CLoSES: A platform for closed-loop intracranial stimulation in humans

The Neurostimulationist will see you now: prescribing direct electrical stimulation therapies for the human brain in epilepsy and beyond

As the pace of research in implantable neurotechnology increases, it is important to take a step back and see if the promise lives up to our intentions. While direct electrical stimulation applied intracranially has been used for the treatment of various neurological disorders, such as Parkinson's, epilepsy, clinical depression, and Obsessive-compulsive disorder, the effectiveness can be highly variable. One perspective is that the inability to consistently treat these neurological disorders in a standardized way is due to multiple, interlaced factors, including stimulation parameters, location, and differences in underlying network connectivity, leading to a trial-and-error stimulation approach in the clinic. An alternate view, based on a growing knowledge from neural data, is that variability in this input (stimulation) and output (brain response) relationship may be more predictable and amenable to standardization, personalization, and, ultimately, therapeutic implementation. In this review, we assert that the future of human brain neurostimulation, via direct electrical stimulation, rests on deploying standardized, constrained models for easier clinical implementation and informed by intracranial data sets, such that diverse, individualized therapeutic parameters can efficiently produce similar, robust, positive outcomes for many patients closer to a prescriptive model. We address the pathway needed to arrive at this future by addressing three questions, namely: (1) why aren't we already at this prescriptive future?; (2) how do we get there?; (3) how far are we from this Neurostimulationist prescriptive future? We first posit that there are limited and predictable ways, constrained by underlying networks, for direct electrical stimulation to induce changes in the brain based on past literature. We then address how identifying underlying individual structural and functional brain connectivity which shape these standard responses enable targeted and personalized neuromodulation, bolstered through large-scale efforts, including machine learning techniques, to map and reverse engineer these input-output relationships to produce a good outcome and better identify underlying mechanisms. This understanding will not only be a major advance in enabling intelligent and informed design of neuromodulatory therapeutic tools for a wide variety of neurological diseases, but a shift in how we can predictably, and therapeutically, prescribe stimulation treatments the human brain.

Brain-machine interactive neuromodulation research tool with edge AI computing

Closed-loop neuromodulation with intelligence methods has shown great potentials in providing novel neuro-technology for treating neurological and psychiatric diseases. Development of brain-machine interactive neuromodulation strategies could lead to breakthroughs in precision and personalized electronic medicine. The neuromodulation research tool integrating artificial intelligent computing and performing neural sensing and stimulation in real-time could accelerate the development of closed-loop neuromodulation strategies and translational research into clinical application. In this study, we developed a brain-machine interactive neuromodulation research tool (BMINT), which has capabilities of neurophysiological signals sensing, computing with mainstream machine learning algorithms and delivering electrical stimulation pulse by pulse in real-time. The BMINT research tool achieved system time delay under 3 ms, and computing capabilities in feasible computation cost, efficient deployment of machine learning algorithms and acceleration process. Intelligent computing framework embedded in the BMINT enable real-time closed-loop neuromodulation developed with mainstream AI ecosystem resources. The BMINT could provide timely contribution to accelerate the translational research of intelligent neuromodulation by integrating neural sensing, edge AI computing and stimulation with AI ecosystems.

A scalable platform for acquisition of high-fidelity human intracranial EEG with minimal clinical burden

Human neuroscience research has been significantly advanced by neuroelectrophysiological studies from people with refractory epilepsy-the only routine clinical intervention that acquires multi-day, multi-electrode human intracranial electroencephalography (iEEG). While a sampling rate below 2 kHz is sufficient for manual iEEG review by epileptologists, computational methods and research studies may benefit from higher resolution, which requires significant technical development. At adult and pediatric Stanford hospitals, research ports of commercial clinical acquisition systems were configured to collect 10 kHz iEEG of up to 256 electrodes simultaneously with the clinical data. The research digital stream was designed to be acquired post-digitization, resulting in no loss in clinical signal quality. This novel framework implements a near-invisible research platform to facilitate the secure, routine collection of high-resolution iEEG that minimizes research hardware footprint and clinical workflow interference. The addition of a pocket-sized router in the patient room enabled an encrypted tunnel to securely transmit research-quality iEEG across hospital networks to a research computer within the hospital server room, where data was coded, de-identified, and uploaded to cloud storage. Every eligible patient undergoing iEEG clinical evaluation at both hospitals since September 2017 has been recruited; participant recruitment is ongoing. Over 350+ terabytes (representing 1000+ days) of neuroelectrophysiology were recorded across 200+ participants of diverse demographics. To our knowledge, this is the first report of such a research integration within a hospital setting. It is a promising approach to promoting equitable participant enrollment and building comprehensive data repositories with consistent, high-fidelity specifications towards new discoveries in human neuroscience.

Modular pipeline for reconstruction and localization of implanted intracranial ECoG and sEEG electrodes

Implantation of electrodes in the brain has been used as a clinical tool for decades to stimulate and record brain activity. As this method increasingly becomes the standard of care for several disorders and diseases, there is a growing need to quickly and accurately localize the electrodes once they are placed within the brain. We share here a protocol pipeline for localizing electrodes implanted in the brain, which we have applied to more than 260 patients, that is accessible to multiple skill levels and modular in execution. This pipeline uses multiple software packages to prioritize flexibility by permitting multiple different parallel outputs while minimizing the number of steps for each output. These outputs include co-registered imaging, electrode coordinates, 2D and 3D visualizations of the implants, automatic surface and volumetric localizations of the brain regions per electrode, and anonymization and data sharing tools. We demonstrate here some of the pipeline's visualizations and automatic localization algorithms which we have applied to determine appropriate stimulation targets, to conduct seizure dynamics analysis, and to localize neural activity from cognitive tasks in previous studies. Further, the output facilitates the extraction of information such as the probability of grey matter intersection or the nearest anatomic structure per electrode contact across all data sets that go through the pipeline. We expect that this pipeline will be a useful framework for researchers and clinicians alike to localize implanted electrodes in the human brain.

Closed-loop enhancement and neural decoding of cognitive control in humans

Deficits in cognitive control-that is, in the ability to withhold a default pre-potent response in favour of a more adaptive choice-are common in depression, anxiety, addiction and other mental disorders. Here we report proof-of-concept evidence that, in participants undergoing intracranial epilepsy monitoring, closed-loop direct stimulation of the internal capsule or striatum, especially the dorsal sites, enhances the participants' cognitive control during a conflict task. We also show that closed-loop stimulation upon the detection of lapses in cognitive control produced larger behavioural changes than open-loop stimulation, and that task performance for single trials can be directly decoded from the activity of a small number of electrodes via neural features that are compatible with existing closed-loop brain implants. Closed-loop enhancement of cognitive control might remediate underlying cognitive deficits and aid the treatment of severe mental disorders.

A wearable platform for closed-loop stimulation and recording of single-neuron and local field potential activity in freely moving humans

Advances in technologies that can record and stimulate deep brain activity in humans have led to impactful discoveries within the field of neuroscience and contributed to the development of novel therapies for neurological and psychiatric disorders. Further progress, however, has been hindered by device limitations in that recording of single-neuron activity during freely moving behaviors in humans has not been possible. Additionally, implantable neurostimulation devices, currently approved for human use, have limited stimulation programmability and restricted full-duplex bidirectional capability. In this study, we developed a wearable bidirectional closed-loop neuromodulation system (Neuro-stack) and used it to record single-neuron and local field potential activity during stationary and ambulatory behavior in humans. Together with a highly flexible and customizable stimulation capability, the Neuro-stack provides an opportunity to investigate the neurophysiological basis of disease, develop improved responsive neuromodulation therapies, explore brain function during naturalistic behaviors in humans and, consequently, bridge decades of neuroscientific findings across species.

Manipulating single-unit theta phase-locking with PhaSER: An open-source tool for real-time phase estimation and manipulation

The precise timing of neuronal spiking relative to the brain's endogenous oscillations (i.e., phase-locking or spike-phase coupling) has long been hypothesized to coordinate cognitive processes and maintain excitatory-inhibitory homeostasis. Indeed, disruptions in theta phase-locking have been described in models of neurological diseases with associated cognitive deficits and seizures, such as Alzheimer's disease, temporal lobe epilepsy, and autism spectrum disorders. However, due to technical limitations, determining if phase-locking causally contributes to these disease phenotypes has not been possible until recently. To fill this gap and allow for the flexible manipulation of single-unit phase-locking to on-going endogenous oscillations, we developed PhaSER, an open-source tool that allows for phase-specific manipulations. PhaSER can deliver optogenetic stimulation at defined phases of theta in order to shift the preferred firing phase of neurons relative to theta in real-time. Here, we describe and validate this tool in a subpopulation of inhibitory neurons that express somatostatin (SOM) in the CA1 and dentate gyrus (DG) regions of the dorsal hippocampus. We show that PhaSER is able to accurately deliver a photo-manipulation that activates opsin+ SOM neurons at specified phases of theta in real-time in awake, behaving mice. Further, we show that this manipulation is sufficient to alter the preferred firing phase of opsin+ SOM neurons without altering the referenced theta power or phase. All software and hardware requirements to implement real-time phase manipulations during behavior are available online (https://github.com/ShumanLab/PhaSER).

A Scalable Framework for Closed-Loop Neuromodulation with Deep Learning

Closed-loop neuromodulation measures dynamic neural or physiological activity to optimize interventions for clinical and nonclinical behavioral, cognitive, wellness, attentional, or general task performance enhancement. Conventional closed-loop stimulation approaches can contain biased biomarker detection (decoders and error-based triggering) and stimulation-type application. We present and verify a novel deep learning framework for designing and deploying flexible, data-driven, automated closed-loop neuromodulation that is scalable using diverse datasets, agnostic to stimulation technology (supporting multi-modal stimulation: tACS, tDCS, tFUS, TMS), and without the need for personalized ground-truth performance data. Our approach is based on identified periods of responsiveness - detected states that result in a change in performance when stimulation is applied compared to no stimulation. To demonstrate our framework, we acquire, analyze, and apply a data-driven approach to our open sourced GX dataset, which includes concurrent physiological (ECG, EOG) and neuronal (EEG) measures, paired with continuous vigilance/attention-fatigue tracking, and High-Definition transcranial electrical stimulation (HD-tES). Our framework's decision process for intervention application identified 88.26% of trials as correct applications, showed potential improvement with varying stimulation types, or missed opportunities to stimulate, whereas 11.25% of trials were predicted to stimulate at inopportune times. With emerging datasets and stimulation technologies, our unifying and integrative framework; leveraging deep learning (Convolutional Neural Networks - CNNs); demonstrates the adaptability and feasibility of automated multimodal neuromodulation for both clinical and nonclinical applications.

Advances in human intracranial electroencephalography research, guidelines and good practices

Since the second-half of the twentieth century, intracranial electroencephalography (iEEG), including both electrocorticography (ECoG) and stereo-electroencephalography (sEEG), has provided an intimate view into the human brain. At the interface between fundamental research and the clinic, iEEG provides both high temporal resolution and high spatial specificity but comes with constraints, such as the individual's tailored sparsity of electrode sampling. Over the years, researchers in neuroscience developed their practices to make the most of the iEEG approach. Here we offer a critical review of iEEG research practices in a didactic framework for newcomers, as well addressing issues encountered by proficient researchers. The scope is threefold: (i) review common practices in iEEG research, (ii) suggest potential guidelines for working with iEEG data and answer frequently asked questions based on the most widespread practices, and (iii) based on current neurophysiological knowledge and methodologies, pave the way to good practice standards in iEEG research. The organization of this paper follows the steps of iEEG data processing. The first section contextualizes iEEG data collection. The second section focuses on localization of intracranial electrodes. The third section highlights the main pre-processing steps. The fourth section presents iEEG signal analysis methods. The fifth section discusses statistical approaches. The sixth section draws some unique perspectives on iEEG research. Finally, to ensure a consistent nomenclature throughout the manuscript and to align with other guidelines, e.g., Brain Imaging Data Structure (BIDS) and the OHBM Committee on Best Practices in Data Analysis and Sharing (COBIDAS), we provide a glossary to disambiguate terms related to iEEG research.

EEG Activation Does Not Differ in Simple and Complex Episodes of Disorders of Arousal: A Spectral Analysis Study

Purpose

Disorders of arousal (DoA) are characterized by incomplete awakening from NREM sleep, with the admixture of both deep sleep and wake EEG activity. Previous observations suggested that changes in EEG activity could be detected in the seconds preceding DoA episodes. The aims of this work were to characterize the topography of EEG spectral changes prior to DoA episodes and to investigate whether or not behavioral complexity could be predicted by changes in EEG immediately preceding behavioral onsets.

Patients and Methods

We collected 103 consecutive video-polysomnographic recordings of 53 DoA adult patients and classified all episodes as simple, rising and complex arousal movements. For each episode, a 5-second window preceding its motor onset ("pre-event") and a 60-second window from 2 to 3 minutes before the episodes ("baseline") were compared. Subsequently, a between-group comparison was performed for the pre-event of simpler versus the more complex episodes.

Results

Spectral analysis over 325 DoA episodes showed an absolute significant increase prior to DoA episodes in all frequency bands excluding sigma, which displayed the opposite effect. In normalized maps, the increase was relatively higher over the central/anterior areas for both slow and fast frequency bands. No significant differences emerged from the comparison between simpler and more complex episodes.

Conclusion

Taken together, these results show that deep sleep and wake-like EEG rhythms coexist over overlapping areas before DoA episodes, suggesting an alteration of local sleep mechanisms. Episodes of different complexity are preceded by a similar EEG activation, implying that they possibly share a similar pathophysiology.

Direct Discriminative Decoder Models for Analysis of High-Dimensional Dynamical Neural Data

With the accelerated development of neural recording technology over the past few decades, research in integrative neuroscience has become increasingly reliant on data analysis methods that are scalable to high-dimensional recordings and computationally tractable. Latent process models have shown promising results in estimating the dynamics of cognitive processes using individual models for each neuron's receptive field. However, scaling these models to work on high-dimensional neural recordings remains challenging. Not only is it impractical to build receptive field models for individual neurons of a large neural population, but most neural data analyses based on individual receptive field models discard the local history of neural activity, which has been shown to be critical in the accurate inference of the underlying cognitive processes. Here, we propose a novel, scalable latent process model that can directly estimate cognitive process dynamics without requiring precise receptive field models of individual neurons or brain nodes. We call this the direct discriminative decoder (DDD) model. The DDD model consists of (1) a discriminative process that characterizes the conditional distribution of the signal to be estimated, or state, as a function of both the current neural activity and its local history, and (2) a state transition model that characterizes the evolution of the state over a longer time period. While this modeling framework inherits advantages of existing latent process modeling methods, its computational cost is tractable. More important, the solution can incorporate any information from the history of neural activity at any timescale in computing the estimate of the state process. There are many choices in building the discriminative process, including deep neural networks or gaussian processes, which adds to the flexibility of the framework. We argue that these attributes of the proposed methodology, along with its applicability to different modalities of neural data, make it a powerful tool for high-dimensional neural data analysis. We also introduce an extension of these methods, called the discriminative-generative decoder (DGD). The DGD includes both discriminative and generative processes in characterizing observed data. As a result, we can combine physiological correlates like behavior with neural data to better estimate underlying cognitive processes. We illustrate the methods, including steps for inference and model identification, and demonstrate applications to multiple data analysis problems with high-dimensional neural recordings. The modeling results demonstrate the computational and modeling advantages of the DDD and DGD methods.

Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE)

BACKGROUND

Closing the loop between brain activity and behavior is one of the most active areas of development in neuroscience. There is particular interest in developing closed-loop control of neural oscillations. Many studies report correlations between oscillations and functional processes. Oscillation-informed closed-loop experiments might determine whether these relationships are causal and would provide important mechanistic insights which may lead to new therapeutic tools. These closed-loop perturbations require accurate estimates of oscillatory phase and amplitude, which are challenging to compute in real time.

NEW METHOD

We developed an easy to implement, fast and accurate Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE). TORTE operates with the open-source Open Ephys GUI (OEGUI) system, making it immediately compatible with a wide range of acquisition systems and experimental preparations.

RESULTS

TORTE efficiently extracts oscillatory phase and amplitude from a target signal and includes a variety of options to trigger closed-loop perturbations. Implementing these tools into existing experiments is easy and adds minimal latency to existing protocols.

COMPARISON WITH EXISTING METHODS

Most labs use in-house lab-specific approaches, limiting replication and extension of their experiments by other groups. Accuracy of the extracted analytic signal and accuracy of oscillation-informed perturbations with TORTE match presented results by these groups. However, TORTE provides access to these tools in a flexible, easy to use toolkit without requiring proprietary software.

CONCLUSION

We hope that the availability of a high-quality, open-source, and broadly applicable toolkit will increase the number of labs able to perform oscillatory closed-loop experiments, and will improve the replicability of protocols and data across labs.

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.

A Data Driven Experimental System for Individualized Brain Stimulation Design and Validation

Deep brain stimulation (DBS) is an effective clinical treatment for epilepsy. However, the individualized setting and adaptive adjustment of DBS parameters are still facing great challenges. This paper investigates a data-driven hardware-in-the-loop (HIL) experimental system for closed-loop brain stimulation system individualized design and validation. The unscented Kalman filter (UKF) is utilized to estimate critical parameters of neural mass model (NMM) from the electroencephalogram recordings to reconstruct individual neural activity. Based on the reconstructed NMM, we build a digital signal processor (DSP) based virtual brain platform with real time scale and biological signal level scale. Then, the corresponding hardware parts of signal amplification detection and closed-loop controller are designed to form the HIL experimental system. Based on the designed experimental system, the proportional-integral controller for different individual NMM is designed and validated, which proves the effectiveness of the experimental system. This experimental system provides a platform to explore neural activity under brain stimulation and the effects of various closed-loop stimulation paradigms.