Magnetic eye tracking in mice

Systemic pharmacological suppression of neural activity reverses learning impairment in a mouse model of Fragile X syndrome

The enhancement of associative synaptic plasticity often results in impaired rather than enhanced learning. Previously, we proposed that such learning impairments can result from saturation of the plasticity mechanism (Nguyen-Vu et al., 2017), or, more generally, from a history-dependent change in the threshold for plasticity. This hypothesis was based on experimental results from mice lacking two class I major histocompatibility molecules, MHCI H2-Kb and H2-Db (MHCI KbDb-/-), which have enhanced associative long-term depression at the parallel fiber-Purkinje cell synapses in the cerebellum (PF-Purkinje cell LTD). Here, we extend this work by testing predictions of the threshold metaplasticity hypothesis in a second mouse line with enhanced PF-Purkinje cell LTD, the Fmr1 knockout mouse model of Fragile X syndrome (FXS). Mice lacking Fmr1 gene expression in cerebellar Purkinje cells (L7-Fmr1 KO) were selectively impaired on two oculomotor learning tasks in which PF-Purkinje cell LTD has been implicated, with no impairment on LTD-independent oculomotor learning tasks. Consistent with the threshold metaplasticity hypothesis, behavioral pre-training designed to reverse LTD at the PF-Purkinje cell synapses eliminated the oculomotor learning deficit in the L7-Fmr1 KO mice, as previously reported in MHCI KbDb-/-mice. In addition, diazepam treatment to suppress neural activity and thereby limit the induction of associative LTD during the pre-training period also eliminated the learning deficits in L7-Fmr1 KO mice. These results support the hypothesis that cerebellar LTD-dependent learning is governed by an experience-dependent sliding threshold for plasticity. An increased threshold for LTD in response to elevated neural activity would tend to oppose firing rate stability, but could serve to stabilize synaptic weights and recently acquired memories. The metaplasticity perspective could inform the development of new clinical approaches for addressing learning impairments in autism and other disorders of the nervous system.

Excitatory Projections of Wide Field Collicular Neurons to the Nucleus of the Optic Tract in the Rat

The superficial layers of the mammalian superior colliculus (SC) contain neurons that are generally responsive to visual stimuli but can differ considerably in morphology and response properties. To elucidate the structure and function of these neurons, we combined extracellular recording and juxtacellular labeling, detailed anatomical reconstruction, and ultrastructural analysis of the synaptic contacts of labeled neurons, using transmission electron microscopy. Our labeled neurons project to different brainstem nuclei. Of particular importance are neurons that fit the morphological criteria of the wide field (WF) neurons and whose dendrites are horizontally oriented. They display a rather characteristic axonal projection pattern to the nucleus of optic tract (NOT); thus, we call them superior collicular WF projecting to the NOT (SCWFNOT) neurons. We corroborated the morphological characterization of this neuronal type as a distinct neuronal class with the help of unsupervised hierarchical cluster analysis. Our ultrastructural data demonstrate that SCWFNOT neurons establish excitatory connections with their targets in the NOT. Although, in rodents, the literature about the WF neurons has focused on their extensive projection to the lateral posterior nucleus of the thalamus, as a conduit for information to reach the visual association areas of the cortex, our data suggest that this subclass of WF neurons may participate in the optokinetic nystagmus.

Behind mouse eyes: The function and control of eye movements in mice

The mouse visual system has become the most popular model to study the cellular and circuit mechanisms of sensory processing. However, the importance of eye movements only started to be appreciated recently. Eye movements provide a basis for predictive sensing and deliver insights into various brain functions and dysfunctions. A plethora of knowledge on the central control of eye movements and their role in perception and behaviour arose from work on primates. However, an overview of various eye movements in mice and a comparison to primates is missing. Here, we review the eye movement types described to date in mice and compare them to those observed in primates. We discuss the central neuronal mechanisms for their generation and control. Furthermore, we review the mounting literature on eye movements in mice during head-fixed and freely moving behaviours. Finally, we highlight gaps in our understanding and suggest future directions for research.

Systemic pharmacological suppression of neural activity reverses learning impairment in a mouse model of Fragile X syndrome

The enhancement of associative synaptic plasticity often results in impaired rather than enhanced learning. Previously, we proposed that such learning impairments can result from saturation of the plasticity mechanism (Nguyen-Vu et al., 2017), or, more generally, from a history-dependent change in the threshold for plasticity. This hypothesis was based on experimental results from mice lacking two class I major histocompatibility molecules, MHCI H2-Kb and H2Db (MH-CI KbDb-/-), which have enhanced associative long-term depression at the parallel fiber-Purkinje cell synapses in the cerebellum (PF-Purkinje cell LTD). Here, we extend this work by testing predictions of the threshold metaplasticity hypothesis in a second mouse line with enhanced PF-Purkinje cell LTD, the Fmr1 knockout mouse model of Fragile X syndrome (FXS). Mice lacking Fmr1 gene expression in cerebellar Purkinje cells (L7-Fmr1 KO) were selectively impaired on two oculomotor learning tasks in which PF-Purkinje cell LTD has been implicated, with no impairment on LTD-independent oculomotor learning tasks. Consistent with the threshold metaplasticity hypothesis, behavioral pre-training designed to reverse LTD at the PF-Purkinje cell synapses eliminated the oculomotor learning deficit in the L7-Fmr1 KO mice, as previously reported in MHCI KbDb-/-mice. In addition, diazepam treatment to suppress neural activity and thereby limit the induction of associative LTD during the pre-training period also eliminated the learning deficits in L7-Fmr1 KO mice. These results support the hypothesis that cerebellar LTD-dependent learning is governed by an experience-dependent sliding threshold for plasticity. An increased threshold for LTD in response to elevated neural activity would tend to oppose firing rate stability, but could serve to stabilize synaptic weights and recently acquired memories. The metaplasticity perspective could inform the development of new clinical approaches for addressing learning impairments in autism and other disorders of the nervous system.

Hindbrain modules differentially transform activity of single collicular neurons to coordinate movements

Seemingly simple behaviors such as swatting a mosquito or glancing at a signpost involve the precise coordination of multiple body parts. Neural control of coordinated movements is widely thought to entail transforming a desired overall displacement into displacements for each body part. Here we reveal a different logic implemented in the mouse gaze system. Stimulating superior colliculus (SC) elicits head movements with stereotyped displacements but eye movements with stereotyped endpoints. This is achieved by individual SC neurons whose branched axons innervate modules in medulla and pons that drive head movements with stereotyped displacements and eye movements with stereotyped endpoints, respectively. Thus, single neurons specify a mixture of endpoints and displacements for different body parts, not overall displacement, with displacements for different body parts computed at distinct anatomical stages. Our study establishes an approach for unraveling motor hierarchies and identifies a logic for coordinating movements and the resulting pose.

Computational cross-species views of the hippocampal formation

The discovery of place cells and head direction cells in the hippocampal formation of freely foraging rodents has led to an emphasis of its role in encoding allocentric spatial relationships. In contrast, studies in head-fixed primates have additionally found representations of spatial views. We review recent experiments in freely moving monkeys that expand upon these findings and show that postural variables such as eye/head movements strongly influence neural activity in the hippocampal formation, suggesting that the function of the hippocampus depends on where the animal looks. We interpret these results in the light of recent studies in humans performing challenging navigation tasks which suggest that depending on the context, eye/head movements serve one of two roles-gathering information about the structure of the environment (active sensing) or externalizing the contents of internal beliefs/deliberation (embodied cognition). These findings prompt future experimental investigations into the information carried by signals flowing between the hippocampal formation and the brain regions controlling postural variables, and constitute a basis for updating computational theories of the hippocampal system to accommodate the influence of eye/head movements.

Ratphones: An Affordable Tool for Highly Controlled Sound Presentation in Freely Moving Rats

Encoding and processing sensory information is key to understanding the environment and to guiding behavior accordingly. Characterizing the behavioral and neural correlates of these processes requires the experimenter to have a high degree of control over stimuli presentation. For auditory stimulation in animals with relatively large heads, this can be accomplished by using headphones. However, it has proven more challenging in smaller species, such as rats and mice, and has been only partially solved using closed-field speakers in anesthetized or head-restrained preparations. To overcome the limitations of such preparations and to deliver sound with high precision to freely moving animals, we have developed a set of miniature headphones for rats. The headphones consist of a small, skull-implantable base attached with magnets to a fully adjustable structure that holds the speakers and keeps them in the same position with respect to the ears.

Through Hawks’ Eyes: Synthetically Reconstructing the Visual Field of a Bird in Flight

Birds of prey rely on vision to execute flight manoeuvres that are key to their survival, such as intercepting fast-moving targets or navigating through clutter. A better understanding of the role played by vision during these manoeuvres is not only relevant within the field of animal behaviour, but could also have applications for autonomous drones. In this paper, we present a novel method that uses computer vision tools to analyse the role of active vision in bird flight, and demonstrate its use to answer behavioural questions. Combining motion capture data from Harris’ hawks with a hybrid 3D model of the environment, we render RGB images, semantic maps, depth information and optic flow outputs that characterise the visual experience of the bird in flight. In contrast with previous approaches, our method allows us to consider different camera models and alternative gaze strategies for the purposes of hypothesis testing, allows us to consider visual input over the complete visual field of the bird, and is not limited by the technical specifications and performance of a head-mounted camera light enough to attach to a bird’s head in flight. We present pilot data from three sample flights: a pursuit flight, in which a hawk intercepts a moving target, and two obstacle avoidance flights. With this approach, we provide a reproducible method that facilitates the collection of large volumes of data across many individuals, opening up new avenues for data-driven models of animal behaviour.

Why are predator cues in the field not more evocative? A ‘real world’ assay elicits subtle, but meaningful, responses by wild rodents to predator scents

Mismatches between highly-standardized laboratory predatory assays and more realistic environmental conditions may lead to different outcomes. Understanding rodents’ natural responses to predator scents is important. Thus, field studies on the same and related species are essential to corroborate laboratory findings to better understand the contexts and motivational drives that affect laboratory responses to predator scents. However, there are too few field assays to enable researchers to study factors that influence these responses in genetically variable populations of wild rodents. Therefore, we placed laboratory-style chambers and remote-sensing devices near multiple colonies of two species of wild mice (Apodemus agrarius and Apodemus flavicollis) to test dual-motivational drives (appetitive and aversive) in a ‘familiar’, yet natural environment. A highly-palatable food reward was offered daily alongside scents from coyotes, lions, rabbits, and both wet and dry controls. In all but two instances (n = 264), animals entered chambers and remained inside for several minutes. Animals initiated flight twice, but they never froze. Rather, they visited chambers more often and stayed inside longer when predatory scents were deployed. The total time spent inside was highest for lion urine (380% longer than the dry control), followed by coyote scent (75% longer), dry control and lastly, herbivore scents (no difference). Once inside the chamber, animals spent more time physically interacting with predatory scents than the herbivore scent or controls. Our findings support the common assumption that rodents fail to respond as overtly to predatory scents in the field compared to what has been observed in the laboratory, possibly due to their varying motivational levels to obtain food. More time spent interacting with scents in the field was likely a function of ‘predator inspection’ (risk assessment) once subjects were in a presumed safe enclosure. We conclude this sort of chamber assay can be useful in understanding the contexts and motivational drives inherent to field studies, and may help interpret laboratory results. Our results also suggest more attention should be given to subtle behaviors such as scent inspection in order to better understand how, and when, environmental stimuli evoke fear in rodents.

An Easily Compatible Eye-tracking System for Freely-moving Small Animals

Measuring eye movement is a fundamental approach in cognitive science as it provides a variety of insightful parameters that reflect brain states such as visual attention and emotions. Combining eye-tracking with multimodal neural recordings or manipulation techniques is beneficial for understanding the neural substrates of cognitive function. Many commercially-available and custom-built systems have been widely applied to awake, head-fixed small animals. However, the existing eye-tracking systems used in freely-moving animals are still limited in terms of their compatibility with other devices and of the algorithm used to detect eye movements. Here, we report a novel system that integrates a general-purpose, easily compatible eye-tracking hardware with a robust eye feature-detection algorithm. With ultra-light hardware and a detachable design, the system allows for more implants to be added to the animal's exposed head and has a precise synchronization module to coordinate with other neural implants. Moreover, we systematically compared the performance of existing commonly-used pupil-detection approaches, and demonstrated that the proposed adaptive pupil feature-detection algorithm allows the analysis of more complex and dynamic eye-tracking data in free-moving animals. Synchronized eye-tracking and electroencephalogram recordings, as well as algorithm validation under five noise conditions, suggested that our system is flexibly adaptable and can be combined with a wide range of neural manipulation and recording technologies.

Superior colliculus drives stimulus-evoked directionally biased saccades and attempted head movements in head-fixed mice

Animals investigate their environments by directing their gaze towards salient stimuli. In the prevailing view, mouse gaze shifts entail head rotations followed by brainstem-mediated eye movements, including saccades to reset the eyes. These 'recentering' saccades are attributed to head movement-related vestibular cues. However, microstimulating mouse superior colliculus (SC) elicits directed head and eye movements resembling SC-dependent sensory-guided gaze shifts in other species, suggesting that mouse gaze shifts may be more flexible than has been recognized. We investigated this possibility by tracking eye and attempted head movements in a head-fixed preparation that eliminates head movement-related sensory cues. We found tactile stimuli evoke directionally biased saccades coincident with attempted head rotations. Differences in saccade endpoints across stimuli are associated with distinct stimulus-dependent relationships between initial eye position and saccade direction and amplitude. Optogenetic perturbations revealed SC drives these gaze shifts. Thus, head-fixed mice make sensory-guided, SC-dependent gaze shifts involving coincident, directionally biased saccades and attempted head movements. Our findings uncover flexibility in mouse gaze shifts and provide a foundation for studying head-eye coupling.

Conservation of locomotion-induced oculomotor activity through evolution in mammals

Efference copies are neural replicas of motor outputs used to anticipate the sensory consequences of a self-generated motor action or to coordinate neural networks involved in distinct motor behaviors.¹ An established example of this motor-to-motor coupling is the efference copy of the propulsive motor command, which supplements classical visuo-vestibular reflexes to ensure gaze stabilization during amphibian larval locomotion.² Such feedforward replica of spinal pattern-generating circuits produces a spino-extraocular motor coupled activity that evokes eye movements, spatiotemporally coordinated to tail undulation independently of any sensory signal.^3,4 Exploiting the developmental stages of the frog,¹ studies in metamorphing Xenopus demonstrated the persistence of this spino-extraocular motor command in adults and its developmental adaptation to tetrapodal locomotion.^5,6 Here, we demonstrate for the first time the existence of a comparable locomotor-to-ocular motor coupling in the mouse. In neonates, ex vivo nerve recordings of brainstem-spinal cord preparations reveal a spino-extraocular motor coupled activity similar to the one described in Xenopus. In adult mice, trans-synaptic rabies virus injections in lateral rectus eye muscle label cervical spinal cord neurons closely connected to abducens motor neurons. Finally, treadmill-elicited locomotion in decerebrated preparations⁷ evokes rhythmic eye movements in synchrony with the limb gait pattern. Overall, our data are evidence for the conservation of locomotor-induced eye movements in vertebrate lineages. Thus, in mammals as in amphibians, CPG-efference copy feedforward signals might interact with sensory feedback to ensure efficient gaze control during locomotion.

Visual pursuit behavior in mice maintains the pursued prey on the retinal region with least optic flow

Mice have a large visual field that is constantly stabilized by vestibular ocular reflex (VOR) driven eye rotations that counter head-rotations. While maintaining their extensive visual coverage is advantageous for predator detection, mice also track and capture prey using vision. However, in the freely moving animal quantifying object location in the field of view is challenging. Here, we developed a method to digitally reconstruct and quantify the visual scene of freely moving mice performing a visually based prey capture task. By isolating the visual sense and combining a mouse eye optic model with the head and eye rotations, the detailed reconstruction of the digital environment and retinal features were projected onto the corneal surface for comparison, and updated throughout the behavior. By quantifying the spatial location of objects in the visual scene and their motion throughout the behavior, we show that the prey image consistently falls within a small area of the VOR-stabilized visual field. This functional focus coincides with the region of minimal optic flow within the visual field and consequently area of minimal motion-induced image-blur, as during pursuit mice ran directly toward the prey. The functional focus lies in the upper-temporal part of the retina and coincides with the reported high density-region of Alpha-ON sustained retinal ganglion cells.

The application of noninvasive, restraint-free eye-tracking methods for use with nonhuman primates

Over the past 50 years there has been a strong interest in applying eye-tracking techniques to study a myriad of questions related to human and nonhuman primate psychological processes. Eye movements and fixations can provide qualitative and quantitative insights into cognitive processes of nonverbal populations such as nonhuman primates, clarifying the evolutionary, physiological, and representational underpinnings of human cognition. While early attempts at nonhuman primate eye tracking were relatively crude, later, more sophisticated and sensitive techniques required invasive protocols and the use of restraint. In the past decade, technology has advanced to a point where noninvasive eye-tracking techniques, developed for use with human participants, can be applied for use with nonhuman primates in a restraint-free manner. Here we review the corpus of recent studies (N=32) that take such an approach. Despite the growing interest in eye-tracking research, there is still little consensus on "best practices," both in terms of deploying test protocols or reporting methods and results. Therefore, we look to advances made in the field of developmental psychology, as well as our own collective experiences using eye trackers with nonhuman primates, to highlight key elements that researchers should consider when designing noninvasive restraint-free eye-tracking research protocols for use with nonhuman primates. Beyond promoting best practices for research protocols, we also outline an ideal approach for reporting such research and highlight future directions for the field.

Population calcium responses of Purkinje cells in the oculomotor cerebellum driven by non-visual input

The climbing fiber input to the cerebellum conveys instructive signals that can induce synaptic plasticity and learning by triggering complex spikes accompanied by large calcium transients in Purkinje cells. In the cerebellar flocculus, which supports oculomotor learning, complex spikes are driven by image motion on the retina, which could indicate an oculomotor error. In the same neurons, complex spikes also can be driven by non-visual signals. It has been shown that the calcium transients accompanying each complex spike can vary in amplitude, even within a given cell, therefore, we compared the calcium responses associated with the visual and non-visual inputs to floccular Purkinje cells. The calcium indicator GCaMP6f was selectively expressed in Purkinje cells, and fiber photometry was used to record the calcium responses from a population of Purkinje cells in the flocculus of awake behaving mice. During visual (optokinetic) stimuli and pairing of vestibular and visual stimuli, the calcium level increased during contraversive retinal image motion. During performance of the vestibulo-ocular reflex in the dark, calcium increased during contraversive head rotation and the associated ipsiverse eye movements. The amplitude of this non-visual calcium response was comparable to that during conditions with retinal image motion present that induce oculomotor learning. Thus, population calcium responses of Purkinje cells in the cerebellar flocculus to visual and non-visual input are similar to what has been reported previously for complex spikes, suggesting that multimodal instructive signals control the synaptic plasticity supporting oculomotor learning.

A low-cost, high-performance video-based binocular eye tracker for psychophysical research

We describe a high-performance, pupil-based binocular eye tracker that approaches the performance of a well-established commercial system, but at a fraction of the cost. The eye tracker is built from standard hardware components, and its software (written in Visual C++) can be easily implemented. Because of its fast and simple linear calibration scheme, the eye tracker performs best in the central 10 degrees of the visual field. The eye tracker possesses a number of useful features: (1) automated calibration simultaneously in both eyes while subjects fixate four fixation points sequentially on a computer screen, (2) automated realtime continuous analysis of measurement noise, (3) automated blink detection, (4) and realtime analysis of pupil centration artifacts. This last feature is critical because it is known that pupil diameter changes can be erroneously registered by pupil-based trackers as a change in eye position. We evaluated the performance of our system against that of a wellestablished commercial system using simultaneous measurements in 10 participants. We propose our low-cost eye tracker as a promising resource for studies of binocular eye movements.

Evaluating Visual Cues Modulates Their Representation in Mouse Visual and Cingulate Cortex

Choosing an action in response to visual cues relies on cognitive processes, such as perception, evaluation, and prediction, which can modulate visual representations even at early processing stages. In the mouse, it is challenging to isolate cognitive modulations of sensory signals because concurrent overt behavior patterns, such as locomotion, can also have brainwide influences. To address this challenge, we designed a task, in which head-fixed mice had to evaluate one of two visual cues. While their global shape signaled the opportunity to earn reward, the cues provided equivalent local stimulation to receptive fields of neurons in primary visual (V1) and anterior cingulate cortex (ACC). We found that mice evaluated these cues within few hundred milliseconds. During this period, ∼30% of V1 neurons became cue-selective, with preferences for either cue being balanced across the recorded population. This selectivity emerged in response to the behavioral demands because the same neurons could not discriminate the cues in sensory control measurements. In ACC, cue evaluation affected a similar fraction of neurons; emerging selectivity, however, was stronger than in V1, and preferences in the recorded population were biased toward the cue promising reward. Such a biased selectivity regime might allow the mouse to infer the promise of reward simply by the overall level of activity. Together, these experiments isolate the impact of task demands on neural responses in mouse cerebral cortex, and document distinct neural signatures of cue evaluation in V1 and ACC.SIGNIFICANCE STATEMENT Performing a cognitive task, such as evaluating visual cues, not only recruits frontal and parietal brain regions, but also modulates sensory processing stages. We trained mice to evaluate two visual cues, and show that, during this task, ∼30% of neurons recorded in V1 became selective for either cue, although they provided equivalent visual stimulation. We also show that, during cue evaluation, mice frequently move their eyes, even under head fixation, and that ignoring systematic differences in eye position can substantially obscure the modulations seen in V1 neurons. Finally, we document that modulations are stronger in ACC, and biased toward the reward-predicting cue, suggesting a transition in the neural representation of task-relevant information across processing stages in mouse cerebral cortex.

Tracking Eye Movements During Sleep in Mice

Eye movement is not only for adjusting the visual field and maintaining the stability of visual information on the retina, but also provides an external manifestation of the cognitive status of the brain. Recent studies showed similarity in eye movement patterns between wakefulness and rapid eye movement (REM) sleep, indicating that the brain status of REM sleep likely resembles that of awake status. REM sleep in humans could be divided into phasic REM and tonic REM sleep according to the difference in eye movement frequencies. Mice are the most commonly used animal model for studying neuronal and molecular mechanisms underlying sleep. However, there was a lack of details for eye movement patterns during REM sleep, hence it remains unknown whether REM sleep can be further divided into different stages in mice. Here we developed a device combining electroencephalogram (EEG), electromyogram (EMG) as well as eye movements recording in mice to study the eye movement patterns during sleep. We implanted a magnet beneath the conjunctiva of eye and tracked eye movements using a magnetic sensor. The magnetic signals showed strong correlation with video-oculography in head-fixed mice, indicating that the magnetic signals reflect the direction and magnitude of eye movement. We also found that the magnet implanted beneath the conjunctiva exhibited good biocompatibility. Finally, we examined eye movement in sleep–wake cycle, and discriminated tonic REM and phasic REM according to the frequency of eye movements, finding that compared to tonic REM, phasic REM exhibited higher oscillation power at 0.50 Hz, and lower oscillation power at 1.50–7.25 Hz and 9.50–12.00 Hz. Our device allowed to simultaneously record EEG, EMG, and eye movements during sleep and wakefulness, providing a convenient and high temporal-spatial resolution tool for studying eye movements in sleep and other researches in mice.

A Direct Comparison of Spatial Attention and Stimulus-Response Compatibility between Mice and Humans

Mice are becoming an increasingly popular model for investigating the neural substrates of visual processing and higher cognitive functions. To validate the translation of mouse visual attention and sensorimotor processing to humans, we compared their performance in the same visual task. Mice and human participants judged the orientation of a grating presented on either the right or left side in the visual field. To induce shifts of spatial attention, we varied the stimulus probability on each side. As expected, human participants showed faster RTs and a higher accuracy for the side with a higher probability, a well-established effect of visual attention. The attentional effect was only present in mice when their response was slow. Although the task demanded a judgment of grating orientation, the accuracy of the mice was strongly affected by whether the side of the stimulus corresponded to the side of the behavioral response. This stimulus-response compatibility (Simon) effect was much weaker in humans and only significant for their fastest responses. Both species exhibited a speed-accuracy trade-off in their responses, because slower responses were more accurate than faster responses. We found that mice typically respond very fast, which contributes to the stronger stimulus-response compatibility and weaker attentional effects, which were only apparent in the trials with slowest responses. Humans responded slower and had stronger attentional effects, combined with a weak influence of stimulus-response compatibility, which was only apparent in trials with fast responses. We conclude that spatial attention and stimulus-response compatibility influence the responses of humans and mice but that strategy differences between species determine the dominance of these effects.

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.

DeepLabStream enables closed-loop behavioral experiments using deep learning-based markerless, real-time posture detection

In general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Most of the available current technologies focus on offline pose estimation with high spatiotemporal resolution. However, to correlate behavior with neuronal activity it is often necessary to detect and react online to behavioral expressions. Here we present DeepLabStream, a versatile closed-loop tool providing real-time pose estimation to deliver posture dependent stimulations. DeepLabStream has a temporal resolution in the millisecond range, can utilize different input, as well as output devices and can be tailored to multiple experimental designs. We employ DeepLabStream to semi-autonomously run a second-order olfactory conditioning task with freely moving mice and optogenetically label neuronal ensembles active during specific head directions.

Mouse entorhinal cortex encodes a diverse repertoire of self-motion signals

Neural circuits generate representations of the external world from multiple information streams. The navigation system provides an exceptional lens through which we may gain insights about how such computations are implemented. Neural circuits in the medial temporal lobe construct a map-like representation of space that supports navigation. This computation integrates multiple sensory cues, and, in addition, is thought to require cues related to the individual's movement through the environment. Here, we identify multiple self-motion signals, related to the position and velocity of the head and eyes, encoded by neurons in a key node of the navigation circuitry of mice, the medial entorhinal cortex (MEC). The representation of these signals is highly integrated with other cues in individual neurons. Such information could be used to compute the allocentric location of landmarks from visual cues and to generate internal representations of space.

Identification of the sleep-wake states in rats using the high-frequency activity of the electroencephalogram

The electroencephalographic signal constitutes the main sign classically used for the identification of states of alertness. However, activities in the high frequency (>100 Hz) range have not been properly studied despite their high potential for sleep scoring in rodents. In the present study, we designed a method for the identification of the sleep-wake states in rats by exclusively using high-frequency activities of the electroencephalogram. By calculating the ratio between the amplitude of the electroencephalographic signal from 110 to 200 Hz and from 110 to 300 Hz, we obtained an index that had values that were low during wakefulness, intermediate during non-REM sleep and high during REM sleep. This high-frequency index (HiFI) allowed the identification of each state without the need to study other signs such as muscle activity or eye movements. To evaluate the performance of the index, we compared it with the conventional scoring of the sleep-wake cycle based upon the study of the electromyogram and delta (0.5-4 Hz), theta (6-9 Hz) and sigma (10-14 Hz) bands of the electroencephalogram. The index had an accuracy of 90.43 ± 1.91% (Cohen's kappa value of 0.82), confirming that the study of the high-frequency activities of the electroencephalogram was sufficient to reliably identify alertness states in the rat. Compared to other sleep-scoring methods, the HiFI has several advantages. It only requires one electroencephalography electrode, thus reducing the severity of the surgical preparation of the experimental animal, and its calculation is very simple, so it can be easily implemented online to classify sleep-wake states in real time.

Unmasking inhibition prolongs neuronal function in retinal degeneration mouse model

All neurodegenerative diseases involve a relatively long period of timeframe from the onset of the disease to complete loss of functions. Extending this timeframe, even at a reduced level of function, would improve the quality of life of patients with these devastating diseases. The retina, as the part of the central nervous system and a frequent site of many distressing neurodegenerative disease, provides an ideal model to investigate the feasibility of extending the functional timeframe through pharmacologic intervention. Retinitis Pigmentosa (RP) is a group of blinding diseases. Although the rate of progression and degree of visual loss varies, there is usually a prolonged time before patients totally lose their photoreceptors and vision. It is believed that inhibitory mechanisms are still intact and may become relatively strong after the gradual loss of photoreceptors in RP patients. Therefore, it is possible that light-evoked responses of retinal ganglion cells and visual information processes in retinal circuits could be "unmasked" by blocking these inhibitory mechanisms restoring some level of visual function. Our results indicate that if the inhibition in the inner retina was unmasked in the retina of the rd10 mouse (the well-characterized RP mimicking, clinically relevant mouse model), the light-evoked responses of many retinal ganglion cells can be induced and restore their normal light sensitivity. GABA A receptor plays a major role in this masking inhibition. ERG b-wave and behavioral tests of spatial vision partly recovered after the application of PTX. Hence, removing retinal inhibition unmasks signalling mediated by surviving cones, thereby restoring some degree of visual function. These results may offer a novel strategy to restore the visual function with the surviving cones in RP patients and other gradual and progressive neurodegenerative diseases.

Dynamics of gaze control during prey capture in freely moving mice

Many studies of visual processing are conducted in constrained conditions such as head- and gaze-fixation, and therefore less is known about how animals actively acquire visual information in natural contexts. To determine how mice target their gaze during natural behavior, we measured head and bilateral eye movements in mice performing prey capture, an ethological behavior that engages vision. We found that the majority of eye movements are compensatory for head movements, thereby serving to stabilize the visual scene. During movement, however, periods of stabilization are interspersed with non-compensatory saccades that abruptly shift gaze position. Notably, these saccades do not preferentially target the prey location. Rather, orienting movements are driven by the head, with the eyes following in coordination to sequentially stabilize and recenter the gaze. These findings relate eye movements in the mouse to other species, and provide a foundation for studying active vision during ethological behaviors in the mouse.

Two Distinct Types of Eye-Head Coupling in Freely Moving Mice

Animals actively interact with their environment to gather sensory information. There is conflicting evidence about how mice use vision to sample their environment. During head restraint, mice make rapid eye movements coupled between the eyes, similar to conjugate saccadic eye movements in humans. However, when mice are free to move their heads, eye movements are more complex and often non-conjugate, with the eyes moving in opposite directions. We combined head and eye tracking in freely moving mice and found both observations are explained by two eye-head coupling types, associated with vestibular mechanisms. The first type comprised non-conjugate eye movements, which compensate for head tilt changes to maintain a similar visual field relative to the horizontal ground plane. The second type of eye movements was conjugate and coupled to head yaw rotation to produce a "saccade and fixate" gaze pattern. During head-initiated saccades, the eyes moved together in the head direction but during subsequent fixation moved in the opposite direction to the head to compensate for head rotation. This saccade and fixate pattern is similar to humans who use eye movements (with or without head movement) to rapidly shift gaze but in mice relies on combined head and eye movements. Both couplings were maintained during social interactions and visually guided object tracking. Even in head-restrained mice, eye movements were invariably associated with attempted head motion. Our results reveal that mice combine head and eye movements to sample their environment and highlight similarities and differences between eye movements in mice and humans.

Understanding the circuit basis of cognitive functions using mouse models

Understanding how cognitive functions arise from computations occurring in the brain requires the ability to measure and perturb neural activity while the relevant circuits are engaged for specific cognitive processes. Rapid technical advances have led to the development of new approaches to transiently activate and suppress neuronal activity as well as to record simultaneously from hundreds to thousands of neurons across multiple brain regions during behavior. To realize the full potential of these approaches for understanding cognition, however, it is critical that behavioral conditions and stimuli are effectively designed to engage the relevant brain networks. Here, we highlight recent innovations that enable this combined approach. In particular, we focus on how to design behavioral experiments that leverage the ever-growing arsenal of technologies for controlling and measuring neural activity in order to understand cognitive functions.

Real-time contextual feedback for close-loop control of navigation

OBJECTIVE

Close-loop control of brain and behavior will benefit from real-time detection of behavioral events to enable low-latency communication with peripheral devices. In animal experiments, this is typically achieved by using sparsely distributed (embedded) sensors that detect animal presence in select regions of interest. High-speed cameras provide high-density sampling across large arenas, capturing the richness of animal behavior, however, the image processing bottleneck prohibits real-time feedback in the context of rapidly evolving behaviors.

APPROACH

Here we developed an open-source software, named PolyTouch, to track animal behavior in large arenas and provide rapid close-loop feedback in ~5.7 ms, ie. average latency from the detection of an event to analog stimulus delivery, e.g. auditory tone, TTL pulse, when tracking a single body. This stand-alone software is written in JAVA. The included wrapper for MATLAB provides experimental flexibility for data acquisition, analysis and visualization.

MAIN RESULTS

As a proof-of-principle application we deployed the PolyTouch for place awareness training. A user-defined portion of the arena was used as a virtual target; visit (or approach) to the target triggered auditory feedback. We show that mice develop awareness to virtual spaces, tend to stay shorter and move faster when they reside in the virtual target zone if their visits are coupled to relatively high stimulus intensity (⩾49 dB). Thus, close-loop presentation of perceived aversive feedback is sufficient to condition mice to avoid virtual targets within the span of a single session (~20 min).

SIGNIFICANCE

Neuromodulation techniques now allow control of neural activity in a cell-type specific manner in spiking resolution. Using animal behavior to drive closed-loop control of neural activity would help to address the neural basis of behavioral state and environmental context-dependent information processing in the brain.

A passive, camera-based head-tracking system for real-time, three-dimensional estimation of head position and orientation in rodents

Tracking head position and orientation in small mammals is crucial for many applications in the field of behavioral neurophysiology, from the study of spatial navigation to the investigation of active sensing and perceptual representations. Many approaches to head tracking exist, but most of them only estimate the 2D coordinates of the head over the plane where the animal navigates. Full reconstruction of the pose of the head in 3D is much more more challenging and has been achieved only in handful of studies, which employed headsets made of multiple LEDs or inertial units. However, these assemblies are rather bulky and need to be powered to operate, which prevents their application in wireless experiments and in the small enclosures often used in perceptual studies. Here we propose an alternative approach, based on passively imaging a lightweight, compact, 3D structure, painted with a pattern of black dots over a white background. By applying a cascade of feature extraction algorithms that progressively refine the detection of the dots and reconstruct their geometry, we developed a tracking method that is highly precise and accurate, as assessed through a battery of validation measurements. We show that this method can be used to study how a rat samples sensory stimuli during a perceptual discrimination task and how a hippocampal place cell represents head position over extremely small spatial scales. Given its minimal encumbrance and wireless nature, our method could be ideal for high-throughput applications, where tens of animals need to be simultaneously and continuously tracked.NEW & NOTEWORTHY Head tracking is crucial in many behavioral neurophysiology studies. Yet reconstruction of the head's pose in 3D is challenging and typically requires implanting bulky, electrically powered headsets that prevent wireless experiments and are hard to employ in operant boxes. Here we propose an alternative approach, based on passively imaging a compact, 3D dot pattern that, once implanted over the head of a rodent, allows estimating the pose of its head with high precision and accuracy.

Paradoxical Rules of Spike Train Decoding Revealed at the Sensitivity Limit of Vision

All sensory information is encoded in neural spike trains. It is unknown how the brain utilizes this neural code to drive behavior. Here, we unravel the decoding rules of the brain at the most elementary level by linking behavioral decisions to retinal output signals in a single-photon detection task. A transgenic mouse line allowed us to separate the two primary retinal outputs, ON and OFF pathways, carrying information about photon absorptions as increases and decreases in spiking, respectively. We measured the sensitivity limit of rods and the most sensitive ON and OFF ganglion cells and correlated these results with visually guided behavior using markerless head and eye tracking. We show that behavior relies only on the ON pathway even when the OFF pathway would allow higher sensitivity. Paradoxically, behavior does not rely on the spike code with maximal information but instead relies on a decoding strategy based on increases in spiking.

Feasibility of Tracking Multiple Implanted Magnets With a Myokinetic Control Interface: Simulation and Experimental Evidence Based on the Point Dipole Model

OBJECTIVE

The quest for an intuitive and physiologically appropriate human-machine interface for the control of dexterous prostheses is far from being completed. To control a hand prosthesis, a possible approach could consist in using information related to the displacement of forearm muscles of an amputee during contraction. We recently proposed that muscle displacement could be monitored by implanting passive magnetic markers (MMs- i.e., permanent magnets) in them. We dubbed this the myokinetic interface. However, besides the system feasibility, how much its accuracy, precision and computation time are affected by the number and distribution of both the MMs and the sensors used to record the MF was not quantified.

METHODS

Here we investigated, through simulations validated with a physical system, the performance of a system capable to track position and orientation of up to 9 MMs using information from up to 112 sensors in a volume resembling the dimensions of the human forearm.

RESULTS

The system was able to track up to 7 MMs in 450 ms, demonstrating position/orientation accuracies in the range of 1 mm/5°. The comparison with the experimental recordings demonstrated a median difference with the simulations in the order of 0.45 mm.

CONCLUSION

We were able to formulate general guidelines for the implementation of magnetic tracking systems.

SIGNIFICANCE

Our results pave the way towards the development of new human-machine interfaces for the control of artificial limbs, but they are also interesting for the whole range of biomedical engineering applications exploiting magnetic tracking.

A Head-Mounted Camera System Integrates Detailed Behavioral Monitoring with Multichannel Electrophysiology in Freely Moving Mice

Breakthroughs in understanding the neural basis of natural behavior require neural recording and intervention to be paired with high-fidelity multimodal behavioral monitoring. An extensive genetic toolkit for neural circuit dissection, and well-developed neural recording technology, make the mouse a powerful model organism for systems neuroscience. However, most methods for high-bandwidth acquisition of behavioral data in mice rely upon fixed-position cameras and other off-animal devices, complicating the monitoring of animals freely engaged in natural behaviors. Here, we report the development of a lightweight head-mounted camera system combined with head-movement sensors to simultaneously monitor eye position, pupil dilation, whisking, and pinna movements along with head motion in unrestrained, freely behaving mice. The power of the combined technology is demonstrated by observations linking eye position to head orientation; whisking to non-tactile stimulation; and, in electrophysiological experiments, visual cortical activity to volitional head movements.

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Eyes, whiskers, head, and neural activity monitored in freely moving mice

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System generates stable video output and leaves mouse behavior largely unchanged

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Close link between eye and head movements at both slow and fast timescales

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Active head movements in the dark strongly modulate primary visual cortex activity

Twitches, Blinks, and Fidgets: Important Generators of Ongoing Neural Activity

Animals and humans continuously engage in small, spontaneous motor actions, such as blinking, whisking, and postural adjustments ("fidgeting"). These movements are accompanied by changes in neural activity in sensory and motor regions of the brain. The frequency of these motions varies in time, is affected by sensory stimuli, arousal levels, and pathology. These fidgeting behaviors can be entrained by sensory stimuli. Fidgeting behaviors will cause distributed, bilateral functional activation in the 0.01 to 0.1 Hz frequency range that will show up in functional magnetic resonance imaging and wide-field calcium neuroimaging studies, and will contribute to the observed functional connectivity among brain regions. However, despite the large potential of these behaviors to drive brain-wide activity, these fidget-like behaviors are rarely monitored. We argue that studies of spontaneous and evoked brain dynamics in awake animals and humans should closely monitor these fidgeting behaviors. Differences in these fidgeting behaviors due to arousal or pathology will "contaminate" ongoing neural activity, and lead to apparent differences in functional connectivity. Monitoring and accounting for the brain-wide activations by these behaviors is essential during experiments to differentiate fidget-driven activity from internally driven neural dynamics.

Cerebellar Purkinje cells control eye movements with a rapid rate code that is invariant to spike irregularity

The rate and temporal pattern of neural spiking each have the potential to influence computation. In the cerebellum, it has been hypothesized that the irregularity of interspike intervals in Purkinje cells affects their ability to transmit information to downstream neurons. Accordingly, during oculomotor behavior in mice and rhesus monkeys, mean irregularity of Purkinje cell spiking varied with mean eye velocity. However, moment-to-moment variations revealed a tight correlation between eye velocity and spike rate, with no additional information conveyed by spike irregularity. Moreover, when spike rate and irregularity were independently controlled using optogenetic stimulation, the eye movements elicited were well-described by a linear population rate code with 3-5 ms temporal precision. Biophysical and random-walk models identified biologically realistic parameter ranges that determine whether spike irregularity influences responses downstream. The results demonstrate cerebellar control of movements through a remarkably rapid rate code, with no evidence for an additional contribution of spike irregularity.