from Layer 2/3 Motor Cortex during A Pressing Movement

Brain-machine interfaces (BMIs) have been promising for not only neuroprosthesis research but also brain function investigation. Electrophysiological recording commonly used in traditional BMIs is spatially sparse and lack of information about neuron types and spatial organization. However, optical imaging methods might avoid these limitations by providing dense, spatially organized and annotated with genetic information over a large field of view. Here, we tried to demonstrate the potential of calcium imaging signals obtained through the one-photon microscope in neural decoding. When mice were trained to perform a lever press task to obtain water as rewards, the calcium signals of neurons in their layer 2/3 motor cortex were recorded by microscope. With the calcium signals, we analyzed the neural activity at both single individual neuron and neuronal population level. We found two typical classes of pressing-related neurons and distinct ensemble activity patterns between a pressing movement and baseline. The decoding results further demonstrated that the movement-related information could be more completely specified by population response structure. Our results suggested that neural signals from more types and a larger amount of neurons, are crucial for accurate decoding in BMI applications.

A Closed-Loop Optogenetic Stimulation Device

Closed-loop optogenetic stimulation devices deliver optical stimulations based on real-time measurement and analysis of neural responses to stimulations. However, the use of large bench-top and tethered devices hinders the naturalistic test environment, which is crucial in pre-clinical neuroscience studies involving small rodent subjects. This paper presents a tetherless, lightweight and miniaturized head-mountable closed-loop optogenetic stimulation device. The device consists of three hardware modules: a hybrid electrode, an action potential detector, and an optogenetic stimulator. In addition, the device includes three software modules: a feature extractor, a control algorithm, and a pulse generator. The details of the design, implementation, and bench-testing of the device are presented. Furthermore, an in vitro test environment is formed using synthetic neural signals, wherein the device is validated for its closed-loop performance. During the in vitro validation, the device was able to identify abnormal neural signals, and trigger optical stimulation. On the other hand, it was able to also distinguish normal neural signals and inhibit optical stimulation. The overall power consumption of the device is 24 mW. The device measures 6 mm in radius and weighs 0.44 g excluding the power source.

Multimaterial and multifunctional neural interfaces: from surface-type and implantable electrodes to fiber-based devices

Development of neural interfaces from surface electrodes to fibers with various type, functionality, and materials.

3D Printed Cranial Window System for Chronic μECoG Recording

Chronic studies of flexible μECoG electrodes and the electrode-brain interface have been limited by the inability to assess tissue response over time. The electrophysiological system presented here combines epidural microelectrocorticographic (μECoG) recording capabilities with the ability to visualize tissue response over time through light microscopy and optical coherence tomography (OCT). With the ability to interchange both the electrode and the electronics, and a flushing port for injection of flushing saline and/or drugs, this 3D printed system has future applications in chronic electrophysiology, optogenetics, and advanced imaging methods.

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.

Wireless opto-electro neural interface for experiments with small freely behaving animals

OBJECTIVE

We have developed a wireless opto-electro interface (WOENI) device, which combines electrocorticogram (ECoG) recording and optical stimulation for bi-directional neuromodulation on small, freely behaving animals, such as rodents.

APPROACH

The device is comprised of two components, a detachable headstage and an implantable polyimide-based substrate. The headstage establishes a bluetooth low energy (BLE) bi-directional data communication with an external custom-designed USB dongle for receiving user commands and optogenetic stimulation patterns, and sending digitalized ECoG data.

MAIN RESULTS

The functionality and stability of the device were evaluated in vivo on freely behaving rats. When the animal received optical stimulation on the primary visual cortex (V1) and visual stimulation via eyes, spontaneous changes in ECoG signals were recorded from both left and right V1 during four consecutive experiments with 7 d intervals over a time span of 21 d following device implantation. Immunostained tissue analyses showed results consistent with ECoG analyses, validating the efficacy of optical stimulation to upregulate the activity of cortical neurons expressing ChR2.

SIGNIFICANCE

The proposed WOENI device is potentially a versatile tool in the studies that involve long-term optogenetic neuromodulation.

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.

A Compact Closed-Loop Optogenetics System Based on Artifact-Free Transparent Graphene Electrodes

Electrophysiology is a decades-old technique widely used for monitoring activity of individual neurons and local field potentials. Optogenetics has revolutionized neuroscience studies by offering selective and fast control of targeted neurons and neuron populations. The combination of these two techniques is crucial for causal investigation of neural circuits and understanding their functional connectivity. However, electrical artifacts generated by light stimulation interfere with neural recordings and hinder the development of compact closed-loop systems for precise control of neural activity. Here, we demonstrate that transparent graphene micro-electrodes fabricated on a clear polyethylene terephthalate film eliminate the light-induced artifact problem and allow development of a compact battery-powered closed-loop optogenetics system. We extensively investigate light-induced artifacts for graphene electrodes in comparison to metal control electrodes. We then design optical stimulation module using micro-LED chips coupled to optical fibers to deliver light to intended depth for optogenetic stimulation. For artifact-free integration of graphene micro-electrode recordings with optogenetic stimulation, we design and develop a compact closed-loop system and validate it for different frequencies of interest for neural recordings. This compact closed-loop optogenetics system can be used for various applications involving optogenetic stimulation and electrophysiological recordings.

A Chronically Implantable Bidirectional Neural Interface for Non-human Primates

Optogenetics has potential applications in the study of epilepsy and neuroprostheses, and for studies on neural circuit dynamics. However, to achieve translation to clinical usage, optogenetic interfaces that are capable of chronic stimulation and monitoring with minimal brain trauma are required. We aimed to develop a chronically implantable device for photostimulation of the brain of non-human primates. We used a micro-light-emitting diode (LED) array with a flexible polyimide film. The array was combined with a whole-cortex electrocorticographic (ECoG) electrode array for simultaneous photostimulation and recording. Channelrhodopsin-2 (ChR2) was virally transduced into the cerebral cortex of common marmosets, and then the device was epidurally implanted into their brains. We recorded the neural activity during photostimulation of the awake monkeys for 4 months. The neural responses gradually increased after the virus injection for ~8 weeks and remained constant for another 8 weeks. The micro-LED and ECoG arrays allowed semi-invasive simultaneous stimulation and recording during long-term implantation in the brains of non-human primates. The development of this device represents substantial progress in the field of optogenetic applications.

An Integrated Circuit for Simultaneous Extracellular Electrophysiology Recording and Optogenetic Neural Manipulation

OBJECTIVE

The ability to record and to control action potential firing in neuronal circuits is critical to understand how the brain functions. The objective of this study is to develop a monolithic integrated circuit (IC) to record action potentials and simultaneously control action potential firing using optogenetics.

METHODS

A low-noise and high input impedance (or low input capacitance) neural recording amplifier is combined with a high current laser/light-emitting diode (LED) driver in a single IC.

RESULTS

The low input capacitance of the amplifier (9.7 pF) was achieved by adding a dedicated unity gain stage optimized for high impedance metal electrodes. The input referred noise of the amplifier is [Formula: see text], which is lower than the estimated thermal noise of the metal electrode. Thus, the action potentials originating from a single neuron can be recorded with a signal-to-noise ratio of at least 6.6. The LED/laser current driver delivers a maximum current of 330 mA, which is adequate for optogenetic control. The functionality of the IC was tested with an anesthetized Mongolian gerbil and auditory stimulated action potentials were recorded from the inferior colliculus. Spontaneous firings of fifth (trigeminal) nerve fibers were also inhibited using the optogenetic protein Halorhodopsin. Moreover, a noise model of the system was derived to guide the design.

SIGNIFICANCE

A single IC to measure and control action potentials using optogenetic proteins is realized so that more complicated behavioral neuroscience research and the translational neural disorder treatments become possible in the future.

In-vitro validation of a closed-loop optogenetic stimulation device

Closed-loop optogenetic stimulation (CLOS) involves real-time neural data collection and analysis, feedback control, and optical neuromodulation. Despite emergence of the CLOS devices, methods for validating such devices in-vitro are limited. This paper presents a CLOS device and introduces an in-vitro setup for validating CLOS devices. The CLOS device consists of an electrode, a neural detector, a control algorithm, and an optogenetic stimulator. The in-vitro setup consists of saline solution, a neural signal emitter, a photodiode and its amplifier, and a closed-loop simulation program. Synthetic neural signals are delivered to the CLOS device, and based on the sensed optical stimulations from the light source, the properties of the delivered neural signals are changed. Experiments are conducted to evaluate the closed-loop operation of the CLOS device, and verify the capability of the in-vitro setup to for validating the CLOS devices. The in-vitro setup enables refinement of CLOS devices before arduous in-vivo trials.

Endogenous Bioelectric Signaling Networks: Exploiting Voltage Gradients for Control of Growth and Form

Living systems exhibit remarkable abilities to self-assemble, regenerate, and remodel complex shapes. How cellular networks construct and repair specific anatomical outcomes is an open question at the heart of the next-generation science of bioengineering. Developmental bioelectricity is an exciting emerging discipline that exploits endogenous bioelectric signaling among many cell types to regulate pattern formation. We provide a brief overview of this field, review recent data in which bioelectricity is used to control patterning in a range of model systems, and describe the molecular tools being used to probe the role of bioelectrics in the dynamic control of complex anatomy. We suggest that quantitative strategies recently developed to infer semantic content and information processing from ionic activity in the brain might provide important clues to cracking the bioelectric code. Gaining control of the mechanisms by which large-scale shape is regulated in vivo will drive transformative advances in bioengineering, regenerative medicine, and synthetic morphology, and could be used to therapeutically address birth defects, traumatic injury, and cancer.

Implantable optoelectronic probes for in vivo optogenetics

More than a decade has passed since optics and genetics came together and lead to the emerging technologies of optogenetics. The advent of light-sensitive opsins made it possible to optically trigger the neurons into activation or inhibition by using visible light. The importance of spatiotemporally isolating a segment of a neural network and controlling nervous signaling in a precise manner has driven neuroscience researchers and engineers to invest great efforts in designing high precision in vivo implantable devices. These efforts have focused on delivery of sufficient power to deep brain regions, while monitoring neural activity with high resolution and fidelity. In this review, we report the progress made in the field of hybrid optoelectronic neural interfaces that combine optical stimulation with electrophysiological recordings. Different approaches that incorporate optical or electrical components on implantable devices are discussed in detail. Advantages of various different designs as well as practical and fundamental limitations are summarized to illuminate the future of neurotechnology development.

Trends and Challenges in Neuroengineering: Toward "Intelligent" Neuroprostheses through Brain-"Brain Inspired Systems" Communication

Future technologies aiming at restoring and enhancing organs function will intimately rely on near-physiological and energy-efficient communication between living and artificial biomimetic systems. Interfacing brain-inspired devices with the real brain is at the forefront of such emerging field, with the term "neurobiohybrids" indicating all those systems where such interaction is established. We argue that achieving a "high-level" communication and functional synergy between natural and artificial neuronal networks in vivo, will allow the development of a heterogeneous world of neurobiohybrids, which will include "living robots" but will also embrace "intelligent" neuroprostheses for augmentation of brain function. The societal and economical impact of intelligent neuroprostheses is likely to be potentially strong, as they will offer novel therapeutic perspectives for a number of diseases, and going beyond classical pharmaceutical schemes. However, they will unavoidably raise fundamental ethical questions on the intermingling between man and machine and more specifically, on how deeply it should be allowed that brain processing is affected by implanted "intelligent" artificial systems. Following this perspective, we provide the reader with insights on ongoing developments and trends in the field of neurobiohybrids. We address the topic also from a "community building" perspective, showing through a quantitative bibliographic analysis, how scientists working on the engineering of brain-inspired devices and brain-machine interfaces are increasing their interactions. We foresee that such trend preludes to a formidable technological and scientific revolution in brain-machine communication and to the opening of new avenues for restoring or even augmenting brain function for therapeutic purposes.

Optogenetic stimulation of the cochlea-A review of mechanisms, measurements, and first models

This review evaluates the potential of optogenetic methods for the stimulation of the auditory nerve and assesses the feasability of optogenetic cochlear implants (CIs). It provides an overview of all critical steps like opsin targeting strategies, how opsins work, how their function can be modeled and included in neuronal models and the properties of light sources available for optical stimulation. From these foundations, quantitative estimates for the number of independent stimulation channels and the temporal precision of optogenetic stimulation of the auditory nerve are derived and compared with state-of-the-art electrical CIs. We conclude that optogenetic CIs have the potential to increase the number of independent stimulation channels by up to one order of magnitude to about 100, but only if light sources are able to deliver confined illumination patterns independently and parallelly. Already now, opsin variants like ChETA and Chronos enable driving of the auditory nerve up to rates of 200 spikes/s, close to the physiological value of their maximum sustained firing rate. Apart from requiring 10 times more energy than electrical stimulation, optical CIs still face major hurdles concerning the safety of gene transfection and optrode array implantation, for example, before becoming an option to replace electrical CIs.

Portable closed-loop optogenetic stimulation device

This paper presents a closed-loop optogenetic stimulation device to achieve online modulation of neurons. The device is designed to be mountable on small rodents in pre-clinical settings. Considering the size of rodents and the need for portability, a single-piece self-contained device is developed which allows real-time photostimulation based on detected neuronal states. It consists of three components: a neural recorder, a control algorithm, and an optogenetic stimulator. The neural recorder which is realized by analogue circuitry measures the neural signal. The on-off control algorithm analyses the neural signal and controls the stimulation of the target neurons. The optogenetic stimulator performs sampling and digitization of the detected neural signal, runs the control algorithm, and manages the operation of the light source. The configurable neural recorder is capable of 64 dB amplification in the frequency range of 300 Hz to 6 KHz. The outcome of bench testing of the device is reported. The device is portable and headmountable which makes it suitable for use with small rodents in pre-clinical trials.