Neurobiologically realistic neural network enables cross-scale modeling of neural dynamics.

Fundamental principles underlying computation in multi-scale brain networks illustrate how multiple brain areas and their coordinated activity give rise to complex cognitive functions. Whereas brain activity has been studied at the micro- to meso-scale to reveal the connections between the dynamical patterns and the behaviors, investigations of neural population dynamics are mainly limited to single-scale analysis. Our goal is to develop a cross-scale dynamical model for the collective activity of neuronal populations. Here we introduce a bio-inspired deep learning approach, termed NeuroBondGraph Network (NBGNet), to capture cross-scale dynamics that can infer and map the neural data from multiple scales. Our model not only exhibits more than an 11-fold improvement in reconstruction accuracy, but also predicts synchronous neural activity and preserves correlated low-dimensional latent dynamics. We also show that the NBGNet robustly predicts held-out data across a long time scale (2 weeks) without retraining. We further validate the effective connectivity defined from our model by demonstrating that neural connectivity during motor behaviour agrees with the established neuroanatomical hierarchy of motor control in the literature. The NBGNet approach opens the door to revealing a comprehensive understanding of brain computation, where network mechanisms of multi-scale activity are critical.

Spatial resolution enhancement in photon-starved STED imaging using deep learning-based fluorescence lifetime analysis.

As a super-resolution imaging method, stimulated emission depletion (STED) microscopy has unraveled fine intracellular structures and provided insights into nanoscale organizations in cells. Although image resolution can be further enhanced by continuously increasing the STED-beam power, the resulting photodamage and phototoxicity are major issues for real-world applications of STED microscopy. Here we demonstrate that, with 50% less STED-beam power, the STED image resolution can be improved up to 1.45-fold using the separation of photons by a lifetime tuning (SPLIT) scheme combined with a deep learning-based phasor analysis algorithm termed flimGANE (fluorescence lifetime imaging based on a generative adversarial network). This work offers a new approach for STED imaging in situations where only a limited photon budget is available.

Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells.

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to quantify molecular compositions and study molecular states in complex cellular environment as the lifetime readings are not biased by fluorophore concentration or excitation power. However, the current methods to generate FLIM images are either computationally intensive or unreliable when the number of photons acquired at each pixel is low. Here we introduce a new deep learning-based method termed flimGANE (fluorescence lifetime imaging based on Generative Adversarial Network Estimation) that can rapidly generate accurate and high-quality FLIM images even in the photon-starved conditions. We demonstrated our model is up to 2,800 times faster than the gold standard time-domain maximum likelihood estimation (TD_MLE) and that flimGANE provides a more accurate analysis of low-photon-count histograms in barcode identification, cellular structure visualization, Förster resonance energy transfer characterization, and metabolic state analysis in live cells. With its advantages in speed and reliability, flimGANE is particularly useful in fundamental biological research and clinical applications, where high-speed analysis is critical.

Estimating Intrinsic Manifold Dimensionality to Classify Task-Related Information in Human and Non-Human Primate Data.

Feature selection, or dimensionality reduction, has become a standard step in reducing large-scale neural datasets into usable signals for brain-machine interface and neurofeedback decoders. Current techniques in fMRI data reduce the number of voxels (features) by performing statistics on individual voxels or using traditional techniques that utilize linear combinations of features (e.g., principal component analysis (PCA)). However, these methods often do not account for the cross-correlations found across voxels and do not sufficiently reduce the feature space to support efficient real-time feedback. To overcome these limitations, we propose using factor analysis on fMRI data. This technique has become increasingly popular for extracting a minimal number of latent features to explain high-dimensional data in non-human primates (NHPs). Here, we demonstrate these methods in both NHP and human data. In NHP subjects (n=2), we reduced the number of features to an average of 26.86% and 14.86% of the total feature space to build our multinomial classifier. In one NHP subject, the average accuracy of classifying eight target locations over 64 sessions was 62.43% (+/-6.19%) compared to a PCA-based classifier with 60.26% (+/-6.02%). In healthy fMRI subjects, we reduced the feature space to an average of 0.33% of the initial space. Group average (n=5) accuracy of FA-based category classification was 74.33% (+/- 4.91%) compared to a PCA-based classifier with 68.42% (+/-4.79%). FA-based classifiers can maintain the performance fidelity observed with PCA-based decoders. Importantly, FA-based methods allow researchers to address specific hypotheses about how underlying neural activity relates to behavior.

Short-training Algorithm for Online Brain-machine Interfaces Using One-photon Microendoscopic Calcium Imaging.

Calcium imaging has great potential to be applied to online brain-machine interfaces (BMIs). As opposed to two-photon imaging settings, a one-photon microendoscopic imaging device can be chronically implanted and is subject to little motion artifacts. Traditionally, one-photon microendoscopic calcium imaging data are processed using the constrained nonnegative matrix factorization (CNMFe) algorithm, but this batched processing algorithm cannot be applied in real-time. An online analysis of calcium imaging data algorithm (or OnACIDe) has been proposed, but OnACIDe updates the neural components by repeatedly performing neuron identification frame-by-frame, which may decelerate the update speed if applying to online BMIs. For BMI applications, the ability to track a stable population of neurons in real-time has a higher priority over accurately identifying all the neurons in the field of view. By leveraging the fact that 1) microendoscopic recordings are rather stable with little motion artifacts and 2) the number of neurons identified in a short training period is sufficient for potential online BMI tasks such as cursor movements, we proposed the short-training CNMFe algorithm (stCNMFe) that skips motion correction and neuron identification processes to enable a more efficient BMI training program in a one-photon microendoscopic setting.

Multi-scale neural decoding and analysis.

Objective. Complex spatiotemporal neural activity encodes rich information related to behavior and cognition. Conventional research has focused on neural activity acquired using one of many different measurement modalities, each of which provides useful but incomplete assessment of the neural code. Multi-modal techniques can overcome tradeoffs in the spatial and temporal resolution of a single modality to reveal deeper and more comprehensive understanding of system-level neural mechanisms. Uncovering multi-scale dynamics is essential for a mechanistic understanding of brain function and for harnessing neuroscientific insights to develop more effective clinical treatment.Approach. We discuss conventional methodologies used for characterizing neural activity at different scales and review contemporary examples of how these approaches have been combined. Then we present our case for integrating activity across multiple scales to benefit from the combined strengths of each approach and elucidate a more holistic understanding of neural processes.Main results. We examine various combinations of neural activity at different scales and analytical techniques that can be used to integrate or illuminate information across scales, as well the technologies that enable such exciting studies. We conclude with challenges facing future multi-scale studies, and a discussion of the power and potential of these approaches.Significance. This roadmap will lead the readers toward a broad range of multi-scale neural decoding techniques and their benefits over single-modality analyses. This Review article highlights the importance of multi-scale analyses for systematically interrogating complex spatiotemporal mechanisms underlying cognition and behavior.

Head-mounted microendoscopic calcium imaging in dorsal premotor cortex of behaving rhesus macaque.

Microendoscopic calcium imaging with one-photon miniature microscopes enables unprecedented readout of neural circuit dynamics during active behavior in rodents. In this study, we describe successful application of this technology in the rhesus macaque, demonstrating plug-and-play, head-mounted recordings of cellular-resolution calcium dynamics from large populations of neurons simultaneously in bilateral dorsal premotor cortices during performance of a naturalistic motor reach task. Imaging is stable over several months, allowing us to longitudinally track individual neurons and monitor their relationship to motor behavior over time. We observe neuronal calcium dynamics selective for reach direction, which we could use to decode the animal's trial-by-trial motor behavior. This work establishes head-mounted microendoscopic calcium imaging in macaques as a powerful approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and it promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease.

Making the jump: Expert guidance on transitioning to academic independence.

Obtaining a position as an independent investigator is a daunting prospect, and often requires skill sets that are not emphasized during graduate or postdoctoral training. Here, we present insight from a seminar series designed to guide young researchers looking to "make the jump", covering the fundamental steps of the job search (preparation of an application package, Skype/remote interview, campus visit, and negotiations). We summarize the many useful insights distilled throughout these roundtable sessions with the goal of providing information and guidance to a broader community of researchers on the best way to prepare for and tackle the faculty job market.

A wireless and artefact-free 128-channel neuromodulation device for closed-loop stimulation and recording in non-human primates.

Closed-loop neuromodulation systems aim to treat a variety of neurological conditions by delivering and adjusting therapeutic electrical stimulation in response to a patient's neural state, recorded in real time. Existing systems are limited by low channel counts, lack of algorithmic flexibility, and the distortion of recorded signals by large and persistent stimulation artefacts. Here, we describe an artefact-free wireless neuromodulation device that enables research applications requiring high-throughput data streaming, low-latency biosignal processing, and simultaneous sensing and stimulation. The device is a miniaturized neural interface capable of closed-loop recording and stimulation on 128 channels, with on-board processing to fully cancel stimulation artefacts. In addition, it can detect neural biomarkers and automatically adjust stimulation parameters in closed-loop mode. In a behaving non-human primate, the device enabled long-term recordings of local field potentials and the real-time cancellation of stimulation artefacts, as well as closed-loop stimulation to disrupt movement preparatory activity during a delayed-reach task. The neuromodulation device may help advance neuroscientific discovery and preclinical investigations of stimulation-based therapeutic interventions.

A high-density carbon fiber neural recording array technology.

OBJECTIVE: Microwire and Utah-style neural recording arrays are the predominant devices used for cortical neural recording, but the implanted electrodes cause a significant adverse biological response and suffer from well-studied performance degradation. Recent work has demonstrated that carbon fiber electrodes do not elicit this same adverse response, but these existing designs are not practically scalable to hundreds or thousands of recording sites. We present technology that overcomes these issues while additionally providing fine electrode pitch for spatial oversampling. APPROACH: We present a 32-channel carbon fiber monofilament-based intracortical neural recording array fabricated through a combination of bulk silicon microfabrication processing and microassembly. This device represents the first truly two-dimensional carbon fiber neural recording array. The density, channel count, and size scale of this array are enabled by an out-of-plane microassembly technique in which individual fibers are inserted through metallized and isotropically conductive adhesive-filled holes in an oxide-passivated microfabricated silicon substrate. MAIN RESULTS: Five-micron diameter fibers are spaced at a pitch of 38 microns, four times denser than state of the art one-dimensional arrays. The fine diameter of the carbon fibers affords both minimal cross-section and nearly three orders of magnitude greater lateral compliance than standard tungsten microwires. Typical [Formula: see text] impedances are on the order of hundreds of kiloohms, and successful in vivo recording is demonstrated in the motor cortex of a rat. 22 total units are recorded on 20 channels, with unit SNR ranging from 1.4 to 8.0. SIGNIFICANCE: This is the highest density microwire-style electrode array to date, and this fabrication technique is scalable to a larger number of electrodes and allows for the potential future integration of microelectronics. Large-scale carbon fiber neural recording arrays are a promising technology for reducing the inflammatory response and increasing the information density, particularly in neural recording applications where microwire arrays are already used.

Recent advances in neural dust: towards a neural interface platform.

The neural dust platform uses ultrasonic power and communication to enable a scalable, wireless, and batteryless system for interfacing with the nervous system. Ultrasound offers several advantages over alternative wireless approaches, including a safe method for powering and communicating with sub mm-sized devices implanted deep in tissue. Early studies demonstrated that neural dust motes could wirelessly transmit high-fidelity electrophysiological data in vivo, and that theoretically, this system could be miniaturized well below the mm-scale. Future developments are focused on further minimization of the platform, better encapsulation methods as a path towards truly chronic neural interfaces, improved delivery mechanisms, stimulation capabilities, and finally refinements to enable deployment of neural dust in the central nervous system.

Caudate Microstimulation Increases Value of Specific Choices.

Value-based decision-making involves an assessment of the value of items available and the actions required to obtain them. The basal ganglia are highly implicated in action selection and goal-directed behavior [1-4], and the striatum in particular plays a critical role in arbitrating between competing choices [5-9]. Previous work has demonstrated that neural activity in the caudate nucleus is modulated by task-relevant action values [6, 8]. Nonetheless, how value is represented and maintained in the striatum remains unclear since decision-making in these tasks relied on spatially lateralized responses, confounding the ability to generalize to a more abstract choice task [6, 8, 9]. Here, we investigate striatal value representations by applying caudate electrical stimulation in macaque monkeys (n = 3) to bias decision-making in a task that divorces the value of a stimulus from motor action. Electrical microstimulation is known to induce neural plasticity [10, 11], and caudate microstimulation in primates has been shown to accelerate associative learning [12, 13]. Our results indicate that stimulation paired with a particular stimulus increases selection of that stimulus, and this effect was stimulus dependent and action independent. The modulation of choice behavior using microstimulation was best modeled as resulting from changes in stimulus value. Caudate neural recordings (n = 1) show that changes in value-coding neuron activity are stimulus value dependent. We argue that caudate microstimulation can differentially increase stimulus values independent of action, and unilateral manipulations of value are sufficient to mediate choice behavior. These results support potential future applications of microstimulation to correct maladaptive plasticity underlying dysfunctional decision-making related to neuropsychiatric conditions.