Real-time in vivo optogenetic neuromodulation and multielectrode electrophysiologic recording with NeuroRighter

Irregular optogenetic stimulation waveforms can induce naturalistic patterns of hippocampal spectral activity

Objective. Therapeutic brain stimulation is conventionally delivered using constant-frequency stimulation pulses. Several recent clinical studies have explored how unconventional and irregular temporal stimulation patterns could enable better therapy. However, it is challenging to understand which irregular patterns are most effective for different therapeutic applications given the massively high-dimensional parameter space.Approach. Here we applied many irregular stimulation patterns in a single neural circuit to demonstrate how they can enable new dimensions of neural control compared to conventional stimulation, to guide future exploration of novel stimulation patterns in translational settings. We optogenetically excited the septohippocampal circuit with constant-frequency, nested pulse, sinusoidal, and randomized stimulation waveforms, systematically varying their amplitude and frequency parameters.Main results.We first found equal entrainment of hippocampal oscillations: all waveforms provided similar gamma-power increase, whereas no parameters increased theta-band power above baseline (despite the mechanistic role of the medial septum in driving hippocampal theta oscillations). We then compared each of the effects of each waveform on high-dimensional multi-band activity states using dimensionality reduction methods. Strikingly, we found that conventional stimulation drove predominantly 'artificial' (different from behavioral activity) effects, whereas all irregular waveforms induced activity patterns that more closely resembled behavioral activity.Significance. Our findings suggest that irregular stimulation patterns are not useful when the desired mechanism is to suppress or enhance a single frequency band. However, novel stimulation patterns may provide the greatest benefit for neural control applications where entraining a particular mixture of bands (e.g. if they are associated with different symptoms) or behaviorally-relevant activity is desired.

Optogenetic modulation of hippocampal oscillations ameliorates spatial cognition and hippocampal dysrhythmia following early-life seizures

There is increasing human and animal evidence that brain oscillations play a critical role in the development of spatial cognition. In rat pups, disruption of hippocampal rhythms via optogenetic stimulation during the critical period for memory development impairs spatial cognition. Early-life seizures are associated with long-term deficits in spatial cognition and aberrant hippocampal oscillatory activity. Here we asked whether modulation of hippocampal rhythms following early-life seizures can reverse or improve hippocampal connectivity and spatial cognition. We used optogenetic stimulation of the medial septum to induce physiological 7 Hz theta oscillations in the hippocampus during the critical period of spatial cognition following early-life seizures. Optogenetic stimulation of the medial septum in control and rats subjected to early-life seizures resulted in precisely regulated frequency-matched hippocampal oscillations. Rat pups receiving active blue light stimulation performed better than the rats receiving inert yellow light in a test of spatial cognition. The improvement in spatial cognition in these rats was associated with a faster theta frequency and higher theta power, coherence and phase locking value in the hippocampus than rats with early-life seizures receiving inert yellow light. These findings indicate that following early life seizures, modification of hippocampal rhythms may be a potential novel therapeutic modality.

Tracking motion kinematics and tremor with intrinsic oscillatory property of instrumental mechanics

Tracking kinematic details of motor behaviors is a foundation to study the neuronal mechanism and biology of motor control. However, most of the physiological motor behaviors and movement disorders, such as gait, balance, tremor, dystonia, and myoclonus, are highly dependent on the overall momentum of the whole-body movements. Therefore, tracking the targeted movement and overall momentum simultaneously is critical for motor control research, but it remains an unmet need. Here, we introduce the intrinsic oscillatory property (IOP), a fundamental mechanical principle of physics, as a method for motion tracking in a force plate. The overall kinetic energy of animal motions can be transformed into the oscillatory amplitudes at the designed IOP frequency of the force plate, while the target movement has its own frequency features and can be tracked simultaneously. Using action tremor as an example, we reported that force plate-based IOP approach has superior performance and reliability in detecting both tremor severity and tremor frequency, showing a lower level of coefficient of variation (CV) compared with video- and accelerometer-based motion tracking methods and their combination. Under the locomotor suppression effect of medications, therapeutic effects on tremor severity can still be quantified by dynamically adjusting the overall locomotor activity detected by IOP. We further validated IOP method in optogenetic-induced movements and natural movements, confirming that IOP can represent the intensity of general rhythmic and nonrhythmic movements, thus it can be generalized as a common approach to study kinematics.

A Review: Research Progress of Neural Probes for Brain Research and Brain-Computer Interface

Neural probes, as an invasive physiological tool at the mesoscopic scale, can decipher the code of brain connections and communications from the cellular or even molecular level, and realize information fusion between the human body and external machines. In addition to traditional electrodes, two new types of neural probes have been developed in recent years: optoprobes based on optogenetics and magnetrodes that record neural magnetic signals. In this review, we give a comprehensive overview of these three kinds of neural probes. We firstly discuss the development of microelectrodes and strategies for their flexibility, which is mainly represented by the selection of flexible substrates and new electrode materials. Subsequently, the concept of optogenetics is introduced, followed by the review of several novel structures of optoprobes, which are divided into multifunctional optoprobes integrated with microfluidic channels, artifact-free optoprobes, three-dimensional drivable optoprobes, and flexible optoprobes. At last, we introduce the fundamental perspectives of magnetoresistive (MR) sensors and then review the research progress of magnetrodes based on it.

A Miniaturized Closed-Loop Optogenetic Brain Stimulation Device

This paper presents a tetherless and miniaturized closed-loop optogenetic brain stimulation device, designed as a back mountable device for laboratory mice. The device has the ability to sense the biomarkers corresponding to major depressive disorder (MDD) from local field potential (LFP), and produces a feedback signal to control the closed-loop operation after on-device processing of the sensed signals. MDD is a chronic neurological disorder and there are still many unanswered questions about the underlying neurological mechanisms behind its occurrence. Along with other brain stimulation paradigms, optogenetics has recently proved effective in the study of MDD. Most of these experiments have used tethered and connected devices. However, the use of tethered devices in optogenetic brain stimulation experiments has the drawback of hindering the free movement of the laboratory animal subjects undergoing stimulation. To address this issue, the proposed device is small, light-weight, untethered, and back-mountable. The device consists of: (i) an optrode which houses an electrode for collecting neural signals, an optical source for delivering light stimulations, and a temperature sensor for monitoring the temperature increase at the stimulation site, (ii) a neural sensor for acquisition and pre-processing of the neural signals to obtain LFP signals in the frequency range of 4 to 200 Hz, as electrophysiological biomarkers of MDD (iii) a classifier for classification of the signal into four classes: normal, abnormal alpha, abnormal theta, and abnormal gamma oscillations, (iv) a control algorithm to select stimulation parameters based on the input class, and (v) a stimulator for generating light stimulations. The design, implementation, and evaluation of the device are presented, and the results are discussed. The neural sensor and the stimulator are circular in shape with a radius of 8 mm. Pre-recorded neural signals from the mouse hippocampus are used for the evaluation of the device.

Flexible Neural Probes with Electrochemical Modified Microelectrodes for Artifact-Free Optogenetic Applications

With the rapid increase in the use of optogenetics to investigate nervous systems, there is high demand for neural interfaces that can simultaneously perform optical stimulation and electrophysiological recording. However, high-magnitude stimulation artifacts have prevented experiments from being conducted at a desirably high temporal resolution. Here, a flexible polyimide-based neural probe with polyethylene glycol (PEG) packaged optical fiber and Pt-Black/PEDOT-GO (graphene oxide doped poly(3,4-ethylene-dioxythiophene)) modified microelectrodes was developed to reduce the stimulation artifacts that are induced by photoelectrochemical (PEC) and photovoltaic (PV) effects. The advantages of this design include quick and accurate implantation and high-resolution recording capacities. Firstly, electrochemical performance of the modified microelectrodes is significantly improved due to the large specific surface area of the GO layer. Secondly, good mechanical and electrochemical stability of the modified microelectrodes is obtained by using Pt-Black as bonding layer. Lastly, bench noise recordings revealed that PEC noise amplitude of the modified neural probes could be reduced to less than 50 µV and no PV noise was detected when compared to silicon-based neural probes. The results indicate that this device is a promising optogenetic tool for studying local neural circuits.

Optogenetic Methods for the Study of Circadian Rhythms

A fundamental feature of circadian clock neurons across species is that they express circadian rhythms in spontaneous spike frequency. Spike frequency rhythms serve as both output timing signals of clock neurons as well as resonant elements of rhythms generation. Importantly, optogenetics, as applied to clock neurons, can enable investigation of the roles of clock neuron electrical activity in circadian timing. Here we describe protocols for using both in vitro and in vivo optogenetics directed to mammalian clock neurons in the suprachiasmatic nucleus to study circadian physiology and behavior. Optogenetic stimulation via channelrhodopsin, or inhibition via halorhodopsin, allows for the precise manipulation of neuronal firing rates across the SCN, and within specific neuronal subpopulations thereof, and can be combined with actigraphy and gene expression analysis.

Disruption of hippocampal rhythms via optogenetic stimulation during the critical period for memory development impairs spatial cognition

BACKGROUND

Hippocampal oscillations play a critical role in the ontogeny of allocentric memory in rodents. During the critical period for memory development, hippocampal theta is the driving force behind the temporal coordination of neuronal ensembles underpinning spatial memory. While known that hippocampal oscillations are necessary for normal spatial cognition, whether disrupted hippocampal oscillatory activity during the critical period impairs long-term spatial memory is unknown. Here we investigated whether disruption of normal hippocampal rhythms during the critical period have enduring effects on allocentric memory in rodents.

OBJECTIVE/HYPOTHESIS

We hypothesized that disruption of hippocampal oscillations via artificial regulation of the medial septum during the critical period for memory development results in long-standing deficits in spatial cognition.

METHODS

After demonstrating that pan-neuronal medial septum (MS) optogenetic stimulation (465 nm activated) regulated hippocampal oscillations in weanling rats we used a random pattern of stimulation frequencies to disrupt hippocampal theta rhythms for either 1Hr or 5hr a day between postnatal (P) days 21-25. Non-stimulated and yellow light-stimulated (590 nm) rats served as controls. At P50-60 all rats were tested for spatial cognition in the active avoidance task. Rats were then sacrificed, and the MS and hippocampus assessed for cell loss. Power spectrum density of the MS and hippocampus, coherences and voltage correlations between MS and hippocampus were evaluated at baseline for a range of stimulation frequencies from 0.5 to 110 Hz and during disruptive hippocampal stimulation. Unpaired t-tests and ANOVA were used to compare oscillatory parameters, behavior and cell density in all animals.

RESULTS

Non-selective optogenetic stimulation of the MS in P21 rats resulted in precise regulation of hippocampal oscillations with 1:1 entrainment between stimulation frequency (0.5-110 Hz) and hippocampal local field potentials. Across bandwidths MS stimulation increased power, coherence and voltage correlation at all frequencies whereas the disruptive stimulation increased power and reduced coherence and voltage correlations with most statistical measures highly significant (p < 0.001, following correction for false detection). Rats receiving disruptive hippocampal stimulation during the critical period for memory development for either 1Hr or 5hr had marked impairment in spatial learning as measured in active avoidance test compared to non-stimulated or yellow light-control rats (p < 0.001). No cell loss was measured between the blue-stimulated and non-stimulated or yellow light-stimulated controls in either the MS or hippocampus.

CONCLUSION

The results demonstrated that robust regulation of hippocampal oscillations can be achieved with non-selective optogenetic stimulation of the MS in rat pups. A disruptive hippocampal stimulation protocol, which markedly increases power and reduces coherence and voltage correlations between the MS and hippocampus during the critical period of memory development, results in long-standing spatial cognitive deficits. This spatial cognitive impairment is not a result of optogenetic stimulation-induced cell loss.

Optimizing neuromodulation based on surrogate neural states for seizure suppression in a rat temporal lobe epilepsy model

OBJECTIVE

Developing a new neuromodulation method for epilepsy treatment requires a large amount of time and resources to find effective stimulation parameters and often fails due to inter-subject variability in stimulation effect. As an alternative, we present a novel data-driven surrogate approach which can optimize the neuromodulation efficiently by investigating the stimulation effect on surrogate neural states.

APPROACH

Medial septum (MS) optogenetic stimulation was applied for modulating electrophysiological activities of the hippocampus in a rat temporal lobe epilepsy model. For the new approach, we implemented machine learning techniques to describe the pathological neural states and to optimize the stimulation parameters. Specifically, first, we found neural state surrogates to estimate a seizure susceptibility based on hippocampal local field potentials. Second, we modulated the neural state surrogates in a desired way with the subject-specific optimal stimulation parameters found by in vivo Bayesian optimization. Finally, we tested whether modulating the neural state surrogates affected seizure frequency.

MAIN RESULTS

We found two neural state surrogates: The first was hippocampal theta power by considering its well-known relationship with epilepsy, and the second was the output of pre-ictal state model (PriSM) which was built by characterizing the hippocampal activity during the pre-ictal period. The optimal stimulation parameters found by Bayesian optimization outperformed the other parameters in terms of modulating the surrogates toward anti-seizure neural state. When treatment efficacy was tested, the subject-specific optimal parameters for increasing theta power were more effective to suppress seizures than fixed stimulation parameter (7 Hz). However, modulation of the other neural state surrogate, PriSM, did not suppress seizures.

SIGNIFICANCE

The surrogate approach can save enormous time and resources to find subject-specific optimal stimulation parameters which can effectively modulate neural states and further improve therapeutic effectiveness. This approach can also be used for improving neuromodulation treatment of other neurological or psychiatric diseases.

A Systematic Review of Closed-Loop Feedback Techniques in Sleep Studies-Related Issues and Future Directions

Advances in computer processing technology have enabled researchers to analyze real-time brain activity and build real-time closed-loop paradigms. In many fields, the effectiveness of these closed-loop protocols has proven to be better than that of the simple open-loop paradigms. Recently, sleep studies have attracted much attention as one possible application of closed-loop paradigms. To date, several studies that used closed-loop paradigms have been reported in the sleep-related literature and recommend a closed-loop feedback system to enhance specific brain activity during sleep, which leads to improvements in sleep's effects, such as memory consolidation. However, to the best of our knowledge, no report has reviewed and discussed the detailed technical issues that arise in designing sleep closed-loop paradigms. In this paper, we reviewed the most recent reports on sleep closed-loop paradigms and offered an in-depth discussion of some of their technical issues. We found 148 journal articles strongly related with 'sleep and stimulation' and reviewed 20 articles on closed-loop feedback sleep studies. We focused on human sleep studies conducting any modality of feedback stimulation. Then we introduced the main component of the closed-loop system and summarized several open-source libraries, which are widely used in closed-loop systems, with step-by-step guidelines for closed-loop system implementation for sleep. Further, we proposed future directions for sleep research with closed-loop feedback systems, which provide some insight into closed-loop feedback systems.

Artifact-free and high-temporal-resolution in vivo opto-electrophysiology with microLED optoelectrodes

The combination of in vivo extracellular recording and genetic-engineering-assisted optical stimulation is a powerful tool for the study of neuronal circuits. Precise analysis of complex neural circuits requires high-density integration of multiple cellular-size light sources and recording electrodes. However, high-density integration inevitably introduces stimulation artifact. We present minimal-stimulation-artifact (miniSTAR) μLED optoelectrodes that enable effective elimination of stimulation artifact. A multi-metal-layer structure with a shielding layer effectively suppresses capacitive coupling of stimulation signals. A heavily boron-doped silicon substrate silences the photovoltaic effect induced from LED illumination. With transient stimulation pulse shaping, we reduced stimulation artifact on miniSTAR μLED optoelectrodes to below 50 μVpp, much smaller than a typical spike detection threshold, at optical stimulation of >50 mW mm-2 irradiance. We demonstrated high-temporal resolution (<1 ms) opto-electrophysiology without any artifact-induced signal quality degradation during in vivo experiments. MiniSTAR μLED optoelectrodes will facilitate functional mapping of local circuits and discoveries in the brain.

Long-term Intracellular Recording of Optogenetically-induced Electrical Activities using Vertical Nanowire Multi Electrode Array

Continuous recording of intracellular activities in single cells is required for deciphering rare, dynamic and heterogeneous cell responses, which are missed by population or brief single-cell recording. Even if the field of intracellular recording is constantly proceeding, several technical challenges are still remained to conquer this important approach. Here, we demonstrate long-term intracellular recording by combining a vertical nanowire multi electrode array (VNMEA) with optogenetic stimulation to minimally disrupt cell survival and functions during intracellular access and measurement. We synthesized small-diameter and high-aspect-ratio silicon nanowires to spontaneously penetrate into single cells, and used light to modulate the cell's responsiveness. The light-induced intra- and extracellular activities of individual optogenetically-modified cells were measured simultaneously, and each cell showed distinctly different measurement characteristics according to the cell-electrode configuration. Intracellular recordings were achieved continuously and reliably without signal interference and attenuation over 24 hours. The integration of two controllable techniques, vertically grown nanowire electrodes and optogenetics, expands the strategies for discovering the mechanisms for crucial physiological and dynamic processes in various types of cells.

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.

Real-time contextual feedback for close-loop control of navigation

OBJECTIVE

Close-loop control of brain and behavior will benefit from real-time detection of behavioral events to enable low-latency communication with peripheral devices. In animal experiments, this is typically achieved by using sparsely distributed (embedded) sensors that detect animal presence in select regions of interest. High-speed cameras provide high-density sampling across large arenas, capturing the richness of animal behavior, however, the image processing bottleneck prohibits real-time feedback in the context of rapidly evolving behaviors.

APPROACH

Here we developed an open-source software, named PolyTouch, to track animal behavior in large arenas and provide rapid close-loop feedback in ~5.7 ms, ie. average latency from the detection of an event to analog stimulus delivery, e.g. auditory tone, TTL pulse, when tracking a single body. This stand-alone software is written in JAVA. The included wrapper for MATLAB provides experimental flexibility for data acquisition, analysis and visualization.

MAIN RESULTS

As a proof-of-principle application we deployed the PolyTouch for place awareness training. A user-defined portion of the arena was used as a virtual target; visit (or approach) to the target triggered auditory feedback. We show that mice develop awareness to virtual spaces, tend to stay shorter and move faster when they reside in the virtual target zone if their visits are coupled to relatively high stimulus intensity (⩾49 dB). Thus, close-loop presentation of perceived aversive feedback is sufficient to condition mice to avoid virtual targets within the span of a single session (~20 min).

SIGNIFICANCE

Neuromodulation techniques now allow control of neural activity in a cell-type specific manner in spiking resolution. Using animal behavior to drive closed-loop control of neural activity would help to address the neural basis of behavioral state and environmental context-dependent information processing in the brain.

A characterization of epileptogenesis presented in hippocampal neural activity in a rat tetanus toxin model

We built a regression model to describe the progress of epileptogenesis in a rat intrahippocampal tetanus toxin (TeNT) epilepsy model by identifying informative neural features from hippocampal local field potentials (LFPs). The LFPs were recorded from the awake and freely behaving animals during the latent period and the active-seizure period. Frequency domain neural features including power spectral density, coherence and phase coherence were calculated from the hippocampal LFPs. A least angle regression with elastic net regularization (LARS-ENR) model successfully predicted a relative day from the first seizure in multiple rats (R²_test = 0.724±0.025). By leveraging a characteristic of LARS-ENR which reduces unnecessary features, we identified the neural features related to epileptogenesis in a TeNT model.

A Machine Learning Approach to Characterize the Modulation of the Hippocampal Rhythms Via Optogenetic Stimulation of the Medial Septum

The medial septum (MS) is a potential target for modulating hippocampal activity. However, given the multiple cell types involved, the changes in hippocampal neural activity induced by MS stimulation have not yet been fully characterized. We combined MS optogenetic stimulation with local field potential (LFP) recordings from the hippocampus and leveraged machine learning techniques to explore how activating or inhibiting multiple MS neuronal subpopulations using different optical stimulation parameters affects hippocampal LFP biomarkers. First, of the seven different optogenetic viral vectors used for modulating different neuronal subpopulations, only two induced a substantial change in hippocampal LFP. Second, we found hippocampal low-gamma band to be most effectively modulated by the stimulation. Third, the hippocampal biomarkers were sensitive to the optogenetic virus type and the stimulation frequency, establishing those parameters as the critical ones for the regulation of hippocampal biomarker activity. Last, we built a Gaussian process regression model to describe the relationship between stimulation parameters and activity of the biomarker as well as to identify the optimal parameters for biomarker modulation. This new machine learning approach can further our understanding of the effects of neural stimulation and guide the selection of optimal parameters for neural control.

Optogenetic entrainment of neural oscillations with hybrid fiber probes

OBJECTIVE

Optogenetic modulation of neural activity is a ubiquitous tool for basic investigation of brain circuits. While the majority of optogenetic paradigms rely on short light pulses to evoke synchronized activity of optically sensitized cells, many neurobiological processes are associated with slow local field potential (LFP) oscillations. Therefore, we developed a hybrid fiber probe capable of simultaneous electrophysiological recording and optical stimulation and used it to investigate the utility of sinusoidal light stimulation for evoking oscillatory neural activity in vivo across a broad frequency range.

APPROACH

We fabricated hybrid fiber probes comprising a hollow cylindrical array of 9 electrodes and a flexible optical waveguide integrated within the core. We implanted these probes in the hippocampus of transgenic Thy1-ChR2-YFP mice that broadly express the blue-light sensitive cation channel channelrhodopsin 2 (ChR2) in excitatory neurons across the brain. The effects of the sinusoidal light stimulation were characterized and contrasted with those corresponding to pulsed stimulation in the frequency range of physiological LFP rhythms (3-128 Hz).

MAIN RESULTS

Within hybrid probes, metal electrode surfaces were vertically aligned with the waveguide tip, which minimized optical stimulation artifacts in neurophysiological recordings. Sinusoidal stimulation resulted in reliable and coherent entrainment of LFP oscillations up to 70 Hz, the cutoff frequency of ChR2, with response amplitudes inversely scaling with the stimulation frequencies. Effectiveness of the stimulation was maintained for two months following implantation.

SIGNIFICANCE

Alternative stimulation patterns complementing existing pulsed protocols, in particular sinusoidal light stimulation, are a prerequisite for investigating the physiological mechanisms underlying brain rhythms. So far, studies applying sinusoidal stimulation in vivo were limited to single stimulation frequencies. We show the feasibility of sinusoidal stimulation in vivo to induce coherent LFP oscillations across the entire frequency spectrum supported by the gating dynamics of ChR2 and introduce a hybrid fiber probe tailored to continuous light stimulation.

Optogenetic Modulation of a Minor Fraction of Parvalbumin-Positive Interneurons Specifically Affects Spatiotemporal Dynamics of Spontaneous and Sensory-Evoked Activity in Mouse Somatosensory Cortex in Vivo

Parvalbumin (PV) positive interneurons exert strong effects on the neocortical excitatory network, but it remains unclear how they impact the spatiotemporal dynamics of sensory processing in the somatosensory cortex. Here, we characterized the effects of optogenetic inhibition and activation of PV interneurons on spontaneous and sensory-evoked activity in mouse barrel cortex in vivo. Inhibiting PV interneurons led to a broad-spectrum power increase both in spontaneous and sensory-evoked activity. Whisker-evoked responses were significantly increased within 20 ms after stimulus onset during inhibition of PV interneurons, demonstrating high temporal precision of PV-shaped inhibition. Multiunit activity was strongly enhanced in neighboring cortical columns, but not at the site of transduction, supporting a central and highly specific role of PV interneurons in lateral inhibition. Inversely, activating PV interneurons drastically decreased spontaneous and whisker-evoked activity in the principal column and exerted strong lateral inhibition. Histological assessment of transduced cells combined with quantitative modeling of light distribution and spike sorting revealed that only a minor fraction (~10%) of the local PV population comprising no more than a few hundred neurons is optogenetically modulated, mediating the observed prominent and widespread effects on neocortical processing.

Multimed: An Integrated, Multi-Application Platform for the Real-Time Recording and Sub-Millisecond Processing of Biosignals

Enhanced understanding and control of electrophysiology mechanisms are increasingly being hailed as key knowledge in the fields of modern biology and medicine. As more and more excitable cell mechanics are being investigated and exploited, the need for flexible electrophysiology setups becomes apparent. With that aim, we designed Multimed, which is a versatile hardware platform for the real-time recording and processing of biosignals. Digital processing in Multimed is an arrangement of generic processing units from a custom library. These can freely be rearranged to match the needs of the application. Embedded onto a Field Programmable Gate Array (FPGA), these modules utilize full-hardware signal processing to lower processing latency. It achieves constant latency, and sub-millisecond processing and decision-making on 64 channels. The FPGA core processing unit makes Multimed suitable as either a reconfigurable electrophysiology system or a prototyping platform for VLSI implantable medical devices. It is specifically designed for open- and closed-loop experiments and provides consistent feedback rules, well within biological microseconds timeframes. This paper presents the specifications and architecture of the Multimed system, then details the biosignal processing algorithms and their digital implementation. Finally, three applications utilizing Multimed in neuroscience and diabetes research are described. They demonstrate the system’s configurability, its multi-channel, real-time processing, and its feedback control capabilities.

Bioelectronic organ-based sensor for microfluidic real-time analysis of the demand in insulin

On-line and real-time analysis of micro-organ activity permits to use the endogenous analytical power of cellular signal transduction algorithms as biosensors. We have developed here such a sensor using only a few pancreatic endocrine islets and the avoidance of transgenes or chemical probes reduces bias and procures general usage. Nutrient and hormone-induced changes in islet ion fluxes through channels provide the first integrative read-out of micro-organ activity. Using extracellular electrodes we captured this read-out non-invasively as slow potentials which reflect glucose concentration-dependent (3-15 mM) micro-organ activation and coupling. Custom-made PDMS-based microfluidics with platinum black micro-electrode arrays required only some tens of islets and functioned at flow rates of 1-10 µl/min which are compatible with microdialysis. We developed hardware solutions for on-line real-time analysis on a reconfigurable Field-Programmable Gate Array (FPGA) that offered resource-efficient architecture and storage of intermediary processing stages. Moreover, real-time adaptive and reconfigurable algorithms accounted for signal disparities and noise distribution. Based on islet slow potentials, this integrated set-up allowed within less than 40 μs the discrimination and precise automatic ranking of small increases (2 mM steps) of glucose concentrations in real time and within the physiological glucose range. This approach shall permit further development in continuous monitoring of the demand for insulin in type 1 diabetes as well as monitoring of organs-on-chip or maturation of stem-cell derived islets.

Stretchable Transparent Electrode Arrays for Simultaneous Electrical and Optical Interrogation of Neural Circuits in Vivo

Recent developments of transparent electrode arrays provide a unique capability for simultaneous optical and electrical interrogation of neural circuits in the brain. However, none of these electrode arrays possess the stretchability highly desired for interfacing with mechanically active neural systems, such as the brain under injury, the spinal cord, and the peripheral nervous system (PNS). Here, we report a stretchable transparent electrode array from carbon nanotube (CNT) web-like thin films that retains excellent electrochemical performance and broad-band optical transparency under stretching and is highly durable under cyclic stretching deformation. We show that the CNT electrodes record well-defined neuronal response signals with negligible light-induced artifacts from cortical surfaces under optogenetic stimulation. Simultaneous two-photon calcium imaging through the transparent CNT electrodes from cortical surfaces of GCaMP-expressing mice with epilepsy shows individual activated neurons in brain regions from which the concurrent electrical recording is taken, thus providing complementary cellular information in addition to the high-temporal-resolution electrical recording. Notably, the studies on rats show that the CNT electrodes remain operational during and after brain contusion that involves the rapid deformation of both the electrode array and brain tissue. This enables real-time, continuous electrophysiological monitoring of cortical activity under traumatic brain injury. These results highlight the potential application of the stretchable transparent CNT electrode arrays in combining electrical and optical modalities to study neural circuits, especially under mechanically active conditions, which could potentially provide important new insights into the local circuit dynamics of the spinal cord and PNS as well as the mechanism underlying traumatic injuries of the nervous system.

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.

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.

Predicting the stimulation effectiveness using pre-stimulation neural states via optogenetic activation of the medial septum glutamatergic neurons modulating the hippocampal neural activity

In this study, we explored the role of pre-stimulation neural states on the effectiveness of optogenetic stimulation. Optogenetic stimulation was applied to the medial septum glutamatergic neurons to modulate the hippocampal neural activity in a rat tetanus toxin seizure model. The hippocampal local field potential was recorded using a multi electrode array in an awake and behaving rat. Optical stimulation with a 465nm light source was applied at 35Hz in a 20 seconds off / 20 seconds on pattern with simultaneous recording from the hippocampus. Both the baseline and the stimulation period recordings were divided into 2 second segments and used for the further analysis. In the first experiment, a support vector machine (SVM) model classified the neural states by using spectral features between 0 and 50Hz. 447 out of 545 segments (82.02%) were correctly labeled as `Baseline' while only 326 out of 544 (59.93%) segments from the stimulation period were correctly labeled as `Stimulation.' As the ratio of mislabels is significantly higher for the stimulation period (chi-squared, p<;0.01), we concluded that the stimulation was not always effective. In the second experiment, an SVM model predicted the stimulation effectiveness using the spectral features of the pre-stimulation segments. The classification result shows that 63.7% of the pre-stimulation segments correctly predicted the stimulation effectiveness. These findings suggest that the prediction of the stimulation effectiveness may improve the stimulation efficacy by implementing a state-based stimulation protocol.

Closed Loop Experiment Manager (CLEM)-An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM). CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC) and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs). We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA) that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level.

Utah optrode array customization using stereotactic brain atlases and 3-D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates

As the optogenetic field expands, the need for precise targeting of neocortical circuits only grows more crucial. This work demonstrates a technique for using Solidworks^® computer-aided design (CAD) and readily available stereotactic brain atlases to create a three-dimensional (3-D) model of the dorsal region of area visual cortex 4 (V4D) of the macaque monkey (Macaca fascicularis) visual cortex. The 3-D CAD model of the brain was used to customize an [Formula: see text] Utah optrode array (UOA) after it was determined that a high-density ([Formula: see text]) UOA caused extensive damage to marmoset (Callithrix jacchus) primary visual cortex as assessed by electrophysiological recording of spiking activity through a 1.5-mm-diameter through glass via. The [Formula: see text] UOA was customized for optrode length ([Formula: see text]), optrode width ([Formula: see text]), optrode pitch ([Formula: see text]), backplane thickness ([Formula: see text]), and overall form factor ([Formula: see text]). Two [Formula: see text] UOAs were inserted into layer VI of macaque V4D cortices with minimal damage as assessed in fixed tissue cytochrome oxidase staining in nonrecoverable surgeries. Additionally, two [Formula: see text] arrays were implanted in mice (Mus musculus) motor cortices, providing early evidence for long-term tolerability (over 6 months), and for the ability to integrate the UOA with a Holobundle light delivery system toward patterned optogenetic stimulation of cortical networks.

Maskless wafer-level microfabrication of optical penetrating neural arrays out of soda-lime glass: Utah Optrode Array

Borrowing from the wafer-level fabrication techniques of the Utah Electrode Array, an optical array capable of delivering light for neural optogenetic studies is presented in this paper: the Utah Optrode Array. Utah Optrode Arrays are micromachined out of sheet soda-lime-silica glass using standard backend processes of the semiconductor and microelectronics packaging industries such as precision diamond grinding and wet etching. 9 × 9 arrays with 1100μ m × 100μ m optrodes and a 500μ m back-plane are repeatably reproduced on 2i n wafers 169 arrays at a time. This paper describes the steps and some of the common errors of optrode fabrication.

A machine learning approach to characterizing the effect of asynchronous distributed electrical stimulation on hippocampal neural dynamics in vivo

Asynchronous distributed microelectrode theta stimulation (ADMETS) of the hippocampus has been shown to reduce seizure frequency in the tetanus toxin rat model of mesial temporal lobe epilepsy suggesting a hypothesis that ADMETS induces a seizure resistant state. Here we present a machine learning approach to characterize the nature of neural state changes induced by distributed stimulation. We applied the stimulation to two animals under sham and ADMETS conditions and used a combination of machine learning techniques on intra-hippocampal recordings of Local Field Potentials (LFPs) to characterize the difference in the neural state between sham and ADMETS. By iteratively fitting a logistic regression with data from the inter-stimulation interval under sham and ADMETS condition we found that the classification performance improves for both animals until 90s post stimulation before leveling out at AUC of 0.64 ± 0.2 and 0.67 ± 0.02 when all inter-stimulation data is included. The models for each animal were re-fit using elastic net regularization to force many of the model coefficients to 0, identifying those that do not optimally contribute to the classifier performance. We found that there is significant variation in the non-zero coefficients between animals (p <; 0.01), suggesting that the ADMETS induced state is represented differently between subject. These findings lay the foundation for using machine learning to robustly and quantitatively characterize neural state.

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.

Efficacy of nonselective optogenetic control of the medial septum over hippocampal oscillations: the influence of speed and implications for cognitive enhancement

Optogenetics holds great promise for both the dissection of neural circuits and the evaluation of theories centered on the temporal organizing properties of oscillations that underpin cognition. To date, no studies have examined the efficacy of optogenetic stimulation for altering hippocampal oscillations in freely moving wild-type rats, or how these alterations would affect performance on behavioral tasks. Here, we used an AAV virus to express ChR2 in the medial septum (MS) of wild-type rats, and optically stimulated septal neurons at 6 Hz and 30 Hz. We measured the corresponding effects of these stimulations on the oscillations of the MS and hippocampal subfields CA1 and CA3 in three different contexts: (1) With minimal movement while the rats sat in a confined chamber; (2) Explored a novel open field; and (3) Learned and performed a T-maze behavioral task. While control yellow light stimulation did not affect oscillations, 6-Hz blue light septal stimulations altered hippocampal theta oscillations in a manner that depended on the animal's mobility and speed. While the 30 Hz blue light septal stimulations only altered theta frequency in CA1 while the rat had limited mobility, it robustly increased the amplitude of hippocampal signals at 30 Hz in both regions in all three recording contexts. We found that animals were more likely to make a correct choice during Day 1 of T-maze training during both MS stimulation protocols than during control stimulation, and that improved performance was independent of theta frequency alterations.

A framework for identification of brain network dynamics using a novel binary noise modulated electrical stimulation pattern

Modeling and identification of brain network dynamics is of great importance both for understanding brain function and for closed-loop control of brain states. In this work, we present a multi-input-multi-output (MIMO) linear state-space model (LSSM) to describe the brain network dynamics in response to electrical stimulation. The LSSM maps the parameters of electrical stimulation, such as frequency, amplitude and pulse-width to recorded brain signals such as electrocorticography (ECoG) and electroencephalography (EEG). Effective identification of the LSSM in open-loop stimulation experiments, however, is strongly dependent on the open-loop input stimulation design. We propose a novel input design to accurately identify the LSSM by integrating the concept of binary noise (BN) with practical constraints on stimulation waveforms. The designed input pattern is a pulse train modulated by stochastic BN parameters. We show that this input pattern both satisfies the necessary spectral condition for accurate system identification and can incorporate any desired pulse shape. Using numerical experiments, we show that the quality of identification depends heavily on the input signal pattern and the proposed binary noise modulated pattern achieves satisfactory identification results, reducing the relative estimation error more than 300 times compared with step sequence modulated, single-sinusoid modulated and multi-sinusoids modulated input patterns.

Implantable neurotechnologies: bidirectional neural interfaces--applications and VLSI circuit implementations

A bidirectional neural interface is a device that transfers information into and out of the nervous system. This class of devices has potential to improve treatment and therapy in several patient populations. Progress in very large-scale integration has advanced the design of complex integrated circuits. System-on-chip devices are capable of recording neural electrical activity and altering natural activity with electrical stimulation. Often, these devices include wireless powering and telemetry functions. This review presents the state of the art of bidirectional circuits as applied to neuroprosthetic, neurorepair, and neurotherapeutic systems.

Direct detection of optogenetically evoked oscillatory neuronal electrical activity in rats using SLOE sequence

The direct detection of neuronal electrical activity is one of the most challenging goals in non-BOLD fMRI research. Previous work has demonstrated its feasibility in phantom and cell culture studies, but attempts in in vivo studies remain few and far between. Most recent in vivo studies used T2*-weighted sequences to directly detect neuronal electrical activity evoked by sensory stimulus. As neuronal electrical signal is usually comprised of a series of spectrally distributed oscillatory waveforms rather than being a direct current, it is most likely to be detected using oscillatory current sensitive sequences. In this study, we explored the potential of using the spin-lock oscillatory excitation (SLOE) sequence with spiral readout to directly detect optogenetically evoked oscillatory neuronal electrical activity, whose main spectral component can be manipulated artificially to match the resonance frequency of spin-lock RF field. In addition, experiments using the stimulus-induced rotary saturation (SIRS) sequence with spiral readout were also performed. Electrophysiological recording and MRI data acquisition were conducted on separate animals. Robust optogenetically evoked oscillatory LFP signals were observed and significant BOLD signals were acquired with the GE-EPI sequence before and after the whole SLOE and SIRS acquisitions, but no significant neuronal current MRI (ncMRI) signal changes were detected. These results indicate that the sensitivity of oscillatory current sensitive sequences needs to be further improved for direct detection of neuronal electrical activity.

Mechanics of mouse ocular motor plant quantified by optogenetic techniques

Rigorous descriptions of ocular motor mechanics are often needed for models of ocular motor circuits. The mouse has become an important tool for ocular motor studies, yet most mechanical data come from larger species. Recordings of mouse abducens neurons indicate the mouse mechanics share basic viscoelastic properties with larger species but have considerably longer time constants. Time constants can also be extracted from the rate at which the eye re-centers when released from an eccentric position. The displacement can be accomplished by electrically stimulating ocular motor nuclei, but electrical stimulation may also activate nearby ocular motor circuitry. We achieved specific activation of abducens motoneurons through photostimulation in transgenic mice expressing channelrhodopsin in cholinergic neurons. Histology confirmed strong channelrhodopsin expression in the abducens nucleus with relatively little expression in nearby ocular motor structures. Stimulation was delivered as 20- to 1,000-ms pulses and 40-Hz trains. Relaxations were modeled best by a two-element viscoelastic system. Time constants were sensitive to stimulus duration. Analysis of isometric relaxation of isolated mouse extraocular muscles suggest the dependence is attributable to noninstantaneous decay of active forces in non-twitch fibers following stimulus offset. Time constants were several times longer than those obtained in primates, confirming that the mouse ocular motor mechanics are relatively sluggish. Finally, we explored the effects of 0.1- to 20-Hz sinusoidal photostimuli and demonstrated their potential usefulness in characterizing ocular motor mechanics, although this application will require further data on the temporal relationship between photostimulation and neuronal firing in extraocular motoneurons.

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.

The inhibitory avoidance discrimination task to investigate accuracy of memory

The present study was aimed at developing a new inhibitory avoidance task, based on training and/or testing rats in multiple contexts, to investigate accuracy of memory. In the first experiment, male Sprague-Dawley rats were given footshock in an inhibitory avoidance apparatus and, 48 h later, retention latencies of each rat were assessed in the training apparatus (Shock box) as well as in a novel, contextually modified, apparatus. Retention latencies in the Shock box were significantly longer than those in the Novel box, indicating accurate memory of the training context. When the noradrenergic stimulant yohimbine (0.3 mg/kg, sc) was administered after the training, 48-h retention latencies in the Shock box, but not Novel box, were increased, indicating that the noradrenergic activation enhanced memory of the training experience without reducing memory accuracy. In the second experiment, rats were trained on an inhibitory avoidance discrimination task: They were first trained in an inhibitory avoidance apparatus without footshock (Non-Shock box), followed 1 min later by footshock training in a contextually modified apparatus (Shock box). Forty-eight-hour retention latencies in the Shock and Non-Shock boxes did not differ from each other but were both significantly longer than those in a Novel box, indicating that rats remembered the two training contexts but did not have episodic-like memory of the association of footshock with the correct training context. When the interval between the two training episodes was increased to 2 min, rats showed accurate memory of the association of footshock with the training context. Yohimbine administered after the training also enhanced rats' ability to remember in which training context they had received actual footshock. These findings indicate that the inhibitory avoidance discrimination task is a novel variant of the well-established inhibitory avoidance task suitable to investigate accuracy of memory.