Virtual Reality system for freely-moving rodents

Spatial navigation, active sensing, and most cognitive functions rely on a tight link between motor output and sensory input. Virtual reality (VR) systems simulate the sensorimotor loop, allowing flexible manipulation of enriched sensory input. Conventional rodent VR systems provide 3D visual cues linked to restrained locomotion on a treadmill, leading to a mismatch between visual and most other sensory inputs, sensory-motor conflicts, as well as restricted naturalistic behavior. To rectify these limitations, we developed a VR system (ratCAVE) that provides realistic and low-latency visual feedback directly to head movements of completely unrestrained rodents. Immersed in this VR system, rats displayed naturalistic behavior by spontaneously interacting with and hugging virtual walls, exploring virtual objects, and avoiding virtual cliffs. We further illustrate the effect of ratCAVE-VR manipulation on hippocampal place fields. The newly-developed methodology enables a wide range of experiments involving flexible manipulation of visual feedback in freely-moving behaving animals

WhiskEras: A New Algorithm for Accurate Whisker Tracking

Rodents engage in active touch using their facial whiskers: they explore their environment by making rapid back-and-forth movements. The fast nature of whisker movements, during which whiskers often cross each other, makes it notoriously difficult to track individual whiskers of the intact whisker field. We present here a novel algorithm, WhiskEras, for tracking of whisker movements in high-speed videos of untrimmed mice, without requiring labeled data. WhiskEras consists of a pipeline of image-processing steps: first, the points that form the whisker centerlines are detected with sub-pixel accuracy. Then, these points are clustered in order to distinguish individual whiskers. Subsequently, the whiskers are parameterized so that a single whisker can be described by four parameters. The last step consists of tracking individual whiskers over time. We describe that WhiskEras performs better than other whisker-tracking algorithms on several metrics. On our four video segments, WhiskEras detected more whiskers per frame than the Biotact Whisker Tracking Tool. The signal-to-noise ratio of the output of WhiskEras was higher than that of Janelia Whisk. As a result, the correlation between reflexive whisker movements and cerebellar Purkinje cell activity appeared to be stronger than previously found using other tracking algorithms. We conclude that WhiskEras facilitates the study of sensorimotor integration by markedly improving the accuracy of whisker tracking in untrimmed mice

Integrative function in rat visual system

A vital function of the brain is to acquire information about the events in the environment and to respond appropriately. The brain needs to integrate the incoming information from multiple senses to improve the quality of the sensory signal. It also needs to be able to distribute the processing resources to optimise the integration across modalities based on the reliability and salience of the incoming signals. This thesis aimed to investigate two aspects of the way in which the brain integrates information from the external environment: multisensory integration and selective attention. The hooded rat was used as the experimental animal model. In Chapter 2 of this thesis, I investigate the multisensory properties of neurons in superior colliculus (SC), a midbrain structure involved in attentive and orienting behaviours. I first establish that in rat SC, spiking activity is elevated by whisker or visual stimuli, but rarely both, when those stimuli are presented in isolation. I then show that visually responsive sites are mainly found in superficial layers whereas whisker responsive sites were in intermediate layers. Finally I show that there are robust suppressive interactions between these two modalities. In Chapter 3, I develop a rodent behavioural paradigm that can easily be paired with electrophysiological measurements. The design is adaptable to a variety of detection and discrimination tasks. Head position is restricted in the central nose-poke without head-fixation and the eyes can be constantly monitored via video camera. In Chapter 4, I ask whether selective spatial visual attention can be demonstrated in rats utilising the paradigms developed in Chapter 3. Selective attention is the process by which brain focuses on significant external events. Does being able to predict the likely side of the stimulus modulate the speed and accuracy of stimulus detection? To address this question, I varied the probability with which the signal was presented on left or right screen. My results suggest that rats have the capacity for spatial attention engaged by top-down mechanisms that have access to the predictability of stimulus location. In summary, my thesis presents a paradigm to study visual behaviour, multisensory integration and selective spatial attention in rats. Over the last decade, rats have gained popularity as a viable animal model in sensory systems neuroscience because of the access to the array of genetic tools and in vivo electrophysiology and imaging techniques. As such the paradigms developed here provide a useful preparation to complement the existing well-established primate models

The development, validation and demonstration of an automated rodent tracker and whisker detector

Quantitatively assessing behaviour to measure animal behaviour and motor control is challenging because there is a lack of unobtrusive behavioural models. Some studies have suggested that measuring whisker movements might be a good, quantitative behavioural model. However, whiskers are very thin, small and move very fast; and there is not yet an automated program that can detect whiskers in a fully-intact, freely-moving animal. Therefore, this thesis develops, validates and demonstrates a novel, fullyautomated rodent tracker and a whisker annotator, that simultaneously measures locomotion and exploration behaviours as well as whisker movements. The �rst step in designing an automated rodent tracker and whisker detector, is to extract a reliable ground truth from which to compare any tracked points to. Therefore, the Manual Whisker Annotator (MWA) was designed as a validator and calibrator for the subsequent trackers and detectors. The second step is to provide a reliable body and head contour. Therefore, the Automated Rodent Tracker (ART) was developed and validated, compared to a semi-automated tracker (Ethovision) and the MWA. Finally, a fully-automated whisker detector (FAWD) was designed and validated, using two existing semi-automatic whisker trackers (BWTT and Whisk) and the MWA. FAWD incorporates a variety of image-processing algorithms, including super sampling, dilation and subtraction and frangi �ltering to reliably detect whiskers. Both ART and FAWD were also successfully demonstrated on videos collected from SOD1 mice, a model of Amyotrophic Lateral Sclerosis, from day 30 to 120. The development of this software enables whisker movements and locomotion to be tracked in a repeatable fashion, and the fully-automated nature of the software means that many videos can be collected and quickly processed with minimal user input. This thesis develops and validates a suite of behavioural software that provides robust and quantitative measures of rodent behaviour for basic research or drug discovery. Future work will be to demonstrate this software on a larger range of rodent models of neurodegeneration, to further showcase the exibility and quantitative nature of this behavioural model

Two-photon all-optical interrogation of mouse barrel cortex during sensory discrimination

The neocortex supports a rich repertoire of cognitive and behavioural functions, yet the rules, or neural ‘codes’, that determine how patterns of cortical activity drive perceptual processes remain enigmatic. Experimental neuroscientists study these codes through measuring and manipulating neuronal activity in awake behaving subjects, which allows links to be identified between patterns of neural activity and ongoing behaviour functions. In this thesis, I detail the application of novel optical techniques for simultaneously recording and manipulating neurons with cellular resolution to examine how tactile signals are processed in sparse neuronal ensembles in mouse somatosensory ‘barrel’ cortex. To do this, I designed a whisker-based perceptual decision-making task for head-fixed mice, that allows precise control over sensory input and interpretable readout of perceptual choice. Through several complementary experimental approaches, I show that task performance is exquisitely coupled to barrel cortical activity. Using two- photon calcium imaging to simultaneously record from populations of barrel cortex neurons, I demonstrate that different subpopulations of neurons in layer 2/3 (L2/3) show selectivity for contralateral and ipsilateral whisker input during behaviour. To directly test whether these stimulus-tuned groups of neurons differentially impact perceptual decision-making I performed patterned photostimulation experiments to selectively activate these functionally defined sets of neurons and assessed the resulting impact on behaviour and the local cortical network in layer 2/3. In contrast with the expected results, stimulation of sensory-coding neurons appeared to have little perceptual impact on task performance. However, activation of non- stimulus coding neurons did drive decision biases. These results challenge the conventional view that strongly sensory responsive neurons carry more perceptual weight than non-responsive sensory neurons during perceptual decision-making. Furthermore, patterned photostimulation revealed and imposed potent surround suppression in L2/3, which points to strong lateral inhibition playing a dominant role in shaping spatiotemporally sparse activity patterns. These results showcase the utility of combined patterned photostimulation methods and population calcium imaging for revealing and testing neural circuit function during sensorimotor behaviour and provide new perspectives on sensory coding in barrel cortex

On Neuromechanical Approaches for the Study of Biological Grasp and Manipulation

Biological and robotic grasp and manipulation are undeniably similar at the level of mechanical task performance. However, their underlying fundamental biological vs. engineering mechanisms are, by definition, dramatically different and can even be antithetical. Even our approach to each is diametrically opposite: inductive science for the study of biological systems vs. engineering synthesis for the design and construction of robotic systems. The past 20 years have seen several conceptual advances in both fields and the quest to unify them. Chief among them is the reluctant recognition that their underlying fundamental mechanisms may actually share limited common ground, while exhibiting many fundamental differences. This recognition is particularly liberating because it allows us to resolve and move beyond multiple paradoxes and contradictions that arose from the initial reasonable assumption of a large common ground. Here, we begin by introducing the perspective of neuromechanics, which emphasizes that real-world behavior emerges from the intimate interactions among the physical structure of the system, the mechanical requirements of a task, the feasible neural control actions to produce it, and the ability of the neuromuscular system to adapt through interactions with the environment. This allows us to articulate a succinct overview of a few salient conceptual paradoxes and contradictions regarding under-determined vs. over-determined mechanics, under- vs. over-actuated control, prescribed vs. emergent function, learning vs. implementation vs. adaptation, prescriptive vs. descriptive synergies, and optimal vs. habitual performance. We conclude by presenting open questions and suggesting directions for future research. We hope this frank assessment of the state-of-the-art will encourage and guide these communities to continue to interact and make progress in these important areas

Streaming Aggregation using Reconfigurable Hardware

High throughput and low latency streaming aggregation is essential for many applications that analyze massive volumes of data in real-time. In many cases, high speed stream aggregation can be achieved incrementally by computing partial results for multiple windows. However, for particular problems, temporarily storing all incoming raw data to a single window before processing is more efficient or even the only option. This thesis presents the first FPGA-based single window stream aggregation designs for tuple-based and time-based windowing policies. The proposed approach is able to support challenging queries required in realistic stream processing problems. More precisely, holistic, distributive, and algebraic aggregation functions, as well as custom ones can be supported. Our designs offer aggregation for large number of concurrently active keys and handles large window sizes and frequent aggregations. Maxeler\u27s dataflow engines (DFEs), which suit well the stream processing characteristics, are used to implement the designs. DFEs have a direct feed of incoming data from the network as well as direct access to off-chip DRAM. The tuple-based single window DFE processes up to 8 million tuples-per-second (1.1 Gbps) offering 1-2 orders of magnitude higher throughput than a state-of-the-art stream processing software system. The processing latency is less than 4 usec, 4 orders of magnitude lower latency than software. The time-based single-window stream aggregation DFE offers high processing throughput, up to 150 Mtuples/sec, similar to related GPU systems, which however do not support both time-based and single windows. It also offers an ultra-low processing latency of 1-10 usec, at least 4 orders of magnitude lower than software-based solutions

Optogenetic feedback control of neural activity

Optogenetic techniques enable precise excitation and inhibition of firing in specified neuronal populations and artifact-free recording of firing activity. Several studies have suggested that optical stimulation provides the precision and dynamic range requisite for closed-loop neuronal control, but no approach yet permits feedback control of neuronal firing. Here we present the ‘optoclamp’, a feedback control technology that provides continuous, real-time adjustments of bidirectional optical stimulation in order to lock spiking activity at specified targets over timescales ranging from seconds to days. We demonstrate how this system can be used to decouple neuronal firing levels from ongoing changes in network excitability due to multi-hour periods of glutamatergic or GABAergic neurotransmission blockade in vitro as well as impinging vibrissal sensory drive in vivo. This technology enables continuous, precise optical control of firing in neuronal populations in order to disentangle causally related variables of circuit activation in a physiologically and ethologically relevant manner.National Science Foundation (U.S.). Graduate Research FellowshipNational Science Foundation (U.S.). Integrative Graduate Education and Research Traineeshi