Coordinated head direction representations in mouse anterodorsal thalamic nucleus and retrosplenial cortex.

The sense of direction is critical for survival in changing environments and relies on flexibly integrating self-motion signals with external sensory cues. While the anatomical substrates involved in head direction (HD) coding are well known, the mechanisms by which visual information updates HD representations remain poorly understood. Retrosplenial cortex (RSC) plays a key role in forming coherent representations of space in mammals and it encodes a variety of navigational variables, including HD. Here, we use simultaneous two-area tetrode recording to show that RSC HD representation is nearly synchronous with that of the anterodorsal nucleus of thalamus (ADn), the obligatory thalamic relay of HD to cortex, during rotation of a prominent visual cue. Moreover, coordination of HD representations in the two regions is maintained during darkness. We further show that anatomical and functional connectivity are consistent with a strong feedforward drive of HD information from ADn to RSC, with anatomically restricted corticothalamic feedback. Together, our results indicate a concerted global HD reference update across cortex and thalamus.

A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/sec) and low closed-loop latencies (<1ms) that uses a novel 0.3 mm thin tether to minimize behavioral impact. Head position and rotation are tracked in 3D and used to drive active commutation without torque measurements. ONIX can acquire from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, 3D-trackers, and other data sources. We used ONIX to perform uninterrupted, long (~7 hours) neural recordings in mice as they traversed complex 3-dimensional terrain. ONIX allowed exploration with similar mobility as non-implanted animals, in contrast to conventional tethered systems which restricted movement. By combining long recordings with full mobility, our technology will enable new progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

Differential dendritic integration of long-range inputs in association cortex via subcellular changes in synaptic AMPA-to-NMDA receptor ratio.

Synaptic NMDA receptors can produce powerful dendritic supralinearities that expand the computational repertoire of single neurons and their respective circuits. This form of supralinearity may represent a general principle for synaptic integration in thin dendrites. However, individual cortical neurons receive many diverse classes of input that may require distinct postsynaptic decoding schemes. Here, we show that sensory, motor, and thalamic inputs preferentially target basal, apical oblique, and distal tuft dendrites, respectively, in layer 5b pyramidal neurons of the mouse retrosplenial cortex, a visuospatial association area. These dendritic compartments exhibited differential expression of NMDA receptor-mediated supralinearity due to systematic changes in the AMPA-to-NMDA receptor ratio. Our results reveal a new schema for integration in cortical pyramidal neurons, in which dendrite-specific changes in synaptic receptors support input-localized decoding. This coexistence of multiple modes of dendritic integration in single neurons has important implications for synaptic plasticity and cortical computation.

Systems Neuroscience of Natural Behaviors in Rodents.

Animals evolved in complex environments, producing a wide range of behaviors, including navigation, foraging, prey capture, and conspecific interactions, which vary over timescales ranging from milliseconds to days. Historically, these behaviors have been the focus of study for ecology and ethology, while systems neuroscience has largely focused on short timescale behaviors that can be repeated thousands of times and occur in highly artificial environments. Thanks to recent advances in machine learning, miniaturization, and computation, it is newly possible to study freely moving animals in more natural conditions while applying systems techniques: performing temporally specific perturbations, modeling behavioral strategies, and recording from large numbers of neurons while animals are freely moving. The authors of this review are a group of scientists with deep appreciation for the common aims of systems neuroscience, ecology, and ethology. We believe it is an extremely exciting time to be a neuroscientist, as we have an opportunity to grow as a field, to embrace interdisciplinary, open, collaborative research to provide new insights and allow researchers to link knowledge across disciplines, species, and scales. Here we discuss the origins of ethology, ecology, and systems neuroscience in the context of our own work and highlight how combining approaches across these fields has provided fresh insights into our research. We hope this review facilitates some of these interactions and alliances and helps us all do even better science, together.

Layer 6 ensembles can selectively regulate the behavioral impact and layer-specific representation of sensory deviants.

Predictive models can enhance the salience of unanticipated input. Here, we tested a key potential node in neocortical model formation in this process, layer (L) 6, using behavioral, electrophysiological and imaging methods in mouse primary somatosensory neocortex. We found that deviant stimuli enhanced tactile detection and were encoded in L2/3 neural tuning. To test the contribution of L6, we applied weak optogenetic drive that changed which L6 neurons were sensory responsive, without affecting overall firing rates in L6 or L2/3. This stimulation selectively suppressed behavioral sensitivity to deviant stimuli, without impacting baseline performance. This stimulation also eliminated deviance encoding in L2/3 but did not impair basic stimulus responses across layers. In contrast, stronger L6 drive inhibited firing and suppressed overall sensory function. These findings indicate that, despite their sparse activity, specific ensembles of stimulus-driven L6 neurons are required to form neocortical predictions, and to realize their behavioral benefit.

An easy-to-assemble, robust, and lightweight drive implant for chronic tetrode recordings in freely moving animals.

Tetrode arrays are a standard method for neuronal recordings in behaving animals, especially for chronic recordings of many neurons in freely-moving animals. OBJECTIVE: We sought to simplify tetrode drive designs with the aim of enabling building and implanting a 16-tetrode drive in a single day. APPROACH: Our design makes use of recently developed technologies to reduce the complexity of the drive while maintaining a low weight. MAIN RESULTS: The design presents an improvement over existing implants in terms of robustness, weight, and ease of use. We describe two variants: a 16 tetrode implant weighing ∼2 g for mice, bats, tree shrews and similar animals, and a 64 tetrode implant weighing ∼16 g for rats and similar animals. These designs were co-developed and optimized alongside a new class of drive-mounted feature-rich amplifier boards with ultra-thin radio-frequency tethers, as described in an upcoming paper (Newman, Zhang et al in prep). SIGNIFICANCE: This design significantly improves the data yield of chronic electrophysiology experiments.

Twister3: a simple and fast microwire twister.

OBJECTIVE: Twisted wire probes (TWPs, e.g. stereotrodes and tetrodes) provide a cheap and reliable method for obtaining high quality, multiple single-unit neural recordings in freely moving animals. Despite their ubiquity, TWPs are constructed using a tedious procedure consisting of manually folding, turning, and fusing microwire. This imposes a significant labor burden on research personnel who use TWPs in their experiments. APPROACH: To address this issue, we created Twister3, an open-source microwire twisting machine. This machine features a quick-draw wire feeder that eliminates manual wire folding, an auto-aligning motor attachment mechanism which results in consistently straight probes, and a high speed motor for rapid probe turning. MAIN RESULTS: Twister3 greatly increases the speed and repeatability of constructing twisted microwire probes compared to existing options. Users with less than one hour of experience using the device were able to make ~70 tetrodes per hour, on average. It is cheap, well documented, and all associated designs and source code are open-source. SIGNIFICANCE: Twister3 significantly reduces the labor burden of creating high-quality TWPs so electrophysiologists can spend more of their time performing recordings rather than making probes. Therefore, this device is of interest to any lab performing TWP neural recordings, for example, using microdrives.

Somatic and Dendritic Encoding of Spatial Variables in Retrosplenial Cortex Differs during 2D Navigation.

Active amplification of organized synaptic inputs in dendrites can endow individual neurons with the ability to perform complex computations. However, whether dendrites in behaving animals perform independent local computations is not known. Such activity may be particularly important for complex behavior, where neurons integrate multiple streams of information. Head-restrained imaging has yielded important insights into cellular and circuit function, but this approach limits behavior and the underlying computations. We describe a method for full-featured 2-photon imaging in awake mice during free locomotion with volitional head rotation. We examine head direction and position encoding in simultaneously imaged apical tuft dendrites and their respective cell bodies in retrosplenial cortex, an area that encodes multi-modal navigational information. Activity in dendrites was not determined solely by somatic activity but reflected distinct navigational variables, fulfilling the requirements for dendritic computation. Our approach provides a foundation for studying sub-cellular processes during complex behaviors.

Open Ephys electroencephalography (Open Ephys + EEG): a modular, low-cost, open-source solution to human neural recording.

OBJECTIVE: Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. APPROACH: Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys + EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. MAIN RESULTS: The Open Ephys + EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys + EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. SIGNIFICANCE: Open Ephys + EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology.

OBJECTIVE: Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. APPROACH: We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. MAIN RESULTS: In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. SIGNIFICANCE: The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.

Thalamic reticular nucleus induces fast and local modulation of arousal state.

During low arousal states such as drowsiness and sleep, cortical neurons exhibit rhythmic slow wave activity associated with periods of neuronal silence. Slow waves are locally regulated, and local slow wave dynamics are important for memory, cognition, and behaviour. While several brainstem structures for controlling global sleep states have now been well characterized, a mechanism underlying fast and local modulation of cortical slow waves has not been identified. Here, using optogenetics and whole cortex electrophysiology, we show that local tonic activation of thalamic reticular nucleus (TRN) rapidly induces slow wave activity in a spatially restricted region of cortex. These slow waves resemble those seen in sleep, as cortical units undergo periods of silence phase-locked to the slow wave. Furthermore, animals exhibit behavioural changes consistent with a decrease in arousal state during TRN stimulation. We conclude that TRN can induce rapid modulation of local cortical state.

Tactile object localization by anticipatory whisker motion.

Rodents use rhythmic protractions of their whiskers to locate objects in space. The amplitude of these protractions is reduced when whiskers contact objects, leading to a tendency of whiskers to only lightly touch the environment. While the impact of this process on the sensory input has been studied, little is known about how sensory input causes this change in the motor pattern. Here, using high-speed imaging of whisking in mice, we simultaneously measured whisker contacts and the resulting whisking motion. We found that mice precisely target their whisker protractions to the distance at which they expect objects. This modulation does not depend on the current sensory input and remains stable for at least one whisking cycle when there is no object contact or when the object position is changed. As a result, the timing and other information carried by whisker contacts encodes how well each protraction was matched to the object, functioning as an error signal. Whisker contacts can thus encode a mismatch between expected object locations and the actual environment.

Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology.

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors.

Design and fabrication of ultralight weight, adjustable multi-electrode probes for electrophysiological recordings in mice.

The number of physiological investigations in the mouse, mus musculus, has experienced a recent surge, paralleling the growth in methods of genetic targeting for microcircuit dissection and disease modeling. The introduction of optogenetics, for example, has allowed for bidirectional manipulation of genetically-identified neurons, at an unprecedented temporal resolution. To capitalize on these tools and gain insight into dynamic interactions among brain microcircuits, it is essential that one has the ability to record from ensembles of neurons deep within the brain of this small rodent, in both head-fixed and freely behaving preparations. To record from deep structures and distinct cell layers requires a preparation that allows precise advancement of electrodes towards desired brain regions. To record neural ensembles, it is necessary that each electrode be independently movable, allowing the experimenter to resolve individual cells while leaving neighboring electrodes undisturbed. To do both in a freely behaving mouse requires an electrode drive that is lightweight, resilient, and highly customizable for targeting specific brain structures. A technique for designing and fabricating miniature, ultralight weight, microdrive electrode arrays that are individually customizable and easily assembled from commercially available parts is presented. These devices are easily scalable and can be customized to the structure being targeted; it has been used successfully to record from thalamic and cortical regions in a freely behaving animal during natural behavior.

The flexDrive: an ultra-light implant for optical control and highly parallel chronic recording of neuronal ensembles in freely moving mice.

Electrophysiological recordings from ensembles of neurons in behaving mice are a central tool in the study of neural circuits. Despite the widespread use of chronic electrophysiology, the precise positioning of recording electrodes required for high-quality recordings remains a challenge, especially in behaving mice. The complexity of available drive mechanisms, combined with restrictions on implant weight tolerated by mice, limits current methods to recordings from no more than 4-8 electrodes in a single target area. We developed a highly miniaturized yet simple drive design that can be used to independently position 16 electrodes with up to 64 channels in a package that weighs ~2 g. This advance over current designs is achieved by a novel spring-based drive mechanism that reduces implant weight and complexity. The device is easy to build and accommodates arbitrary spatial arrangements of electrodes. Multiple optical fibers can be integrated into the recording array and independently manipulated in depth. Thus, our novel design enables precise optogenetic control and highly parallel chronic recordings of identified single neurons throughout neural circuits in mice.

Unsupervised whisker tracking in unrestrained behaving animals.

Understanding how whisker-based tactile information is represented in the nervous system requires quantification of sensory input and observation of neural activity during whisking and whisker touch. Chronic electrophysiological methods have long been available to study neural responses in awake and behaving animals; however, methods to quantify the sensory input on whiskers have not yet been developed. Here we describe an unsupervised algorithm to track whisker movements in high-speed video recordings and to quantify the statistics of the tactile information on whiskers in freely behaving animals during haptic object exploration. The algorithm does not require human identification of whiskers, nor does it assume the shape, location, orientation, length of whiskers, or direction of the whisker movements. The algorithm performs well on temporary loss of whisker visibility and under low-light/low-contrast conditions even with inherent anisotropic noise and non-Gaussian variability in the signal. Using this algorithm, we define the speed [protraction (P), 1,081 +/- 322; retraction (R), 1,564 +/- 549 degrees /s], duration (P, 34 +/- 10; R, 24 +/- 8 ms), amplitude (P = R, 40 +/- 13 degrees ), and frequency (19 +/- 7 Hz) of active whisking in freely behaving mice. We furthermore quantify whisker deflection induced changes in whisking kinematics and calculate the statistics (i.e., speed, amplitude and duration) of whisker touch and finally show that whisker deprivation does not alter whisking kinematics during haptic exploration.