Large-scale recording of thalamocortical circuits: in vivo electrophysiology with the two-dimensional electronic depth control silicon probe

Propagating population activity patterns during spontaneous slow waves in the thalamus of rodents

Slow waves (SWs) represent the most prominent electrophysiological events in the thalamocortical system under anesthesia and during deep sleep. Recent studies have revealed that SWs have complex spatiotemporal dynamics and propagate across neocortical regions. However, it is still unclear whether neuronal activity in the thalamus exhibits similar propagation properties during SWs. Here, we report propagating population activity in the thalamus of ketamine/xylazine-anesthetized rats and mice visualized by high-density silicon probe recordings. In both rodent species, propagation of spontaneous thalamic activity during up-states was most frequently observed in dorsal thalamic nuclei such as the higher order posterior (Po), lateral posterior (LP) or laterodorsal (LD) nuclei. The preferred direction of thalamic activity spreading was along the dorsoventral axis, with over half of the up-states exhibiting a gradual propagation in the ventral-to-dorsal direction. Furthermore, simultaneous neocortical and thalamic recordings collected under anesthesia demonstrated that there is a weak but noticeable interrelation between propagation patterns observed during cortical up-states and those displayed by thalamic population activity. In addition, using chronically implanted silicon probes, we detected propagating activity patterns in the thalamus of naturally sleeping rats during slow-wave sleep. However, in comparison to propagating up-states observed under anesthesia, these propagating patterns were characterized by a reduced rate of occurrence and a faster propagation speed. Our findings suggest that the propagation of spontaneous population activity is an intrinsic property of the thalamocortical network during synchronized brain states such as deep sleep or anesthesia. Additionally, our data implies that the neocortex may have partial control over the formation of propagation patterns within the dorsal thalamus under anesthesia.

Scalable Three-Dimensional Recording Electrodes for Probing Biological Tissues

Electrophysiological recording technologies can provide critical insight into the function of the nervous system and other biological tissues. Standard silicon-based probes have limitations, including single-sided recording sites and intrinsic instabilities due to the probe stiffness. Here, we demonstrate high-performance neural recording using double-sided three-dimensional (3D) electrodes integrated in an ultraflexible bioinspired open mesh structure, allowing electrodes to sample fully the 3D interconnected tissue of the brain. In vivo electrophysiological recording using 3D electrodes shows statistically significant increases in the number of neurons per electrode, average spike amplitudes, and signal to noise ratios in comparison to standard two-dimensional electrodes, while achieving stable detection of single-neuron activity over months. The capability of these 3D electrodes is further shown for chronic recording from retinal ganglion cells in mice. This approach opens new opportunities for a comprehensive 3D interrogation, stimulation, and understanding of the complex circuitry of the brain and other electrogenic tissues in live animals over extended time periods.

Semi-Implantable Bioelectronics

Developing techniques to effectively and real-time monitor and regulate the interior environment of biological objects is significantly important for many biomedical engineering and scientific applications, including drug delivery, electrophysiological recording and regulation of intracellular activities. Semi-implantable bioelectronics is currently a hot spot in biomedical engineering research area, because it not only meets the increasing technical demands for precise detection or regulation of biological activities, but also provides a desirable platform for externally incorporating complex functionalities and electronic integration. Although there is less definition and summary to distinguish it from the well-reviewed non-invasive bioelectronics and fully implantable bioelectronics, semi-implantable bioelectronics have emerged as highly unique technology to boost the development of biochips and smart wearable device. Here, we reviewed the recent progress in this field and raised the concept of "Semi-implantable bioelectronics", summarizing the principle and strategies of semi-implantable device for cell applications and in vivo applications, discussing the typical methodologies to access to intracellular environment or in vivo environment, biosafety aspects and typical applications. This review is meaningful for understanding in-depth the design principles, materials fabrication techniques, device integration processes, cell/tissue penetration methodologies, biosafety aspects, and applications strategies that are essential to the development of future minimally invasive bioelectronics.

Do not waste your electrodes-principles of optimal electrode geometry for spike sorting

Objective. This study examines how the geometrical arrangement of electrodes influences spike sorting efficiency, and attempts to formalise principles for the design of electrode systems enabling optimal spike sorting performance.Approach. The clustering performance of KlustaKwik, a popular toolbox, was evaluated using semi-artificial multi-channel data, generated from a library of real spike waveforms recorded in the CA1 region of mouse Hippocampusin vivo.Main results. Based on spike sorting results under various channel configurations and signal levels, a simple model was established to describe the efficiency of different electrode geometries. Model parameters can be inferred from existing spike waveform recordings, which allowed quantifying both the cooperative effect between channels and the noise dependence of clustering performance.Significance. Based on the model, analytical and numerical results can be derived for the optimal spacing and arrangement of electrodes for one- and two-dimensional electrode systems, targeting specific brain areas.

Spatial Information Based OSort for Real-Time Spike Sorting Using FPGA

OBJECTIVE

Spiking activity of individual neurons can be separated from the acquired multi-unit activity with spike sorting methods. Processing the recorded high-dimensional neural data can take a large amount of time when performed on general-purpose computers.

METHODS

In this paper, an FPGA-based real-time spike sorting system is presented which takes into account the spatial correlation between the electrical signals recorded with closely-packed recording sites to cluster multi-channel neural data. The system uses a spatial window-based version of the Online Sorting algorithm, which uses unsupervised template-matching for clustering.

RESULTS

The test results show that the proposed system can reach an average accuracy of 86% using simulated data (16-32 neurons, 4-10 dB Signal-to-Noise Ratio), while the single-channel clustering version achieves only 74% average accuracy in the same cases on a 128-channel electrode array. The developed system was also tested on in vivo cortical recordings obtained from an anesthetized rat.

CONCLUSION

The proposed FPGA-based spike sorting system can process more than 11000 spikes/second, so it can be used during in vivo experiments providing real-time feedback on the location and electrophysiological properties of well-separable single units.

SIGNIFICANCE

The proposed spike sorting system could be used to reduce the positioning error of the closely-packed recording site during a neural measurement.

High-density electrophysiological recordings in macaque using a chronically implanted 128-channel passive silicon probe

OBJECTIVE

The analysis of interactions among local populations of neurons in the cerebral cortex (e.g. within cortical microcolumns) requires high resolution and high channel count recordings from chronically implanted laminar microelectrode arrays. The request for high-density recordings of a large number of recording sites can presently only be accomplished by probes realized using complementary metal-oxide-semiconductor (CMOS) technology. In preparation for their use in non-human primates, we aimed for neural probe validation in a head-fixed approach analyzing the long-term recording capability.

APPROACH

We examined chronically implanted silicon-based laminar probes, realized using a CMOS technology in combination with micromachining, to record from the primary visual cortex (V1) of a monkey. We used a passive CMOS probe that had 128 electrodes arranged at a pitch of 22.5 µm in four columns and 32 rows on a slender shank. In order to validate the performance of a dedicated microdrive, the overall dimensions of probe and interface boards were chosen to be compatible with the final active CMOS probe comprising integrated circuitry.

MAIN RESULTS

Using the passive probe, we recorded simultaneously local field potentials (LFP) and spiking multiunit activity (MUA) in V1 of an awake behaving macaque monkey. We found that an insertion through the dura and subsequent readjustments of the chronically implanted neural probe was possible and allowed us to record stable LFPs for more than five months. The quality of MUA degraded within the first month but remained sufficiently high to permit mapping of receptive fields during the full recording period.

SIGNIFICANCE

We conclude that the passive silicon probe enables semi-chronic recordings of high quality of LFP and MUA for a time span exceeding five months. The new microdrive compatible with a commercial recording chamber successfully demonstrated the readjustment of the probe position while the implemented plug structure effectively reduced brain tissue movement relative to the probe.

The neural tissue around SU-8 implants: A quantitative in vivo biocompatibility study

The use of SU-8 material in the production of neural sensors has grown recently. Despite its widespread application, a detailed systematic quantitative analysis concerning its biocompatibility in the central nervous system is lacking. In this immunohistochemical study, we quantified the neuronal preservation and the severity of astrogliosis around SU-8 devices implanted in the neocortex of rats, after a 2 months survival. We found that the density of neurons significantly decreased up to a distance of 20 μm from the implant, with an averaged density decrease to 24 ± 28% of the control. At 20 to 40 μm distance from the implant, the majority of the neurons was preserved (74 ± 39% of the control) and starting from 40 μm distance from the implant, the neuron density was control-like. The density of synaptic contacts - examined at the electron microscopic level - decreased in the close vicinity of the implant, but it recovered to the control level as close as 24 μm from the implant track. The intensity of the astroglial staining significantly increased compared to the control region, up to 560 μm and 480 μm distance from the track in the superficial and deep layers of the neocortex, respectively. Electron microscopic examination revealed that the thickness of the glial scar was around 5-10 μm thin, and the ratio of glial processes in the neuropil was not more than 16% up to a distance of 12 μm from the implant. Our data suggest that neuronal survival is affected only in a very small area around the implant. The glial scar surrounding the implant is thin, and the presence of glial elements is low in the neuropil, although the signs of astrogliosis could be observed up to about 500 μm from the track. Subsequently, the biocompatibility of the SU-8 material is high. Due to its low cost fabrication and more flexible nature, SU-8 based devices may offer a promising approach to experimental and clinical applications in the future.

Intra-"cortical" activity during avian non-REM and REM sleep: variant and invariant traits between birds and mammals

Several mammalian-based theories propose that the varying patterns of neuronal activity occurring in wakefulness and sleep reflect different modes of information processing. Neocortical slow-waves, hippocampal sharp-wave ripples, and thalamocortical spindles occurring during mammalian non-rapid eye-movement (NREM) sleep are proposed to play a role in systems-level memory consolidation. Birds show similar NREM and REM (rapid eye-movement) sleep stages to mammals; however, it is unclear whether all neurophysiological rhythms implicated in mammalian memory consolidation are also present. Moreover, it is unknown whether the propagation of slow-waves described in the mammalian neocortex occurs in the avian "cortex" during natural NREM sleep. We used a 32-channel silicon probe connected to a transmitter to make intracerebral recordings of the visual hyperpallium and thalamus in naturally sleeping pigeons (Columba livia). As in the mammalian neocortex, slow-waves during NREM sleep propagated through the hyperpallium. Propagation primarily occurred in the thalamic input layers of the hyperpallium, regions that also showed the greatest slow-wave activity (SWA). Spindles were not detected in both the visual hyperpallium, including regions receiving thalamic input, and thalamus, using a recording method that readily detects spindles in mammals. Interestingly, during REM sleep fast gamma bursts in the hyperpallium (when present) were restricted to the thalamic input layers. In addition, unlike mice, the decrease in SWA from NREM to REM sleep was the greatest in these layers. Taken together, these variant and invariant neurophysiological aspects of avian and mammalian sleep suggest that there may be associated mechanistic and functional similarities and differences between avian and mammalian sleep.

Focal inputs are a potential origin of local field potential (LFP) in the brain regions without laminar structure

Current sinks and sources spatially separated between the apical and basal dendrites have been believed to be essential in generating local field potentials (LFPs). According to this theory, LFPs would not be large enough to be observed in the regions without laminar structures, such as striatum and thalamus. However, LFPs are experimentally recorded in these regions. We hypothesized that focal excitatory input induces a concentric current sink and source generating LFPs in these regions. In this study, we tested this hypothesis by the numerical simulations of multicompartment neuron models and the analysis of simplified models. Both confirmed that focal excitatory input can generate LFPs on the order of 0.1 mV in a region without laminar structures. The present results suggest that LFPs in subcortical nuclei indicate localized excitatory input.

Nanoenabled Direct Contact Interfacing of Syringe-Injectable Mesh Electronics

Polymer-based electronics with low bending stiffnesses and high flexibility, including recently reported macroporous syringe-injectable mesh electronics, have shown substantial promise for chronic studies of neural circuitry in the brains of live animals. A central challenge for exploiting these highly flexible materials for in vivo studies has centered on the development of efficient input/output (I/O) connections to an external interface with high yield, low bonding resistance, and long-term stability. Here we report a new paradigm applied to the challenging case of injectable mesh electronics that exploits the high flexibility of nanoscale thickness two-sided metal I/O pads that can deform and contact standard interface cables in high yield with long-term electrical stability. First, we describe the design and facile fabrication of two-sided metal I/O pads that allow for contact without regard to probe orientation. Second, systematic studies of the contact resistance as a function of I/O pad design and mechanical properties demonstrate the key role of the I/O pad bending stiffness in achieving low-resistance stable contacts. Additionally, computational studies provide design rules for achieving high-yield multiplexed contact interfacing in the case of angular misalignment such that adjacent channels are not shorted. Third, the in vitro measurement of 32-channel mesh electronics probes bonded to interface cables using the direct contact method shows a reproducibly high yield of electrical connectivity. Finally, in vivo experiments with 32-channel mesh electronics probes implanted in live mice demonstrate the chronic stability of the direct contact interface, enabling consistent tracking of single-unit neural activity over at least 2 months without a loss of channel recording. The direct contact interfacing methodology paves the way for scalable long-term connections of multiplexed mesh electronics neural probes for neural recording and modulation and moreover could be used to facilitate a scalable interconnection of other flexible electronics in biological studies and therapeutic applications.

Novel electrode technologies for neural recordings

Neural recording electrode technologies have contributed considerably to neuroscience by enabling the extracellular detection of low-frequency local field potential oscillations and high-frequency action potentials of single units. Nevertheless, several long-standing limitations exist, including low multiplexity, deleterious chronic immune responses and long-term recording instability. Driven by initiatives encouraging the generation of novel neurotechnologies and the maturation of technologies to fabricate high-density electronics, novel electrode technologies are emerging. Here, we provide an overview of recently developed neural recording electrode technologies with high spatial integration, long-term stability and multiple functionalities. We describe how these emergent neurotechnologies can approach the ultimate goal of illuminating chronic brain activity with minimal disruption of the neural environment, thereby providing unprecedented opportunities for neuroscience research in the future.

In vivo Recording Quality of Mechanically Decoupled Floating Versus Skull-Fixed Silicon-Based Neural Probes

Throughout the past decade, silicon-based neural probes have become a driving force in neural engineering. Such probes comprise sophisticated, integrated CMOS electronics which provide a large number of recording sites along slender probe shanks. Using such neural probes in a chronic setting often requires them to be mechanically anchored with respect to the skull. However, any relative motion between brain and implant causes recording instabilities and tissue responses such as glial scarring, thereby shielding recordable neurons from the recording sites integrated on the probe and thus decreasing the signal quality. In the current work, we present a comparison of results obtained using mechanically fixed and floating silicon neural probes chronically implanted into the cortex of a non-human primate. We demonstrate that the neural signal quality estimated by the quality of the spiking and local field potential (LFP) recordings over time is initially superior for the floating probe compared to the fixed device. Nonetheless, the skull-fixed probe also allowed long-term recording of multi-unit activity (MUA) and low frequency signals over several months, especially once pulsations of the brain were properly controlled.

Long-term recording performance and biocompatibility of chronically implanted cylindrically-shaped, polymer-based neural interfaces

Stereo-electroencephalography depth electrodes, regularly implanted into drug-resistant patients with focal epilepsy to localize the epileptic focus, have a low channel count (6–12 macro- or microelectrodes), limited spatial resolution (0.5–1 cm) and large contact area of the recording sites (~mm2). Thus, they are not suited for high-density local field potential and multiunit recordings. In this paper, we evaluated the long-term electrophysiological recording performance and histocompatibility of a neural interface consisting of 32 microelectrodes providing a physical shape similar to clinical devices. The cylindrically-shaped depth probes made of polyimide (PI) were chronically implanted for 13 weeks into the brain of rats, while cortical or thalamic activity (local field potentials, single-unit and multi-unit activity) was recorded regularly to monitor the temporal change of several features of the electrophysiological performance. To examine the tissue reaction around the probe, neuron-selective and astroglia-selective immunostaining methods were applied. Stable single-unit and multi-unit activity were recorded for several weeks with the implanted depth probes and a weak or moderate tissue reaction was found around the probe track. Our data on biocompatibility presented here and in vivo experiments in non-human primates provide a strong indication that this type of neural probe can be applied in stereo-electroencephalography recordings of up to 2 weeks in humans targeting the localization of epileptic foci providing an increased spatial resolution and the ability to monitor local field potentials and neuronal spiking activity.

Multifunctional Fibers as Tools for Neuroscience and Neuroengineering

Multifunctional devices for modulation and probing of neuronal activity during free behavior facilitate studies of functions and pathologies of the nervous system. Probes composed of stiff materials, such as metals and semiconductors, exhibit elastic and chemical mismatch with the neural tissue, which is hypothesized to contribute to sustained tissue damage and gliosis. Dense glial scars have been found to encapsulate implanted devices, corrode their surfaces, and often yield poor recording quality in long-term experiments. Motivated by the hypothesis that reducing the mechanical stiffness of implanted probes may improve their long-term reliability, a variety of probes based on soft materials have been developed. In addition to enabling electrical neural recording, these probes have been engineered to take advantage of genetic tools for optical neuromodulation. With the emergence of optogenetics, it became possible to optically excite or inhibit genetically identifiable cell types via expression of light-sensitive opsins. Optogenetics experiments often demand implantable multifunctional devices to optically stimulate, deliver viral vectors and drugs, and simultaneously record electrophysiological signals from the specified cells within the nervous system. Recent advances in microcontact printing and microfabrication techniques have equipped flexible probes with microscale light-emitting diodes (μLEDs), waveguides, and microfluidic channels. Complementary to these approaches, fiber drawing has emerged as a scalable route to integration of multiple functional features within miniature and flexible neural probes. The thermal drawing process relies on the fabrication of macroscale models containing the materials of interest, which are then drawn into microstructured fibers with predefined cross-sectional geometries. We have recently applied this approach to produce fibers integrating conductive electrodes for extracellular recording of single- and multineuron potentials, low-loss optical waveguides for optogenetic neuromodulation, and microfluidic channels for drug and viral vector delivery. These devices allowed dynamic investigation of the time course of opsin expression across multiple brain regions and enabled pairing of optical stimulation with local pharmacological intervention in behaving animals. Neural probes designed to interface with the spinal cord, a viscoelastic tissue undergoing repeated strain during normal movement, rely on the integration of soft and flexible materials to avoid injury and device failure. Employing soft substrates, such as parylene C and poly-(dimethylsiloxane), for electrode and μLED arrays permitted stimulation and recording of neural activity on the surface of the spinal cord. Similarly, thermally drawn flexible and stretchable optoelectronic fibers that resemble the fibrous structure of the spinal cord were implanted without any significant inflammatory reaction in the vicinity of the probes. These fibers enabled simultaneous recording and optogenetic stimulation of neural activity in the spinal cord. In this Account, we review the applications of multifunctional fibers and other integrated devices for optoelectronic probing of neural circuits and discuss engineering directions that may facilitate future studies of nerve repair and accelerate the development of bioelectronic medical devices.

Neural Parallel Engine: A toolbox for massively parallel neural signal processing

BACKGROUND

Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings.

NEW METHOD

In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation.

RESULTS

Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows.

COMPARISON WITH EXISTING METHODS

Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing.

CONCLUSIONS

A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels.

Time Multiplexed Active Neural Probe with 1356 Parallel Recording Sites

We present a high electrode density and high channel count CMOS (complementary metal-oxide-semiconductor) active neural probe containing 1344 neuron sized recording pixels (20 µm × 20 µm) and 12 reference pixels (20 µm × 80 µm), densely packed on a 50 µm thick, 100 µm wide, and 8 mm long shank. The active electrodes or pixels consist of dedicated in-situ circuits for signal source amplification, which are directly located under each electrode. The probe supports the simultaneous recording of all 1356 electrodes with sufficient signal to noise ratio for typical neuroscience applications. For enhanced performance, further noise reduction can be achieved while using half of the electrodes (678). Both of these numbers considerably surpass the state-of-the art active neural probes in both electrode count and number of recording channels. The measured input referred noise in the action potential band is 12.4 µVrms, while using 678 electrodes, with just 3 µW power dissipation per pixel and 45 µW per read-out channel (including data transmission).