Incorporating 3D-printing technology in the design of head-caps and electrode drives for recording neurons in multiple brain regions

SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain

To understand the neural basis of behavior, it is essential to measure spiking dynamics across many interacting brain regions. Although new technologies, such as Neuropixels probes, facilitate multi-regional recordings, significant surgical and procedural hurdles remain for these experiments to achieve their full potential. Here, we describe skull-shaped hemispheric implants enabling large-scale electrophysiology datasets (SHIELD). These 3D-printed skull-replacement implants feature customizable insertion holes, allowing dozens of cortical and subcortical structures to be recorded in a single mouse using repeated multi-probe insertions over many days. We demonstrate the procedure's high success rate, biocompatibility, lack of adverse effects on behavior, and compatibility with imaging and optogenetics. To showcase SHIELD's scientific utility, we use multi-probe recordings to reveal novel insights into how alpha rhythms organize spiking activity across visual and sensorimotor networks. Overall, this method enables powerful, large-scale electrophysiological experiments for the study of distributed neural computation.

Months-long tracking of neuronal ensembles spanning multiple brain areas with Ultra-Flexible Tentacle Electrodes

We introduce Ultra-Flexible Tentacle Electrodes (UFTEs), packing many independent fibers with the smallest possible footprint without limitation in recording depth using a combination of mechanical and chemical tethering for insertion. We demonstrate a scheme to implant UFTEs simultaneously into many brain areas at arbitrary locations without angle-of-insertion limitations, and a 512-channel wireless logger. Immunostaining reveals no detectable chronic tissue damage even after several months. Mean spike signal-to-noise ratios are 1.5-3x compared to the state-of-the-art, while the highest signal-to-noise ratios reach 89, and average cortical unit yields are ~1.75/channel. UFTEs can track the same neurons across sessions for at least 10 months (longest duration tested). We tracked inter- and intra-areal neuronal ensembles (neurons repeatedly co-activated within 25 ms) simultaneously from hippocampus, retrosplenial cortex, and medial prefrontal cortex in freely moving rodents. Average ensemble lifetimes were shorter than the durations over which we can track individual neurons. We identify two distinct classes of ensembles. Those tuned to sharp-wave ripples display the shortest lifetimes, and the ensemble members are mostly hippocampal. Yet, inter-areal ensembles with members from both hippocampus and cortex have weak tuning to sharp wave ripples, and some have unusual months-long lifetimes. Such inter-areal ensembles occasionally remain inactive for weeks before re-emerging.

In vivo recordings in freely behaving mice using independent silicon probes targeting multiple brain regions

In vivo recordings in freely behaving animals are crucial to understand the neuronal circuit basis of behavior. Although current multi-channel silicon probes provide unparalleled sampling density, the study of interacting neuronal populations requires the implantation of multiple probes across different regions of the brain. Ideally, these probes should be independently adjustable, to maximize the yield, and recoverable, to mitigate costs. In this work, we describe the implementation of a miniaturized 3D-printed headgear system for chronic in vivo recordings in mice using independently movable silicon probes targeting multiple brain regions. We successfully demonstrated the performance of the headgear by simultaneously recording the neuronal activity in the prelimbic cortex and dorsal hippocampus. The system proved to be sturdy, ensuring high-quality stable recordings and permitted reuse of the silicon probes, with no observable interference in mouse innate behaviors.

A method for chronic and semi-chronic microelectrode array implantation in deep brain structures using image guided neuronavigation

BACKGROUND

Accurate targeting of brain structures for in-vivo electrophysiological recordings is essential for basic as well as clinical neuroscience research. Although methodologies for precise targeting and recording from the cortical surface are abundant, such protocols are scarce for deep brain structures.

NEW METHOD

We have incorporated stable fiducial markers within a custom cranial cap for improved image-guided neuronavigation targeting of subcortical structures in macaque monkeys. Anchor bolt chambers allowed for a minimally invasive entrance into the brain for chronic recordings. A 3D-printed microdrive allowed for semi-chronic applications.

RESULTS

We achieved an average Euclidean targeting error of 1.6 mm and a radial error of 1.2 mm over three implantations in two animals. Chronic and semi-chronic implantations allowed for recording of extracellular neuronal activity, with single-neuron activity examples shown from one macaque monkey.

COMPARISON WITH EXISTING METHOD(S)

Traditional stereotactic methods ignore individual anatomical variability. Our targeting approach allows for a flexible, subject-specific surgical plan with targeting errors lower than what is reported in humans, and equal to or lower than animal models using similar methods. Utilizing an anchor bolt as a chamber reduced the craniotomy size needed for electrode implantation, compared to conventional large access chambers which are prone to infection. Installation of an in-house, 3D-printed, screw-to-mount mechanical microdrive is in contrast to existing semi-chronic methods requiring fabrication, assembly, and installation of complex parts.

CONCLUSIONS

Leveraging commercially available tools for implantation, our protocol decreases the risk of infection from open craniotomies, and improves the accuracy of chronic electrode implantations targeting deep brain structures in large animal models.

Rhythmic oscillations in the midbrain dopaminergic nuclei in mice

Introduction

Dopamine release in the forebrain by midbrain ventral tegmental nucleus (VTA) and substantia nigra pars compacta (SNc) neurons is implicated in reward processing, goal-directed learning, and decision-making. Rhythmic oscillations of neural excitability underlie coordination of network processing, and have been reported in these dopaminergic nuclei at several frequency bands. This paper provides a comparative characterization of several frequencies of oscillations of local field potential and single unit activity, highlighting some behavioral correlates.

Methods

We recorded from optogenetically identified dopaminergic sites in four mice training in operant olfactory and visual discrimination tasks.

Results

Rayleigh and Pairwise Phase Consistency (PPC) analyses revealed some VTA/SNc neurons phase-locked to each frequency range, with fast spiking interneurons (FSIs) prevalent at 1-2.5 Hz (slow) and 4 Hz bands, and dopaminergic neurons predominant in the theta band. More FSIs than dopaminergic neurons were phase-locked in the slow and 4 Hz bands during many task events. The highest incidence of phase-locking in neurons was in the slow and 4 Hz bands, and occurred during the delay between the operant choice and trial outcome (reward or punishment) signals.

Discussion

These data provide a basis for further examination of rhythmic coordination of activity of dopaminergic nuclei with other brain structures, and its impact for adaptive behavior.

Development of a synchronous recording and photo-stimulating electrode in multiple brain neurons

The investigation of brain networks and neural circuits involves the crucial aspects of observing and modulating neurophysiological activity. Recently, opto-electrodes have emerged as an efficient tool for electrophysiological recording and optogenetic stimulation, which has greatly facilitated the analysis of neural coding. However, implantation and electrode weight control have posed significant challenges in achieving long-term and multi-regional brain recording and stimulation. To address this issue, we have developed a mold and custom-printed circuit board-based opto-electrode. We report successful opto-electrode placement and high-quality electrophysiological recordings from the default mode network (DMN) of the mouse brain. This novel opto-electrode facilitates synchronous recording and stimulation in multiple brain regions and holds promise for advancing future research on neural circuits and networks.

The Hybrid Drive: a chronic implant device combining tetrode arrays with silicon probes for layer-resolved ensemble electrophysiology in freely moving mice

Objective. Understanding the function of brain cortices requires simultaneous investigation at multiple spatial and temporal scales and to link neural activity to an animal's behavior. A major challenge is to measure within- and across-layer information in actively behaving animals, in particular in mice that have become a major species in neuroscience due to an extensive genetic toolkit. Here we describe the Hybrid Drive, a new chronic implant for mice that combines tetrode arrays to record within-layer information with silicon probes to simultaneously measure across-layer information.Approach. The design of our device combines up to 14 tetrodes and 2 silicon probes, that can be arranged in custom arrays to generate unique areas-specific (and multi-area) layouts.Main Results. We show that large numbers of neurons and layer-resolved local field potentials can be recorded from the same brain region across weeks without loss in electrophysiological signal quality. The drive's lightweight structure (~3.5 g) leaves animal behavior largely unchanged, compared to other tetrode drives, during a variety of experimental paradigms. We demonstrate how the data collected with the Hybrid Drive allow state-of-the-art analysis in a series of experiments linking the spiking activity of CA1 pyramidal layer neurons to the oscillatory activity across hippocampal layers.Significance. Our new device fits a gap in the existing technology and increases the range and precision of questions that can be addressed about neural computations in freely behaving mice.

Metal microdrive and head cap system for silicon probe recovery in freely moving rodent

High-yield electrophysiological extracellular recording in freely moving rodents provides a unique window into the temporal dynamics of neural circuits. Recording from unrestrained animals is critical to investigate brain activity during natural behaviors. The use and implantation of high-channel-count silicon probes represent the largest cost and experimental complexity associated with such recordings making a recoverable and reusable system desirable. To address this, we have designed and tested a novel 3D printed head-gear system for freely moving mice and rats. The system consists of a recoverable microdrive printed in stainless steel and a plastic head cap system, allowing researchers to reuse the silicon probes with ease, decreasing the effective cost, and the experimental effort and complexity. The cap designs are modular and provide structural protection and electrical shielding to the implanted hardware and electronics. We provide detailed procedural instructions allowing researchers to adapt and flexibly modify the head-gear system.

Reconfigurable 3D-Printed headplates for reproducible and rapid implantation of EEG, EMG and depth electrodes in mice

BACKGROUND

Mouse models are beneficial to understanding neural networks given a wide array of transgenic mice and cell-selective techniques. However, instrumentation of mice for neurophysiological studies is difficult. Often surgery is prolonged with experimental error arising from non-concurrent and variable implantations.

NEW METHOD

We describe a method for the rapid, reproducible and customizable instrumentation of mice. We constructed a headplate that conforms to the mouse skull surface using script-based computer aided design. This headplate was then modified to enable the friction-fit assembly prior to surgery and printed with a high-resolution resin-based 3D printer. Using this approach, we describe an easily customized headplate with dural screws for electrocorticography (ECoG), electromyogram (EMG) electrodes, cannula hole and two microdrives for local field potential (LFP) electrodes.

RESULTS

Implantation of the headplate reliably takes less than 40 min, enabling a cohort of eight mice to be implanted in one day. Good quality recordings were obtained after surgical recovery and the headplate was stable for at least four weeks. LFP electrode placement was found to be accurate.

COMPARISON WITH EXISTING METHODS

While similar approaches with microelectrodes have been used in rats before, and related approaches exist for targeting one brain region with tetrodes, we do not know of similar head-plates for mice, nor a strictly source-code and easily reconfigurable approach.

CONCLUSIONS

3D printing and friction-fit pre-assembly of mouse headplates offers a rapid, easily reconfigurable, consistent, and cost-effective way to implant larger numbers of mice in a highly reproducible way, reducing surgical time and mitigating experimental error.

A Novel 3D-Printed Multi-Drive System for Synchronous Electrophysiological Recording in Multiple Brain Regions

Extracellular electrophysiology has been widely applied in neural network studies. Local field potentials and single-unit activities can be recorded with high-density electrodes, which facilitate the decoding of neural codes. However, the chronic multi-regional recording is still a challenging task for achieving high placement accuracy and long-term stability. Here, we present a novel electrode design with low-cost 3D-printed parts and custom printed circuits boards. This new design could facilitate precise electrode placement in multiple brain regions simultaneously and reduce the working time for surgical procedures as well. In this paper, the design and fabrication of the 3D printed multi-channel microdrive are explained in detail. We also show the result of high-quality electrophysiological recordings in eight pain-related areas from rats and the electrode placement accuracy. This novel 3D-printed multi-drive system could achieve synchronous electrophysiological recording in multiple brain regions and facilitate future neural network research.

Closed-loop control of gamma oscillations in the amygdala demonstrates their role in spatial memory consolidation

Gamma is a ubiquitous brain rhythm hypothesized to support cognitive, perceptual, and mnemonic functions by coordinating neuronal interactions. While much correlational evidence supports this hypothesis, direct experimental tests have been lacking. Since gamma occurs as brief bursts of varying frequencies and durations, most existing approaches to manipulate gamma are either too slow, delivered irrespective of the rhythm's presence, not spectrally specific, or unsuitable for bidirectional modulation. Here, we overcome these limitations with an approach that accurately detects and modulates endogenous gamma oscillations, using closed-loop signal processing and optogenetic stimulation. We first show that the rat basolateral amygdala (BLA) exhibits prominent gamma oscillations during the consolidation of contextual memories. We then boost or diminish gamma during consolidation, in turn enhancing or impairing subsequent memory strength. Overall, our study establishes the role of gamma oscillations in memory consolidation and introduces a versatile method for studying fast network rhythms in vivo.

A model-based approach for targeted neurophysiology in the behaving non-human primate

Acute neurophysiology in the behaving primate typically relies on traditional manufacturing approaches for the instrumentation necessary for recording. For example, our previous approach consisted of distributing single microelectrodes in a fixed plane situated over a circular patch of frontal cortex using conventionally-milled recording grids. With the advent of robust, multisite linear probes, and the introduction of commercially-available, high-resolution rapid prototyping systems, we have been able to improve upon traditional approaches. Here, we report our methodology for producing flexible, MR-informed recording platforms that allow us to precisely target brain structures of interest, including those that would be unreachable using previous methods. We have increased our single-session recording yields by an order of magnitude and recorded neural activity from widely-distributed regions using only a single recording chamber. This approach both speeds data collection, reduces the damage done to neural tissue over the course of a single experiment, and reduces the number of surgical procedures experienced by the animal.

Detection of Multiway Gamma Coordination Reveals How Frequency Mixing Shapes Neural Dynamics

A principle of communication technology, frequency mixing, describes how novel oscillations are generated when rhythmic inputs converge on a nonlinearly activating target. As expected given that neurons are nonlinear integrators, it was demonstrated that neuronal networks exhibit mixing in response to imposed oscillations of known frequencies. However, determining when mixing occurs in spontaneous conditions, where weaker or more variable rhythms prevail, has remained impractical. Here, we show that, by exploiting the predicted phase (rather than frequency) relationships between oscillations, the contributions of mixing can be readily identified, even in small samples of noisy data. Assessment of extracellular data using this approach revealed that frequency mixing is widely expressed in a state- and region-dependent manner and that oscillations emerging from mixing entrain unit activity. Frequency mixing is thus intrinsic to the structure of neural activity and contributes importantly to neural dynamics.

Gamma Oscillations in the Basolateral Amygdala: Biophysical Mechanisms and Computational Consequences

The basolateral nucleus of the amygdala (BL) is thought to support numerous emotional behaviors through specific microcircuits. These are often thought to be comprised of feedforward networks of principal cells (PNs) and interneurons. Neither well-understood nor often considered are recurrent and feedback connections, which likely engender oscillatory dynamics within BL. Indeed, oscillations in the gamma frequency range (40 − 100 Hz) are known to occur in the BL, and yet their origin and effect on local circuits remains unknown. To address this, we constructed a biophysically and anatomically detailed model of the rat BL and its local field potential (LFP) based on the physiological and anatomical literature, along with in vivo and in vitro data we collected on the activities of neurons within the rat BL. Remarkably, the model produced intermittent gamma oscillations (∼50 − 70 Hz) whose properties matched those recorded in vivo, including their entrainment of spiking. BL gamma-band oscillations were generated by the intrinsic circuitry, depending upon reciprocal interactions between PNs and fast-spiking interneurons (FSIs), while connections within these cell types affected the rhythm’s frequency. The model allowed us to conduct experimentally impossible tests to characterize the synaptic and spatial properties of gamma. The entrainment of individual neurons to gamma depended on the number of afferent connections they received, and gamma bursts were spatially restricted in the BL. Importantly, the gamma rhythm synchronized PNs and mediated competition between ensembles. Together, these results indicate that the recurrent connectivity of BL expands its computational and communication repertoire.

The systemDrive: a Multisite, Multiregion Microdrive with Independent Drive Axis Angling for Chronic Multimodal Systems Neuroscience Recordings in Freely Behaving Animals

A multielectrode system that can address widely separated targets at multiple sites across multiple brain regions with independent implant angling is needed to investigate neural function and signaling in systems and circuits of small animals. Here, we present the systemDrive, a novel multisite, multiregion microdrive that is capable of moving microwire electrode bundles into targets along independent and nonparallel drive trajectories. Our design decouples the stereotaxic surgical placement of individual guide cannulas for each trajectory from the placement of a flexible drive structure. This separation enables placement of many microwire multitrodes along widely spaced and independent drive axes with user-set electrode trajectories and depths from a single microdrive body, and achieves stereotaxic precision with each. The system leverages tight tube-cannula tolerances and geometric constraints on flexible drive axes to ensure concentric alignment of electrode bundles within guide cannulas. Additionally, the headmount and microdrive both have an open-center design to allow for the placement of additional sensing modalities. This design is the first, in the context of small rodent chronic research, to provide the capability to finely position microwires through multiple widely distributed cell groups, each with stereotaxic precision, along arbitrary and nonparallel trajectories that are not restricted to emanate from a single source. We demonstrate the use of the systemDrive in male Long-Evans rats to observe simultaneous single-unit and multiunit activity from multiple widely separated sleep-wake regulatory brainstem cell groups, along with cortical and hippocampal activity, during free behavior over multiple many-day continuous recording periods.

Multisite Electrophysiology Recordings in Mice to Study Cross-Regional Communication During Anxiety

Recording neural activity in awake, freely moving mice is a powerful and flexible technique for dissecting the neural circuit mechanisms underlying pathological behavior. This unit describes protocols for designing a drive and recording single neurons and local field potentials during anxiety-related paradigms. We also include protocols for integrating pharmacologic and optogenetic means for circuit manipulations, which, when combined with electrophysiological recordings, demonstrate input-specific and cell-specific contributions to circuit-wide activity. We discuss the planning, execution, and troubleshooting of physiology experiments during anxiety-like behavior. © 2017 by John Wiley & Sons, Inc.

Micro-drive and headgear for chronic implant and recovery of optoelectronic probes

Silicon probes are multisite electrodes used for the electrophysiological recording of large neuronal ensembles. Optoelectronic probes (OEPs) are recent upgrades that allow, in parallel, the delivery of local optical stimuli. The procedures to use these delicate electrodes for chronic experiments in mice are still underdeveloped and typically assume one-time uses. Here, we developed a micro-drive, a support for OEPs optical fibers, and a hat enclosure, which fabrications consist in fitting and fastening together plastic parts made with 3D printers. Excluding two parts, all components and electrodes are relatively simple to recover after the experiments, via the loosening of screws. To prevent the plugging of OEPs laser sources from altering the stability of recordings, the OEPs fibers can be transiently anchored to the hat via the tightening of screws. We test the stability of recordings in the mouse hippocampus under three different conditions: acute head-fixed, chronic head-fixed, and chronic freely moving. Drift in spike waveforms is significantly smaller in chronic compared to acute conditions, with the plugging/unplugging of head-stage and fiber connectors not affecting much the recording stability. Overall, these tools generate stable recordings of place cell in chronic conditions, and make the recovery and reuse of electrode packages relatively simple.

Scalable, Lightweight, Integrated and Quick-to-Assemble (SLIQ) Hyperdrives for Functional Circuit Dissection

Independently adjustable multielectrode arrays are routinely used to interrogate neuronal circuit function, enabling chronic in vivo monitoring of neuronal ensembles in freely behaving animals at a single-cell, single spike resolution. Despite the importance of this approach, its widespread use is limited by highly specialized design and fabrication methods. To address this, we have developed a Scalable, Lightweight, Integrated and Quick-to-assemble multielectrode array platform. This platform additionally integrates optical fibers with independently adjustable electrodes to allow simultaneous single unit recordings and circuit-specific optogenetic targeting and/or manipulation. In current designs, the fully assembled platforms are scalable from 2 to 32 microdrives, and yet range 1–3 g, light enough for small animals. Here, we describe the design process starting from intent in computer-aided design, parameter testing through finite element analysis and experimental means, and implementation of various applications across mice and rats. Combined, our methods may expand the utility of multielectrode recordings and their continued integration with other tools enabling functional dissection of intact neural circuits.

Intra- and interregional cortical interactions related to sharp-wave ripples and dentate spikes

The hippocampus generates population events termed sharp-wave ripples (SWRs) and dentate spikes (DSs). While little is known about DSs, SWR-related hippocampal discharges during sleep are thought to replay prior waking activity, reactivating the cortical networks that encoded the initial experience. During slow-wave sleep, such reactivations likely occur during up-states, when most cortical neurons are depolarized. However, most studies have examined the relationship between SWRs and up-states measured in single neocortical regions. As a result, it is currently unclear whether SWRs are associated with particular patterns of widely distributed cortical activity. Additionally, no such investigation has been carried out for DSs. The present study addressed these questions by recording SWRs and DSs from the dorsal hippocampus simultaneously with prefrontal, sensory (visual and auditory), perirhinal, and entorhinal cortices in naturally sleeping rats. We found that SWRs and DSs were associated with up-states in all cortical regions. Up-states coinciding with DSs and SWRs exhibited increased unit activity, power in the gamma band, and intraregional gamma coherence. Unexpectedly, interregional gamma coherence rose much more strongly in relation to DSs than to SWRs. Whereas the increase in gamma coherence was time locked to DSs, that seen in relation to SWRs was not. These observations suggest that SWRs are related to the strength of up-state activation within individual regions throughout the neocortex but not so much to gamma coherence between different regions. Perhaps more importantly, DSs coincided with stronger periods of interregional gamma coherence, suggesting that they play a more important role than previously assumed.

NEW & NOTEWORTHY

Off-line cortico-hippocampal interactions are thought to support memory consolidation. We surveyed the relationship between hippocampal sharp-wave ripples (SWRs) and dentate spikes (DSs) with up-states across multiple cortical regions. SWRs and DSs were associated with increased cortical gamma oscillations. Interregional gamma coherence rose much more strongly in relation to DSs than to SWRs. Moreover, it was time locked to DSs but not SWRs. These results have important implications for current theories of systems memory consolidation during sleep.

Three-Dimensional Fabrication for Microfluidics by Conventional Techniques and Equipment Used in Mass Production

This paper presents a simple three-dimensional (3D) fabrication method based on soft lithography techniques and laminated object manufacturing. The method can create 3D structures that have undercuts with general machines for mass production and laboratory scale prototyping. The minimum layer thickness of the method is at least 4 µm and bonding strength between layers is over 330 kPa. The performance reaches conventional fabrication techniques used for two-dimensionally (2D)-designed microfluidic devices. We fabricated some 3D structures, i.e., fractal structures, spiral structures, and a channel-in-channel structure, in microfluidic channels and demonstrated 3D microfluidics. The fabrication method can be achieved with a simple black light for bio-molecule detection; thus, it is useful for not only lab-scale rapid prototyping, but also for commercial manufacturing.

Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas

Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest due to the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome, and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3-D computerized tomography (CT) images of intact rat brains implanted with metal electrode bundles to a Magnetic Resonance Imaging Histology (MRH) Atlas. Our method allows accurate visualization of each electrode bundle's trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by "re-slicing" the images along different planes of view. Further, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience.