Head-fixed Mice Research Articles

Pupil Dynamics-derived Sleep Stage Classification of a Head-fixed Mouse Using a Recurrent Neural Network.

The standard method for sleep state classification is thresholding the amplitudes of electroencephalography (EEG) and electromyography (EMG) data, followed by manual correction by an expert. Although popular, this method has some shortcomings: (1) the time-consuming manual correction by human experts is sometimes a bottleneck hindering sleep studies, (2) EEG electrodes on the skull interfere with wide-field imaging of the cortical activity of a head-fixed mouse under a microscope, (3) invasive surgery to fix the electrodes on the thin mouse skull risks brain tissue injury, and (4) metal electrodes for EEG and EMG recording are difficult to apply to some experimental apparatus such as that for functional magnetic resonance imaging. To overcome these shortcomings, we propose a pupil dynamics-based vigilance state classification method for a head-fixed mouse using a long short-term memory (LSTM) model, a variant of a recurrent neural network, for multi-class labeling of NREM, REM, and WAKE states. For supervisory hypnography, EEG and EMG recording were performed on head-fixed mice. This setup was combined with left eye pupillometry using a USB camera and a markerless tracking toolbox, DeepLabCut. Our open-source LSTM model with feature inputs of pupil diameter, pupil location, pupil velocity, and eyelid opening for 10 s at a 10 Hz sampling rate achieved vigilance state estimation with a higher classification performance (macro F1 score, 0.77; accuracy, 86%) than a feed-forward neural network. Findings from a diverse range of pupillary dynamics implied possible subdivision of the vigilance states defined by EEG and EMG. Pupil dynamics-based hypnography can expand the scope of alternatives for sleep stage scoring of head-fixed mice.

Electrophysiological Recordings from Identified Cell Types in the Olfactory Cortex of Awake Mice.

Neural circuits consist of a myriad of distinct cell types, each with specific intrinsic properties and patterns of synaptic connectivity, which transform neural input and convey this information to downstream targets. Understanding how different features of an odor stimulus are encoded and relayed to their appropriate targets will require selective identification and manipulation of these different elements of the circuit. Here, we describe methods to obtain dense, extracellular electrophysiological recordings of odor-evoked activity in olfactory (piriform) cortex of awake, head-fixed mice, and optogenetic tools and procedures to identify genetically defined cell types within this circuit.

Relating Pupil Diameter and Blinking to Cortical Activity and Hemodynamics across Arousal States.

Arousal state affects neural activity and vascular dynamics in the cortex, with sleep associated with large changes in the local field potential and increases in cortical blood flow. We investigated the relationship between pupil diameter and blink rate with neural activity and blood volume in the somatosensory cortex in male and female unanesthetized, head-fixed mice. We monitored these variables while the mice were awake, during periods of rapid eye movement (REM), and non-rapid eye movement (NREM) sleep. Pupil diameter was smaller during sleep than in the awake state. Changes in pupil diameter were coherent with both gamma-band power and blood volume in the somatosensory cortex, but the strength and sign of this relationship varied with arousal state. We observed a strong negative correlation between pupil diameter and both gamma-band power and blood volume during periods of awake rest and NREM sleep, although the correlations between pupil diameter and these signals became positive during periods of alertness, active whisking, and REM. Blinking was associated with increases in arousal and decreases in blood volume when the mouse was asleep. Bilateral coherence in gamma-band power and in blood volume dropped following awake blinking, indicating a reset of neural and vascular activity. Using only eye metrics (pupil diameter and eye motion), we could determine the arousal state of the mouse ('Awake,' 'NREM,' 'REM') with >90% accuracy with a 5 s resolution. There is a strong relationship between pupil diameter and hemodynamics signals in mice, reflecting the pronounced effects of arousal on cerebrovascular dynamics.SIGNIFICANCE STATEMENT Determining arousal state is a critical component of any neuroscience experiment. Pupil diameter and blinking are influenced by arousal state, as are hemodynamics signals in the cortex. We investigated the relationship between cortical hemodynamics and pupil diameter and found that pupil diameter was strongly related to the blood volume in the cortex. Mice were more likely to be awake after blinking than before, and blinking resets neural activity. Pupil diameter and eye motion can be used as a reliable, noninvasive indicator of arousal state. As mice transition from wake to sleep and back again over a timescale of seconds, monitoring pupil diameter and eye motion permits the noninvasive detection of sleep events during behavioral or resting-state experiments.

Acute head-fixed recordings in awake mice with multiple Neuropixels probes.

Multi-electrode arrays such as Neuropixels probes enable electrophysiological recordings from large populations of single neurons with high temporal resolution. By using such probes, the activity from functionally interacting, yet distinct, brain regions can be measured simultaneously by inserting multiple probes into the same subject. However, the use of multiple probes in small animals such as mice requires the removal of a sizable fraction of the skull, while also minimizing tissue damage and keeping the brain stable during the recordings. Here, we describe a step-by-step process designed to facilitate reliable recordings from up to six Neuropixels probes simultaneously in awake, head-fixed mice. The procedure involves four stages: the implantation of a headframe and a removable glass coverslip, the precise positioning of the Neuropixels probes at targeted points on the brain surface, the placement of a perforated plastic imaging window and the insertion of the probes into the brain of an awake mouse. The approach provides access to multiple brain regions and has been successfully applied across hundreds of mice. The procedure has been optimized for dense recordings from the mouse visual system, but it can be adapted for alternative recording configurations to target multiple probes in other brain areas. The protocol is suitable for users with experience in stereotaxic surgery in mice.

Visual experience has opposing influences on the quality of stimulus representation in adult primary visual cortex.

Transient dark exposure, typically 7-10 days in duration, followed by light reintroduction is an emerging treatment for improving the restoration of vision in amblyopic subjects whose occlusion is removed in adulthood. Dark exposure initiates homeostatic mechanisms that together with light-induced changes in cellular signaling pathways result in the re-engagement of juvenile-like plasticity in the adult such that previously deprived inputs can gain cortical territory. It is possible that dark exposure itself degrades visual responses, and this could place constraints on the optimal duration of dark exposure treatment. To determine whether eight days of dark exposure has a lasting negative impact on responses to classic grating stimuli, neural activity was recorded before and after dark exposure in awake head-fixed mice using two-photon calcium imaging. Neural discriminability, assessed using classifiers, was transiently reduced following dark exposure; a decrease in response reliability across a broad range of spatial frequencies likely contributed to the disruption. Both discriminability and reliability recovered. Fixed classifiers were used to demonstrate that stimulus representation rebounded to the original, pre-deprivation state, thus dark exposure did not appear to have a lasting negative impact on visual processing. Unexpectedly, we found that dark exposure significantly stabilized orientation preference and signal correlation. Our results reveal that natural vision exerts a disrupting influence on the stability of stimulus preference for classic grating stimuli and, at the same time, improves neural discriminability for both low and high-spatial frequency stimuli.

Hemisphere-specific spatial representation by hippocampal granule cells

The dentate gyrus (DG) output plays a key role in the emergence of spatial and contextual map representation within the hippocampus during learning. Differences in neuronal network activity have been observed between left and right CA1-3 areas, implying lateralization in spatial coding properties. Whether bilateral differences of DG granule cell (GC) assemblies encoding spatial and contextual information exist remains largely unexplored. Here, we employed two-photon calcium imaging of the left or the right DG to record the activity of GC populations over five consecutive days in head-fixed mice navigating through familiar and novel virtual environments. Imaging revealed similar mean GC activity on both sides. However, spatial tuning, context-selectivity and run-to-run place field reliability was markedly higher for DG place cells in the left than the right hemisphere. Moreover, the proportion of GCs reconfiguring their place fields between contexts was greater in the left DG. Thus, our data suggest that contextual information is differentially processed by GC populations depending on the hemisphere, with higher context discrimination in the left but a bias towards generalization in the right DG.

Ultraflexible electrode arrays for months-long high-density electrophysiological mapping of thousands of neurons in rodents.

Penetrating flexible electrode arrays can simultaneously record thousands of individual neurons in the brains of live animals. However, it has been challenging to spatially map and longitudinally monitor the dynamics of large three-dimensional neural networks. Here we show that optimized ultraflexible electrode arrays distributed across multiple cortical regions in head-fixed mice and in freely moving rats allow for months-long stable electrophysiological recording of several thousand neurons at densities of about 1,000 neural units per cubic millimetre. The chronic recordings enhanced decoding accuracy during optogenetic stimulation and enabled the detection of strongly coupled neuron pairs at the million-pair and millisecond scales, and thus the inference of patterns of directional information flow. Longitudinal and volumetric measurements of neural couplings may facilitate the study of large-scale neural circuits.

Spatiotemporal Pavlovian head-fixed reversal learning task for mice

Our world is full of uncertainty. Animals, including humans, need to behave flexibly to adjust to ever-changing environments. Reversal learning tasks have been used to assess behavioral flexibility in many species. However, there are some limitations in the traditional free-moving methodology, including (1) sessions to train the animals, (2) within-session number of trials associated with reversals, (3) factors of physical movement unrelated to the task in the maze or operant box, and (4) incompatibility with techniques, such as two-photon imaging. Therefore, to address these limitations, we established a novel spatiotemporal Pavlovian head-fixed reversal learning task for mice. Six experimentally naive adult C57BL/6J mice were used in this study. First, we trained head-fixed mice on a fixed-time schedule task. Sucrose solution was delivered every 10 s with a single drinking spout placed within the licking distance of the mice. After the mice showed anticipatory licking toward the timing of sucrose solution delivery, we began training the mice on the fixed-time schedule reversal learning task with two licking spouts. In this task, sucrose solution was delivered through one of the two drinking spouts. The rewarding spout was switched every 10 trials. Mice quickly learned to switch anticipatory licking to the rewarding side of the spouts, suggesting that they learned this head-fixed reversal learning task. Using the head-fixed experimental design, behavioral measures can be simplified by eliminating the complex behavioral sequences observed in free-moving animals. This novel head-fixed reversal learning task is a useful assay for studying the neurobiological mechanism of behavioral flexibility that is impaired in various psychopathological conditions.

Sound-Evoked Responses of Distinct Neuron Classes from the Tail of the Striatum.

Given its inputs from auditory structures and neuromodulatory systems, the posterior tail of the striatum is ideally positioned to influence behavioral responses to acoustic stimuli according to context and previous rewards. Results from previous studies indicate that neurons in this striatal region display selective responses to sounds. However, it is not clear whether different striatal cell classes code for distinct features of sounds or how different striatal output pathways may use acoustic information to guide behavior. Here we compared the sound-evoked responses of posterior striatal neurons that form the striatal direct pathway (and express the dopamine receptor D1) to the responses of neighboring neurons in naive mice. We achieved this via optogenetic photo-identification of D1-expressing neurons during extracellular electrophysiological recordings in awake head-fixed mice of both sexes. We found that the frequency tuning of sound-responsive direct-pathway striatal neurons is comparable with that of their sound-responsive neighbors. Moreover, we found that both populations encode amplitude-modulated sounds in a similar fashion. These results suggest that different classes of neurons in the posterior striatum of naive animals have similar access to acoustic features conveyed by the auditory system even outside the context of an auditory task.

Task specificity in mouse parietal cortex

Parietal cortex is implicated in a variety of behavioral processes, but it is unknown whether and how its individual neurons participate in multiple tasks. We trained head-fixed mice to perform two visual decision tasks involving a steering wheel or a virtual T-maze and recorded from the same parietal neurons during these two tasks. Neurons that were active during the T-maze task were typically inactive during the steering-wheel task and vice versa. Recording from the same neurons in the same apparatus without task stimuli yielded the same specificity as in the task, suggesting that task specificity depends on physical context. To confirm this, we trained some mice in a third task combining the steering wheel context with the visual environment of the T-maze. This hybrid task engaged the same neurons as those engaged in the steering-wheel task. Thus, participation by neurons in mouse parietal cortex is task specific, and this specificity is determined by physical context.

Development of a spontaneous pain indicator based on brain cellular calcium using deep learning

Chronic pain remains an intractable condition in millions of patients worldwide. Spontaneous ongoing pain is a major clinical problem of chronic pain and is extremely challenging to diagnose and treat compared to stimulus-evoked pain. Although extensive efforts have been made in preclinical studies, there still exists a mismatch in pain type between the animal model and humans (i.e., evoked vs. spontaneous), which obstructs the translation of knowledge from preclinical animal models into objective diagnosis and effective new treatments. Here, we developed a deep learning algorithm, designated AI-bRNN (Average training, Individual test-bidirectional Recurrent Neural Network), to detect spontaneous pain information from brain cellular Ca2+ activity recorded by two-photon microscopy imaging in awake, head-fixed mice. AI-bRNN robustly determines the intensity and time points of spontaneous pain even in chronic pain models and evaluates the efficacy of analgesics in real time. Furthermore, AI-bRNN can be applied to various cell types (neurons and glia), brain areas (cerebral cortex and cerebellum) and forms of somatosensory input (itch and pain), proving its versatile performance. These results suggest that our approach offers a clinically relevant, quantitative, real-time preclinical evaluation platform for pain medicine, thereby accelerating the development of new methods for diagnosing and treating human patients with chronic pain.

Purkinje Cell Activity Resonation Generates Rhythmic Behaviors at the Preferred Frequency of 8 Hz.

Neural activity exhibits oscillations, bursts, and resonance, enhancing responsiveness at preferential frequencies. For example, theta-frequency bursting and resonance in granule cells facilitate synaptic transmission and plasticity mechanisms at the input stage of the cerebellar cortex. However, whether theta-frequency bursting of Purkinje cells is involved in generating rhythmic behavior has remained neglected. We recorded and optogenetically modulated the simple and complex spike activity of Purkinje cells while monitoring whisker movements with a high-speed camera of awake, head-fixed mice. During spontaneous whisking, both simple spike activity and whisker movement exhibit peaks within the theta band. Eliciting either simple or complex spikes at frequencies ranging from 0.5 to 28 Hz, we found that 8 Hz is the preferred frequency around which the largest movement is induced. Interestingly, oscillatory whisker movements at 8 Hz were also generated when simple spike bursting was induced at 2 and 4 Hz, but never via climbing fiber stimulation. These results indicate that 8 Hz is the resonant frequency at which the cerebellar-whisker circuitry produces rhythmic whisking.

State-Dependent Modulation of Activity in Distinct Layer 6 Corticothalamic Neurons in Barrel Cortex of Awake Mice.

Layer 6 corticothalamic (L6 CT) neurons are in a strategic position to control sensory input to the neocortex, yet we understand very little about their functions. Apart from studying their anatomic, physiological, and synaptic properties, most recent efforts have focused on the activity-dependent influences CT cells can exert on thalamic and cortical neurons through causal optogenetic manipulations. However, few studies have attempted to study them during behavior. To address this gap, we performed juxtacellular recordings from optogenetically identified CT neurons in whisker-related primary somatosensory cortex (wS1) of awake, head-fixed mice (either sex) free to rest quietly or self-initiate bouts of whisking and locomotion. We found a rich diversity of response profiles exhibited by CT cells. Their spiking patterns were either modulated by whisking-related behavior (∼28%) or not (∼72%). Whisking-responsive neurons exhibited both increases (activated-type) and decreases in firing rates (suppressed-type) that aligned with whisking onset better than locomotion. We also encountered responsive neurons with preceding modulations in firing rate before whisking onset. Overall, whisking better explained these changes in rates than overall changes in arousal. Whisking-unresponsive CT cells were generally quiet, with many having low spontaneous firing rates (sparse-type) and others being completely silent (silent-type). Remarkably, the sparse firing CT population preferentially spiked at the state transition point when pupil diameter constricted, and the mouse entered quiet wakefulness. Thus, our results demonstrate that L6 CT cells in wS1 show diverse spiking patterns, perhaps subserving distinct functional roles related to precisely timed responses during complex behaviors and transitions between discrete waking states.SIGNIFICANCE STATEMENT Layer 6 corticothalamic neurons provide a massive input to the sensory thalamus and local connectivity within cortex, but their role in thalamocortical processing remains unclear because of difficulty accessing and isolating their activity. Although several recent optogenetic studies reveal that the net influence of corticothalamic actions, suppression versus enhancement, depends critically on the rate these neurons fire, the factors that influence their spiking are poorly understood, particularly during wakefulness. Using the well-established Ntsr1-Cre line to target this elusive population in the whisker somatosensory cortex of awake mice, we found that corticothalamic neurons show diverse state-related responses and modulations in firing rate. These results suggest separate corticothalamic populations can differentially influence thalamocortical excitability during rapid state transitions in awake, behaving animals.

A synaptic signal for novelty processing in the hippocampus

Episodic memory formation and recall are complementary processes that rely on opposing neuronal computations in the hippocampus. How this conflict is resolved in hippocampal circuits is unclear. To address this question, we obtained in vivo whole-cell patch-clamp recordings from dentate gyrus granule cells in head-fixed mice trained to explore and distinguish between familiar and novel virtual environments. We find that granule cells consistently show a small transient depolarisation upon transition to a novel environment. This synaptic novelty signal is sensitive to local application of atropine, indicating that it depends on metabotropic acetylcholine receptors. A computational model suggests that the synaptic response to novelty may bias granule cell population activity, which can drive downstream attractor networks to a new state, favouring the switch from recall to new memory formation when faced with novelty. Such a novelty-driven switch may enable flexible encoding of new memories while preserving stable retrieval of familiar ones.

Olfactory modulation of barrel cortex activity during active whisking and passive whisker stimulation

Rodents depend on olfaction and touch to meet many of their fundamental needs. However, the impact of simultaneous olfactory and tactile inputs on sensory representations in the cortex remains elusive. To study these interactions, we recorded large populations of barrel cortex neurons using 2-photon calcium imaging in head-fixed mice during olfactory and tactile stimulation. Here we show that odors bidirectionally alter activity in a small but significant population of barrel cortex neurons through at least two mechanisms, first by enhancing whisking, and second by a central mechanism that persists after whisking is abolished by facial nerve sectioning. Odor responses have little impact on tactile information, and they are sufficient for decoding odor identity, while behavioral parameters like whisking, sniffing, and facial movements are not odor identity-specific. Thus, barrel cortex activity encodes specific olfactory information that is not linked with odor-induced changes in behavior.

Coordination between Eye Movement and Whisking in Head-Fixed Mice Navigating a Plus Maze.

Navigation through complex environments requires motor planning, motor preparation, and the coordination between multiple sensory–motor modalities. For example, the stepping motion when we walk is coordinated with motion of the torso, arms, head, and eyes. In rodents, movement of the animal through the environment is coordinated with whisking. Even head-fixed mice navigating a plus maze position their whiskers asymmetrically with the bilateral asymmetry signifying the upcoming turn direction. Here we report that, in addition to moving their whiskers, on every trial mice also move their eyes conjugately in the direction of the upcoming turn. Not only do mice move their eyes, but they coordinate saccadic eye movement with the asymmetric positioning of the whiskers. Our analysis shows that asymmetric positioning of whiskers predicted the turn direction that mice will make at an earlier stage than eye movement. Consistent with these results, our observations also revealed that whisker asymmetry increases before saccadic eye movement. Importantly, this work shows that when rodents plan for active behavior, their motor plans can involve both eye and whisker movement. We conclude that, when mice are engaged in and moving through complex real-world environments, their behavioral state can be read out in the movement of both their whiskers and eyes.

Dynamic control of visually guided locomotion through corticosubthalamic projections.

SUMMARYGoal-directed locomotion requires control signals that propagate from higher order areas to regulate spinal mechanisms. The corticosubthalamic hyperdirect pathway offers a short route for cortical information to reach locomotor centers in the brainstem. We developed a task in which head-fixed mice run to a visual landmark and then stop and wait to collect the reward and examined the role of secondary motor cortex (M2) projections to the subthalamic nucleus (STN) in controlling locomotion. Our behavioral modeling, calcium imaging, and optogenetics manipulation results suggest that the M2-STN pathway can be recruited during visually guided locomotion to rapidly and precisely control the pedunculopontine nucleus (PPN) of the mesencephalic locomotor region through the basal ganglia. By capturing the physiological dynamics through a feedback control model and analyzing neuronal signals in M2, PPN, and STN, we find that the corticosubthalamic projections potentially control PPN activity by differentiating an M2 error signal to ensure fast input-output dynamics.

A Novel Device of Reaching, Grasping, and Retrieving Task for Head-Fixed Mice

Reaching, grasping, and retrieving movements are essential to our daily lives and are common in many mammalian species. To understand the mechanism for controlling this movement at the neural circuit level, it is necessary to observe the activity of individual neurons involved in the movement. For stable electrophysiological or optical recordings of neural activity in a behaving animal, head fixation effectively minimizes motion artifacts. Here, we developed a new device that allows mice to perform reaching, grasping, and retrieving movements during head fixation. In this method, agar cubes were presented as target objects in front of water-restricted mice, and the mice were able to reach, grasp, and retrieve them with their forelimb. The agar cubes were supplied by a custom-made automatic dispenser, which uses a microcontroller to control the two motors to push out the agar cubes. This agar presentation system supplied approximately 20 agar cubes in consecutive trials. We confirmed that each agar cube could be presented to the mouse with an average weight of 55 ± 3 mg and positional accuracy of less than 1 mm. Using this system, we showed that head-fixed mice could perform reaching, grasping, and retrieving tasks after 1 week of training. When the agar cube was placed near the mice, they could grasp it with a high success rate without extensive training. On the other hand, when the agar cube was presented far from the mice, the success rate was initially low and increased with subsequent test sessions. Furthermore, we showed that activity in the primary motor cortex is required for reaching movements in this task. Therefore, our system can be used to study neural circuit mechanisms for the control and learning of reaching, grasping, and retrieving movements under head-fixed conditions.

Stay or Go? Neuronal Activity in Medial Frontal Cortex During a Voluntary Tactile Preference Task in Head-fixed Mice

The decision to move is influenced by sensory, attentional, and motivational cues. One such cue is the quality of the tactile input, with noxious or unpleasant sensations causing an animal to move away from the cue. Processing of painful and unpleasant sensation in the cortex involves multiple brain regions, although the specific role of the brain areas involved in voluntary, rather than reflexive movement away from unpleasant stimuli is not well understood. Here, we focused on the medial subdivision of secondary motor cortex, which is proposed to link sensory and contextual cues to motor action, and tested its role in controlling voluntary movement in the context of an aversive tactile cue. We designed a novel, 3D-printed tactile platform consisting of innocuous (grid) and mildly noxious (spiked) surfaces (50:50 % of total area), which enabled monitoring neuronal activity in the medial frontal cortex by two-photon imaging during a sensory preference task in head-fixed mice. We found that freely moving mice spent significantly less time on a spiked-surface, and that this preference was eliminated by administration of a local anesthetic. At the neuronal level, individual neurons were differentially modulated specific to the tactile surface encountered. At the population level, the neuronal activity was analyzed in relation to the events where mice chose to "stop-on" or "go-from" a specific tactile surface and when they "switched" surfaces without stopping. Notably, each of these three scenarios showed population activity that differed significantly between the grid and spiked tactile surfaces. Collectively, these data provide evidence that tactile quality is encoded within medial frontal cortex. The task pioneered in this study provides a valuable tool to better evaluate mouse models of nociception and pain, using a voluntary task that allows simultaneous recording of preference and choice. Grant support from NS109287 (G.A.), NS096246 (Y.U.), DK116624 (Y.U.) and NS113189 (Y.U.), the Iowa Neuroscience Institute, and the Williams- Cannon faculty fellowship (G.A). A.K. was supported by a predoctoral fellowship through NIH T32 Grant GM067795.

Context coding in the mouse nucleus accumbens modulates motivationally relevant information

Neural activity in the nucleus accumbens (NAc) is thought to track fundamentally value-centric quantities linked to reward and effort. However, the NAc also contributes to flexible behavior in ways that are difficult to explain based on value signals alone, raising the question of if and how nonvalue signals are encoded in NAc. We recorded NAc neural ensembles while head-fixed mice performed an odor-based biconditional discrimination task where an initial discrete cue modulated the behavioral significance of a subsequently presented reward-predictive cue. We extracted single-unit and population-level correlates related to the cues and found value-independent coding for the initial, context-setting cue. This context signal occupied a population-level coding space orthogonal to outcome-related representations and was predictive of subsequent behaviorally relevant responses to the reward-predictive cues. Together, these findings support a gating model for how the NAc contributes to behavioral flexibility and provide a novel population-level perspective from which to view NAc computations.