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Much innovation is currently aimed at improving the number, density, and geometry of electrodes on extracellular multielectrode arrays for in vivo recording of neural activity in the mammalian brain. To choose a multielectrode array configuration for a given neuroscience purpose, or to reveal design principles of future multielectrode arrays, it would be useful to have a systematic way of evaluating the spike recording capability of such arrays. We describe an automated system that performs robotic patch-clamp recording of a neuron being simultaneously recorded via an extracellular multielectrode array. By recording a patch-clamp data set from a neuron while acquiring extracellular recordings from the same neuron, we can evaluate how well the extracellular multielectrode array captures the spiking information from that neuron. To demonstrate the utility of our system, we show that it can provide data from the mammalian cortex to evaluate how the spike sorting performance of a close-packed extracellular multielectrode array is affected by bursting, which alters the shape and amplitude of spikes in a train. We also introduce an algorithmic framework to help evaluate how the number of electrodes in a multielectrode array affects spike sorting, examining how adding more electrodes yields data that can be spike sorted more easily. Our automated methodology may thus help with the evaluation of new electrode designs and configurations, providing empirical guidance on the kinds of electrodes that will be optimal for different brain regions, cell types, and species, for improving the accuracy of spike sorting. NEW & NOTEWORTHY We present an automated strategy for evaluating the spike recording performance of an extracellular multielectrode array, by enabling simultaneous recording of a neuron with both such an array and with patch clamp. We use our robot and accompanying algorithms to evaluate the performance of multielectrode arrays on supporting spike sorting.

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We here demonstrate multi-chip heterogeneous integration of microfabricated extracellular recording electrodes with neural amplifiers, highlighting a path to scaling electrode channel counts without the need for more complex monolithic integration. We characterize the noise and impedance performance of the heterogeneously integrated neural recording electrodes, and analyze the design parameters that enable the low-voltage neural input signals to co-exist with the high-frequency and high-voltage digital outputs on the same silicon substrate. This heterogeneous integration approach can enable future scaling efforts for microfabricated neural probes, and provides a design path for modular, fast, and independent scaling innovations in recording electrodes and neural amplifiers.

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OBJECTIVE: Neural recording electrodes are important tools for understanding neural codes and brain dynamics. Neural electrodes that are closely packed, such as in tetrodes, enable spatial oversampling of neural activity, which facilitates data analysis. Here we present the design and implementation of close-packed silicon microelectrodes to enable spatially oversampled recording of neural activity in a scalable fashion. METHODS: Our probes are fabricated in a hybrid lithography process, resulting in a dense array of recording sites connected to submicron dimension wiring. RESULTS: We demonstrate an implementation of a probe comprising 1000 electrode pads, each 9 × 9 µm, at a pitch of 11 µm. We introduce design automation and packaging methods that allow us to readily create a large variety of different designs. SIGNIFICANCE: We perform neural recordings with such probes in the live mammalian brain that illustrate the spatial oversampling potential of closely packed electrode sites.

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Driven by the increasing channel count of neural probes, there is much effort being directed to creating increasingly scalable electrophysiology data acquisition (DAQ) systems. However, all such systems still rely on personal computers for data storage, and thus are limited by the bandwidth and cost of the computers, especially as the scale of recording increases. Here we present a novel architecture in which a digital processor receives data from an analog-to-digital converter, and writes that data directly to hard drives, without the need for a personal computer to serve as an intermediary in the DAQ process. This minimalist architecture may support exceptionally high data throughput, without incurring costs to support unnecessary hardware and overhead associated with personal computers, thus facilitating scaling of electrophysiological recording in the future.

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Optogenetics enables light to be used to control the activity of genetically targeted cells in the living brain. Optical fibers can be used to deliver light to deep targets, and LEDs can be spatially arranged to enable patterned light delivery. In combination, arrays of LED-coupled optical fibers can enable patterned light delivery to deep targets in the brain. Here we describe the process flow for making LED arrays and LED-coupled optical fiber arrays, explaining key optical, electrical, thermal, and mechanical design principles to enable the manufacturing, assembly, and testing of such multi-site targetable optical devices. We also explore accessory strategies such as surgical automation approaches as well as innovations to enable low-noise concurrent electrophysiology.

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In recent years, interest has grown in the ability to manipulate, in a temporally precise fashion, the electrical activity of specific neurons embedded within densely wired brain circuits, in order to reveal how specific neurons subserve behaviors and neural computations, and to open up new horizons on the clinical treatment of brain disorders. Technologies that enable temporally precise control of electrical activity of specific neurons, and not these neurons' neighbors-whose cell bodies or processes might be just tens to hundreds of nanometers away-must involve two components. First, they require as a trigger a transient pulse of energy that supports the temporal precision of the control. Second, they require a molecular sensitizer that can be expressed in specific neurons and which renders those neurons specifically responsive to the triggering energy delivered. Optogenetic tools, such as microbial opsins, can be used to activate or silence neural activity with brief pulses of light. Thermogenetic tools, such as thermosensitive TRP channels, can be used to drive neural activity downstream of increases or decreases in temperature. We here discuss the principles underlying the operation of these two recently developed, but widely used, toolboxes, as well as the directions being taken in the use and improvement of these toolboxes.

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In order to understand how the brain generates behaviors, it is important to be able to determine how neural circuits work together to perform computations. Because neural circuits are made of a great diversity of cell types, it is critical to be able to analyze how these different kinds of cell work together. In recent years, a toolbox of fully genetically encoded molecules has emerged that, when expressed in specific neurons, enables the electrical activity of the targeted neurons to be controlled in a temporally precise fashion by pulses of light. We describe this optogenetic toolbox, how it can be used to analyze neural circuits in the brain and how optogenetics is impacting the study of cognition.

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The majority of mammalian microRNA (miRNA) genes reside within introns of protein-encoding and non-coding genes, yet the mechanisms coordinating primary transcript processing into both mature miRNA and spliced mRNA are poorly understood. Analysis of melanoma invasion suppressor miR-211 expressed from intron 6 of melastatin revealed that microprocessing of miR-211 promotes splicing of the exon 6-exon 7 junction of melastatin by a mechanism requiring the RNase III activity of Drosha. Additionally, mutations in the 5' splice site (5'SS), but not in the 3'SS, branch point, or polypyrimidine tract of intron 6 reduced miR-211 biogenesis and Drosha recruitment to intron 6, indicating that 5'SS recognition by the spliceosome promotes microprocessing of miR-211. Globally, knockdown of U1 splicing factors reduced intronic miRNA expression. Our data demonstrate novel mutually-cooperative microprocessing and splicing activities at an intronic miRNA locus and suggest that the initiation of spliceosome assembly may promote microprocessing of intronic miRNAs.

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Optogenetics, the ability to use light to activate and silence specific neuron types within neural networks in vivo and in vitro, is revolutionizing neuroscientists' capacity to understand how defined neural circuit elements contribute to normal and pathological brain functions. Typically, awake behaving experiments are conducted by inserting an optical fiber into the brain, tethered to a remote laser, or by utilizing an implanted light-emitting diode (LED), tethered to a remote power source. A fully wireless system would enable chronic or longitudinal experiments where long duration tethering is impractical, and would also support high-throughput experimentation. However, the high power requirements of light sources (LEDs, lasers), especially in the context of the extended illumination periods often desired in experiments, precludes battery-powered approaches from being widely applicable. We have developed a headborne device weighing 2 g capable of wirelessly receiving power using a resonant RF power link and storing the energy in an adaptive supercapacitor circuit, which can algorithmically control one or more headborne LEDs via a microcontroller. The device can deliver approximately 2 W of power to the LEDs in steady state, and 4.3 W in bursts. We also present an optional radio transceiver module (1 g) which, when added to the base headborne device, enables real-time updating of light delivery protocols; dozens of devices can be controlled simultaneously from one computer. We demonstrate use of the technology to wirelessly drive cortical control of movement in mice. These devices may serve as prototypes for clinical ultra-precise neural prosthetics that use light as the modality of biological control.

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To understand how brain states and behaviors are generated by neural circuits, it would be useful to be able to perturb precisely the activity of specific cell types and pathways in the nonhuman primate nervous system. We used lentivirus to target the light-activated cation channel channelrhodopsin-2 (ChR2) specifically to excitatory neurons of the macaque frontal cortex. Using a laser-coupled optical fiber in conjunction with a recording microelectrode, we showed that activation of excitatory neurons resulted in well-timed excitatory and suppressive influences on neocortical neural networks. ChR2 was safely expressed, and could mediate optical neuromodulation, in primate neocortex over many months. These findings highlight a methodology for investigating the causal role of specific cell types in nonhuman primate neural computation, cognition, and behavior, and open up the possibility of a new generation of ultraprecise neurological and psychiatric therapeutics via cell-type-specific optical neural control prosthetics.

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Many neural disorders are associated with aberrant activity in specific cell types or neural projection pathways embedded within the densely-wired, heterogeneous matter of the brain. An ideal therapy would permit correction of activity just in specific target neurons, while leaving other neurons unaltered. Recently our lab revealed that the naturally-occurring light-activated proteins channelrhodopsin-2 (ChR2) and halorhodopsin (Halo/NpHR) can, when genetically expressed in neurons, enable them to be safely, precisely, and reversibly activated and silenced by pulses of blue and yellow light, respectively. We here describe the ability to make specific neurons in the brain light-sensitive, using a viral approach. We also reveal the design and construction of a scalable, fully-implantable optical prosthetic capable of delivering light of appropriate intensity and wavelength to targeted neurons at arbitrary 3-D locations within the brain, enabling activation and silencing of specific neuron types at multiple locations. Finally, we demonstrate control of neural activity in the cortex of the non-human primate, a key step in the translation of such technology for human clinical use. Systems for optical targeting of specific neural circuit elements may enable a new generation of high-precision therapies for brain disorders.