Automated Observations of Dogs' Resting Behaviour Patterns Using Artificial Intelligence and Their Similarity to Behavioural Observations

Although direct behavioural observations are widely used, they are time-consuming, prone to error, require knowledge of the observed species, and depend on intra/inter-observer consistency. As a result, they pose challenges to the reliability and repeatability of studies. Automated video analysis is becoming popular for behavioural observations. Sleep is a biological metric that has the potential to become a reliable broad-spectrum metric that can indicate the quality of life and understanding sleep patterns can contribute to identifying and addressing potential welfare concerns, such as stress, discomfort, or health issues, thus promoting the overall welfare of animals; however, due to the laborious process of quantifying sleep patterns, it has been overlooked in animal welfare research. This study presents a system comparing convolutional neural networks (CNNs) with direct behavioural observation methods for the same data to detect and quantify dogs' sleeping patterns. A total of 13,688 videos were used to develop and train the model to quantify sleep duration and sleep fragmentation in dogs. To evaluate its similarity to the direct behavioural observations made by a single human observer, 6000 previously unseen frames were used. The system successfully classified 5430 frames, scoring a similarity rate of 89% when compared to the manually recorded observations. There was no significant difference in the percentage of time observed between the system and the human observer (p > 0.05). However, a significant difference was found in total sleep time recorded, where the automated system captured more hours than the observer (p < 0.05). This highlights the potential of using a CNN-based system to study animal welfare and behaviour research.

Quantitative comparison of 2D and 3D monitoring dimensions in fish behavior analysis

To improve the accuracy and efficiency of fish behavior assessment, this paper focuses on quantitatively exploring the variations and relationships between different monitoring dimensions. A systematic comparison was conducted between 3D and 2D behavioral factors using an infrared tracing system, during both day and night. Significant differences in swimming distance were observed among the different monitoring methods, as determined by two-way ANOVA and Tukey's test. A correction was applied to account for the disparities observed in 2D swimming distance, ensuring accurate measurements. These findings present a cost-effective and efficient approach for obtaining precise 3D distance data. Additionally, a kinematic factor called the "number of U-turns" was proposed to provide a more intuitive characterization of directional changes in fish swimming. Significant differences were observed between 2D and 3D data, with higher percentages of false U-turn counts and missing U-turn counts compared to correct counts in the 2D view. These findings suggest that reducing the monitoring dimension may impact the accurate estimation of swimming motion, potentially resulting in inaccurate outcomes. Finally, the statistical analyses of the non-linear properties of fractal dimension revealed significant differences among the various monitoring methods. This conclusion has practical implications for biologists and physicists, enabling them to improve the accuracy of behavioral phenotyping for organisms exhibiting 3D motion.

Design of mechanosensory feedback during undulatory locomotion to enhance speed and stability

Undulatory locomotion relies on the propagation of a wave of excitation in the spinal cord leading to consequential activation of segmental skeletal muscles along the body. Although this process relies on self-generated oscillations of motor circuits in the spinal cord, mechanosensory feedback is crucial to entrain the underlying oscillatory activity and thereby, to enhance movement power and speed. This effect is achieved through directional projections of mechanosensory neurons either sensing stretching or compression of the trunk along the rostrocaudal axis. Different mechanosensory feedback pathways act in concert to shorten and fasten the excitatory wave propagating along the body. While inhibitory mechanosensory cells feedback inhibition on excitatory premotor interneurons and motor neurons, excitatory mechanosensory cells feedforward excitation to premotor excitatory interneurons. Together, diverse mechanosensory cells coordinate the activity of skeletal muscles controlling the head and tail to optimize speed and stabilize balance during fast locomotion.

Functional trajectories during innate spinal cord repair

Adult zebrafish are capable of anatomical and functional recovery following severe spinal cord injury. Axon growth, glial bridging and adult neurogenesis are hallmarks of cellular regeneration during spinal cord repair. However, the correlation between these cellular regenerative processes and functional recovery remains to be elucidated. Whereas the majority of established functional regeneration metrics measure swim capacity, we hypothesize that gait quality is more directly related to neurological health. Here, we performed a longitudinal swim tracking study for 60 individual zebrafish spanning 8 weeks of spinal cord regeneration. Multiple swim parameters as well as axonal and glial bridging were integrated. We established rostral compensation as a new gait quality metric that highly correlates with functional recovery. Tensor component analysis of longitudinal data supports a correspondence between functional recovery trajectories and neurological outcomes. Moreover, our studies predicted and validated that a subset of functional regeneration parameters measured 1 to 2 weeks post-injury is sufficient to predict the regenerative outcomes of individual animals at 8 weeks post-injury. Our findings established new functional regeneration parameters and generated a comprehensive correlative database between various functional and cellular regeneration outputs.

Optimizing assays of zebrafish larvae swimming performance for drug discovery

INTRODUCTION

Zebrafish larvae are one of the few vertebrates amenable to large-scale drug discovery screens. Larval swimming behavior is often used as an outcome variable and many fields of study have developed assays for evaluating swimming performance. An unintended consequence of this wide interest is that details related to assay methodology and interpretation become scattered across the literature. The aim of this review is to consolidate this information, particularly as it relates to high-throughput approaches.

AREAS COVERED

The authors describe larval swimming behaviors as this forms the basis for understanding their experimentally evoked swimming or spontaneous activity. Next, they detail how swimming activity can serve as an outcome variable, particularly in the multi-well formats used in large-scale screening studies. They also highlight biological and technical factors that can impact the sensitivity and variability of these measurements.

EXPERT OPINION

Careful attention to animal husbandry, experimental design, data acquisition, and interpretation of results can improve screen outcomes by maximizing swimming activity while minimizing intra- and inter-larval variability. The development of more sensitive, quantitative methods of assessing swimming performance that can be incorporated into high-throughput workflows will be important in order to take full advantage of the zebrafish model.

Functional Trajectories during innate spinal cord repair

Adult zebrafish are capable of anatomical and functional recovery following severe spinal cord injury. Axon growth, glial bridging and adult neurogenesis are hallmarks of cellular regeneration during spinal cord repair. However, the correlation between these cellular regenerative processes and functional recovery remains to be elucidated. Whereas the majority of established functional regeneration metrics measure swim capacity, we hypothesize that gait quality is more directly related to neurological health. Here, we performed a longitudinal swim tracking study for sixty individual zebrafish spanning eight weeks of spinal cord regeneration. Multiple swim parameters as well as axonal and glial bridging were integrated. We established rostral compensation as a new gait quality metric that highly correlates with functional recovery. Tensor component analysis of longitudinal data supports a correspondence between functional recovery trajectories and neurological outcomes. Moreover, our studies predicted and validated that a subset of functional regeneration parameters measured 1 to 2 weeks post-injury is sufficient to predict the regenerative outcomes of individual animals at 8 weeks post-injury. Our findings established new functional regeneration parameters and generated a comprehensive correlative database between various functional and cellular regeneration outputs.

A Markerless Pose Estimator Applicable to Limbless Animals

The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available) or use markers to build a skeletal representation of pose. Markers are either physical objects attached to the body (white balls, stickers, or paint) or they are defined in silico using recognizable body structures (e.g., joints, limbs, color patterns). Physical markers often cannot be used if the animals are small, lack prominent body structures on which the markers can be placed, or live in environments such as aquatic ones that might detach the marker. Here, we introduce a marker-free pose-estimator (LACE Limbless Animal traCkEr) that builds the pose of the animal de novo from its contour. LACE detects the contour of the animal and derives the body mid-line, building a pseudo-skeleton by defining vertices and edges. By applying LACE to analyse the pose of larval Drosophila melanogaster and adult zebrafish, we illustrate that LACE allows to quantify, for example, genetic alterations of peristaltic movements and gender-specific locomotion patterns that are associated with different body shapes. As illustrated by these examples, LACE provides a versatile method for assessing position, pose and movement patterns, even in animals without limbs.

Parallel Fish School Tracking Based on Multiple Appearance Feature Detection

A parallel fish school tracking based on multiple-feature fish detection has been proposed in this paper to obtain accurate movement trajectories of a large number of zebrafish. Zebrafish are widely adapted in many fields as an excellent model organism. Due to the non-rigid body, similar appearance, rapid transition, and frequent occlusions, vision-based behavioral monitoring is still a challenge. A multiple appearance feature based fish detection scheme was developed by examining the fish head and center of the fish body based on shape index features. The proposed fish detection has the advantage of locating individual fishes from occlusions and estimating their motion states, which could ensure the stability of tracking multiple fishes. Moreover, a parallel tracking scheme was developed based on the SORT framework by fusing multiple features of individual fish and motion states. The proposed method was evaluated in seven video clips taken under different conditions. These videos contained various scales of fishes, different arena sizes, different frame rates, and various image resolutions. The maximal number of tracking targets reached 100 individuals. The correct tracking ratio was 98.60% to 99.86%, and the correct identification ratio ranged from 97.73% to 100%. The experimental results demonstrate that the proposed method is superior to advanced deep learning-based methods. Nevertheless, this method has real-time tracking ability, which can acquire online trajectory data without high-cost hardware configuration.

Continuous body 3-D reconstruction of limbless animals

Limbless animals such as snakes, limbless lizards, worms, eels and lampreys move their slender, long bodies in three dimensions to traverse diverse environments. Accurately quantifying their continuous body's 3-D shape and motion is important for understanding body-environment interactions in complex terrain, but this is difficult to achieve (especially for local orientation and rotation). Here, we describe an interpolation method to quantify continuous body 3-D position and orientation. We simplify the body as an elastic rod and apply a backbone optimization method to interpolate continuous body shape between end constraints imposed by tracked markers. Despite over-simplifying the biomechanics, our method achieves a higher interpolation accuracy (∼50% error) in both 3-D position and orientation compared with the widely used cubic B-spline interpolation method. Beyond snakes traversing large obstacles as demonstrated, our method applies to other long, slender, limbless animals and continuum robots. We provide codes and demo files for easy application of our method.

Zebrafish tracking using YOLOv2 and Kalman filter

Fish show rapid movements in various behavioral activities or associated with the presence of food. However, in periods of rapid movement, the rate at which occlusion occurs among the fish is quite high, causing inconsistency in the detection and tracking of fish, hindering the fish's identity and behavioral trajectory over a long period of time. Although some algorithms have been proposed to solve these problems, most of their applications were made in groups of fish that swim in shallow water and calm behavior, with few sudden movements. To solve these problems, a convolutional network of object recognition, YOLOv2, was used to delimit the region of the fish heads to optimize individual fish detection. In the tracking phase, the Kalman filter was used to estimate the best state of the fish's head position in each frame and, subsequently, the trajectories of each fish were connected among the frames. The results of the algorithm show adequate performances in the trajectories of groups of zebrafish that exhibited rapid movements.

epiTracker: A Framework for Highly Reliable Particle Tracking for the Quantitative Analysis of Fish Movements in Tanks

Behavioral analysis of moving animals relies on a faithful recording and track analysis to extract relevant parameters of movement. To study group behavior and social interactions, often simultaneous analyses of individuals are required. To detect social interactions, for example to identify the leader of a group as opposed to followers, one needs an error-free segmentation of individual tracks throughout time. While automated tracking algorithms exist that are quick and easy to use, inevitable errors will occur during tracking. To solve this problem, we introduce a robust algorithm called epiTracker for segmentation and tracking of multiple animals in two-dimensional (2D) videos along with an easy-to-use correction method that allows one to obtain error-free segmentation. We have implemented two graphical user interfaces to allow user-friendly control of the functions. Using six labeled 2D datasets, the effort to obtain accurate labels is quantified and compared to alternative available software solutions. Both the labeled datasets and the software are publicly available.

Lateral Oscillation and Body Compliance Help Snakes and Snake Robots Stably Traverse Large, Smooth Obstacles

Snakes can move through almost any terrain. Similarly, snake robots hold the promise as a versatile platform to traverse complex environments such as earthquake rubble. Unlike snake locomotion on flat surfaces which is inherently stable, when snakes traverse complex terrain by deforming their body out of plane, it becomes challenging to maintain stability. Here, we review our recent progress in understanding how snakes and snake robots traverse large, smooth obstacles such as boulders and felled trees that lack "anchor points" for gripping or bracing. First, we discovered that the generalist variable kingsnake combines lateral oscillation and cantilevering. Regardless of step height and surface friction, the overall gait is preserved. Next, to quantify static stability of the snake, we developed a method to interpolate continuous body in three dimensions (3D) (both position and orientation) between discrete tracked markers. By analyzing the base of support using the interpolated continuous body 3-D kinematics, we discovered that the snake maintained perfect stability during traversal, even on the most challenging low friction, high step. Finally, we applied this gait to a snake robot and systematically tested its performance traversing large steps with variable heights to further understand stability principles. The robot rapidly and stably traversed steps nearly as high as a third of its body length. As step height increased, the robot rolled more frequently to the extent of flipping over, reducing traversal probability. The absence of such failure in the snake with a compliant body inspired us to add body compliance to the robot. With better surface contact, the compliant body robot suffered less roll instability and traversed high steps at higher probability, without sacrificing traversal speed. Our robot traversed large step-like obstacles more rapidly than most previous snake robots, approaching that of the animal. The combination of lateral oscillation and body compliance to form a large, reliable base of support may be useful for snakes and snake robots to traverse diverse 3-D environments with large, smooth obstacles.

Spatiotemporal Transition in the Role of Synaptic Inhibition to the Tail Beat Rhythm of Developing Larval Zebrafish

Significant maturation of swimming in zebrafish (Danio rerio) occurs within the first few days of life when fish transition from coiling movements to burst swimming and then to beat-and-glide swimming. This maturation occurs against a backdrop of numerous developmental changes - neurogenesis, a transition from predominantly electrical to chemical-based neurotransmission, and refinement of intrinsic properties. There is evidence that spinal locomotor circuits undergo fundamental changes as the zebrafish transitions from burst to beat-and-glide swimming. Our electrophysiological recordings confirm that the operation of spinal locomotor circuits becomes increasingly reliant on glycinergic neurotransmission for rhythmogenesis governing the rhythm of tail beats. This transition occurred at the same time that we observed a change in rhythmicity of synaptic inhibition to spinal motoneurons (MNs). When we examined whether the transition from weakly to strongly glycinergic dependent rhythmogenesis occurred at a uniform pace across the length of the spinal cord, we found that this transition occurred earlier at caudal segments than at rostral segments of the spinal cord. Furthermore, while this rhythmogenic transition occurred when fish transition from burst swimming to beat-and-glide swimming, these two transitions were not interdependent. These results suggest that there is a developmental transition in the operation of spinal locomotor circuits that is gradually set in place in the spinal cord in a caudo-rostral temporal sequence.

Characterization of spinal cord damage based on automatic video analysis of froglet swimming

Xenopus laevis frogs are a widely used organism to study aspects of modern biology (Harland and Grainger, 2011). Its central nervous system is particularly interesting, because in certain stages of metamorphosis the spinal cord can regenerate after injury and recover swimming. With this in mind, automatic gait analysis could help evaluate the regenerative performance by means of a method that automatically and quantitatively establishes the degree in froglets' limb movement. Here, we present an algorithm that characterizes spinal cord damage in froglets. The proposed method tracks the position of the limbs throughout videos and extracts kinematic features, which posteriorly serve to differentiate froglets with different levels of damage to the spinal cord. The detection algorithm and kinematic features chosen were validated in a pattern recognition experiment in which 90 videos (divided equally in three classes: uninjured, hemisected and transected) were classified. We conclude that our system is effective in the characterization of damage to the spinal cord through video analysis of a swimming froglet with a 97% accuracy. These results potentially validate this methodology to automatically compare the recovery of spinal cord function after different treatments without the need to manually process videos. In addition, the procedure could be used to measure the kinematics and behavioral response of froglets to different experimental conditions such as nutritional state, stress, genetic background and age.

Summary: Automatic video tracking system to measure froglet swimming and characterize the degree of spinal cord damage after spinal cord injury. It can potentially be used to compare the recovery of spinal cord function after different treatments.

Age, but not short-term intensive swimming, affects chondrocyte turnover in zebrafish vertebral cartilage

Both age and intensive exercise are generally considered critical risk factors for osteoarthritis. In this work, we intend to establish zebrafish models to assess the role of these two factors on cartilage homeostasis. We designed a swimming device for zebrafish intensive exercise. The body measurements, bone mineral density (BMD) and the histology of spinal cartilages of 4- and 12-month-old zebrafish, as well the 12-month-old zebrafish before and after a 2-week exercise were compared. Our results indicate that both age and exercise affect the body length and body weight, and the micro-computed tomography reveals that both age and exercise affect the spinal BMD. However, quantitative analysis of immunohistochemistry and histochemistry indicate that short-term intensive exercise does not affect the extracellular matrix (ECM) of spinal cartilage. On the other hand, the cartilage ECM significantly grew from 4 to 12 months of age with an increase in total chondrocytes. dUTP nick end labeling staining shows that the percentages of apoptotic cells significantly increase as the zebrafish grows, whereas the BrdU labeling shows that proliferative cells dramatically decrease from 4 to 12 months of age. A 30-day chase of BrdU labeling shows some retention of labeling in cells in 4-month-old spinal cartilage but not in cartilage from 12-month-old zebrafish. Taken together, our results suggest that zebrafish chondrocytes are actively turned over, and indicate that aging is a critical factor that alters cartilage homeostasis. Zebrafish vertebral cartilage may serve as a good model to study the maturation and homeostasis of articular cartilage.

Zebrafish swimming in the flow: a particle image velocimetry study

Zebrafish is emerging as a species of choice for the study of a number of biomechanics problems, including balance development, schooling, and neuromuscular transmission. The precise quantification of the flow physics around swimming zebrafish is critical toward a mechanistic understanding of the complex swimming style of this fresh-water species. Although previous studies have elucidated the vortical structures in the wake of zebrafish swimming in placid water, the flow physics of zebrafish swimming against a water current remains unexplored. In an effort to illuminate zebrafish swimming in a dynamic environment reminiscent of its natural habitat, we experimentally investigated the locomotion and hydrodynamics of a single zebrafish swimming in a miniature water tunnel using particle image velocimetry. Our results on zebrafish locomotion detail the role of flow speed on tail beat undulations, heading direction, and swimming speed. Our findings on zebrafish hydrodynamics offer a precise quantification of vortex shedding during zebrafish swimming and demonstrate that locomotory patterns play a central role on the flow physics. This knowledge may help clarify the evolutionary advantage of burst and cruise swimming movements in zebrafish.

ToxId: an efficient algorithm to solve occlusions when tracking multiple animals

Video analysis of animal behaviour is widely used in fields such as ecology, ecotoxicology, and evolutionary research. However, when tracking multiple animals, occlusion and crossing are problematic, especially when the identity of each individual needs to be preserved. We present a new algorithm, ToxId, which preserves the identity of multiple animals by linking trajectory segments using their intensity histogram and Hu-moments. We verify the performance and accuracy of our algorithm using video sequences with different animals and experimental conditions. The results show that our algorithm achieves state-of-the-art accuracy using an efficient approach without the need of learning processes, complex feature maps or knowledge of the animal shape. ToxId is also computationally efficient, has low memory requirements, and operates without accessing future or past frames.

Feature point based 3D tracking of multiple fish from multi-view images

A feature point based method is proposed for tracking multiple fish in 3D space. First, a simplified representation of the object is realized through construction of two feature point models based on its appearance characteristics. After feature points are classified into occluded and non-occluded types, matching and association are performed, respectively. Finally, the object's motion trajectory in 3D space is obtained through integrating multi-view tracking results. Experimental results show that the proposed method can simultaneously track 3D motion trajectories for up to 10 fish accurately and robustly.

Behavioral methods for the functional assessment of hair cells in zebrafish

Zebrafish is an emerging animal model for studies on auditory system. This model presents high comparability with humans, good accessibility to the hearing organ, and high throughput capacity. To better utilize this animal model, methodologies need to be used to quantify the hearing function of the zebrafish. Zebrafish displays a series of innate and robust behavior related to its auditory function. Here, we reviewed the advantage of using zebrafish in auditory research and then introduced three behavioral tests, as follows: the startle response, the vestibular-ocular reflex, and rheotaxis. These tests are discussed in terms of their physiological characteristics, up-to-date technical development, and apparatus description. Test limitation and areas to improve are also introduced. Finally, we revealed the feasibility of these applications in zebrafish behavioral assessment and their potential in the high-throughput screening on hearing-related genes and drugs.

Developmental changes in head movement kinematics during swimming in Xenopus laevis tadpoles

During the post-embryonic developmental growth of animals, a number of physiological parameters such as locomotor performance, dynamics and behavioural repertoire are adjusted to match the requirements determined by changes in body size, proportions and shape. Moreover, changes in movement parameters also cause changes in the dynamics of self-generated sensory stimuli, to which motion-detecting sensory systems have to adapt. Here, we examined head movements and swimming kinematics of Xenopus laevis tadpoles with a body length of 10-45 mm (developmental stage 46-54) and compared these parameters with fictive swimming, recorded as ventral root activity in semi-intact in vitro preparations. Head movement kinematics was extracted from high-speed video recordings of freely swimming tadpoles. Analysis of these locomotor episodes indicated that the swimming frequency decreased with development, along with the angular velocity and acceleration of the head, which represent self-generated vestibular stimuli. In contrast, neither head oscillation amplitude nor forward velocity changed with development despite the ∼3-fold increase in body size. The comparison between free and fictive locomotor dynamics revealed very similar swimming frequencies for similarly sized animals, including a comparable developmental decrease of the swimming frequency. Body morphology and the motor output rhythm of the spinal central pattern generator therefore develop concurrently. This study thus describes development-specific naturalistic head motion profiles, which form the basis for more natural stimuli in future studies probing the vestibular system.

Three-dimensional motion tracking reveals a diving component to visual and auditory escape swims in zebrafish larvae

Escape behaviors have been studied in zebrafish by neuroscientists seeking cellular-level descriptions of neural circuits but few studies have examined vertical swimming during escapes. We analyzed three-dimensional swimming paths of zebrafish larvae during visually-evoked and auditory-evoked escapes while the fish were in a cubical tank with equal vertical and lateral range. Visually evoked escapes, elicited by sudden dimming of ambient light, consistently elicited downward spiral swimming (dives) with faster vertical than lateral movement. Auditory taps also elicited rapid escape swimming with equivalent total distance traveled but with significantly less vertical and more lateral movement. Visually evoked dives usually ended with the zebrafish hitting the bottom of the 10 cm³ tank. Therefore, visually evoked dives were also analyzed in a tubular tank with 50 cm of vertical range, and in most cases larvae reached the bottom of that tank during a 120 s dimming stimulus. Light-evoked spiral diving in zebrafish may be an innate defense reflex against specific predation threats. Since visual and auditory escapes are initially similar but dives persist only during visual escapes, our findings lay the groundwork for studying a type of decision-making within zebrafish sensorimotor circuits.

Automated Planar Tracking the Waving Bodies of Multiple Zebrafish Swimming in Shallow Water

Zebrafish (Danio rerio) is one of the most widely used model organisms in collective behavior research. Multi-object tracking with high speed camera is currently the most feasible way to accurately measure their motion states for quantitative study of their collective behavior. However, due to difficulties such as their similar appearance, complex body deformation and frequent occlusions, it is a big challenge for an automated system to be able to reliably track the body geometry of each individual fish. To accomplish this task, we propose a novel fish body model that uses a chain of rectangles to represent fish body. Then in detection stage, the point of maximum curvature along fish boundary is detected and set as fish nose point. Afterwards, in tracking stage, we firstly apply Kalman filter to track fish head, then use rectangle chain fitting to fit fish body, which at the same time further judge the head tracking results and remove the incorrect ones. At last, a tracklets relinking stage further solves trajectory fragmentation due to occlusion. Experiment results show that the proposed tracking system can track a group of zebrafish with their body geometry accurately even when occlusion occurs from time to time.

Automated Reconstruction of Three-Dimensional Fish Motion, Forces, and Torques

Fish can move freely through the water column and make complex three-dimensional motions to explore their environment, escape or feed. Nevertheless, the majority of swimming studies is currently limited to two-dimensional analyses. Accurate experimental quantification of changes in body shape, position and orientation (swimming kinematics) in three dimensions is therefore essential to advance biomechanical research of fish swimming. Here, we present a validated method that automatically tracks a swimming fish in three dimensions from multi-camera high-speed video. We use an optimisation procedure to fit a parameterised, morphology-based fish model to each set of video images. This results in a time sequence of position, orientation and body curvature. We post-process this data to derive additional kinematic parameters (e.g. velocities, accelerations) and propose an inverse-dynamics method to compute the resultant forces and torques during swimming. The presented method for quantifying 3D fish motion paves the way for future analyses of swimming biomechanics.

Revisiting Psychoacoustic Methods for the Assessment of Fish Hearing

Behavioral methods have been critical in the study of auditory perception and discrimination in fishes. In this chapter, we review some of the common methods used in fish psychoacoustics. We discuss associative methods, such as operant, avoidance, and classical conditioning, and their use in constructing audiograms, measuring frequency selectivity, and auditory stream segregation. We also discuss the measurement of innate behavioral responses, such as the acoustic startle response (ASR), prepulse inhibition (PPI), and phonotaxis, and their use in the assessment of fish hearing to determine auditory thresholds and in the testing of mechanisms for sound source localization. For each psychoacoustic method, we provide examples of their use and discuss the parameters and situations where such methods can be best utilized. In the case of the ASR, we show how this method can be used to construct and compare audiograms between two species of larval fishes, the three-spined stickleback (Gasterosteus aculeatus) and the zebrafish (Danio rerio). We also discuss considerations for experimental design with respect to stimulus presentation and threshold criteria and how these techniques can be used in future studies to investigate auditory perception in fishes.

Effects of embryonic exposure to polychlorinated biphenyls (PCBs) on anxiety-related behaviors in larval zebrafish

The zebrafish (Danio rerio) is an excellent model system for assessing the effects of toxicant exposure on behavior and neurodevelopment. In the present study, we examined the effects of sub-chronic embryonic exposure to polychlorinated biphenyls (PCBs), a ubiquitous anthropogenic pollutant, on anxiety-related behaviors. We found that exposure to the PCB mixture, Aroclor (A) 1254, from 2 to 26h post-fertilization (hpf) induced two statistically significant behavioral defects in larvae at 7 days post-fertilization (dpf). First, during 135min of free swimming, larvae that had been exposed to 2ppm, 5ppm or 10ppm A1254 exhibited enhanced thigmotaxis (edge preference) relative to control larvae. Second, during the immediately ensuing 15-min visual startle assay, the 5ppm and 10ppm PCB-exposed larvae reacted differently to a visual threat, a red 'bouncing' disk, relative to control larvae. These results are consistent with the anxiogenic and attention-disrupting effects of PCB exposure documented in children, monkeys and rodents and merit further investigation.

Effect of acute ethanol administration on zebrafish tail-beat motion

Zebrafish is becoming a species of choice in neurobiological and behavioral studies of alcohol-related disorders. In these efforts, the activity of adult zebrafish is typically quantified using indirect activity measures that are either scored manually or identified automatically from the fish trajectory. The analysis of such activity measures has produced important insight into the effect of acute ethanol exposure on individual and social behavior of this vertebrate species. Here, we leverage a recently developed tracking algorithm that reconstructs fish body shape to investigate the effect of acute ethanol administration on zebrafish tail-beat motion in terms of amplitude and frequency. Our results demonstrate a significant effect of ethanol on the tail-beat amplitude as well as the tail-beat frequency, both of which were found to robustly decrease for high ethanol concentrations. Such a direct measurement of zebrafish motor functions is in agreement with evidence based on indirect activity measures, offering a complementary perspective in behavioral screening.

Finite element modelling predicts changes in joint shape and cell behaviour due to loss of muscle strain in jaw development

Abnormal joint morphogenesis is linked to clinical conditions such as Developmental Dysplasia of the Hip (DDH) and to osteoarthritis (OA). Muscle activity is known to be important during the developmental process of joint morphogenesis. However, less is known about how this mechanical stimulus affects the behaviour of joint cells to generate altered morphology. Using zebrafish, in which we can image all joint musculoskeletal tissues at high resolution, we show that removal of muscle activity through anaesthetisation or genetic manipulation causes a change to the shape of the joint between the Meckel's cartilage and Palatoquadrate (the jaw joint), such that the joint develops asymmetrically leading to an overlap of the cartilage elements on the medial side which inhibits normal joint function. We identify the time during which muscle activity is critical to produce a normal joint. Using Finite Element Analysis (FEA), to model the strains exerted by muscle on the skeletal elements, we identify that minimum principal strains are located at the medial region of the joint and interzone during mouth opening. Then, by studying the cells immediately proximal to the joint, we demonstrate that biomechanical strain regulates cell orientation within the developing joint, such that when muscle-induced strain is removed, cells on the medial side of the joint notably change their orientation. Together, these data show that biomechanical forces are required to establish symmetry in the joint during development.

Toward a science of computational ethology

The new field of “Computational Ethology” is made possible by advances in technology, mathematics, and engineering that allow scientists to automate the measurement and the analysis of animal behavior. We explore the opportunities and long-term directions of research in this area.

Automatically detect and track multiple fish swimming in shallow water with frequent occlusion

Due to its universality, swarm behavior in nature attracts much attention of scientists from many fields. Fish schools are examples of biological communities that demonstrate swarm behavior. The detection and tracking of fish in a school are of important significance for the quantitative research on swarm behavior. However, different from other biological communities, there are three problems in the detection and tracking of fish school, that is, variable appearances, complex motion and frequent occlusion. To solve these problems, we propose an effective method of fish detection and tracking. In this method, first, the fish head region is positioned through extremum detection and ellipse fitting; second, The Kalman filtering and feature matching are used to track the target in complex motion; finally, according to the feature information obtained by the detection and tracking, the tracking problems caused by frequent occlusion are processed through trajectory linking. We apply this method to track swimming fish school of different densities. The experimental results show that the proposed method is both accurate and reliable.

Myotonia congenita-associated mutations in chloride channel-1 affect zebrafish body wave swimming kinematics

Myotonia congenita is a human muscle disorder caused by mutations in CLCN1, which encodes human chloride channel 1 (CLCN1). Zebrafish is becoming an increasingly useful model for human diseases, including muscle disorders. In this study, we generated transgenic zebrafish expressing, under the control of a muscle specific promoter, human CLCN1 carrying mutations that have been identified in human patients suffering from myotonia congenita. We developed video analytic tools that are able to provide precise quantitative measurements of movement abnormalities in order to analyse the effect of these CLCN1 mutations on adult transgenic zebrafish swimming. Two new parameters for body-wave kinematics of swimming reveal changes in body curvature and tail offset in transgenic zebrafish expressing the disease-associated CLCN1 mutants, presumably due to their effect on muscle function. The capability of the developed video analytic tool to distinguish wild-type from transgenic zebrafish could provide a useful asset to screen for compounds that reverse the disease phenotype, and may be applicable to other movement disorders besides myotonia congenita.

Quantification of larval zebrafish motor function in multiwell plates using open-source MATLAB applications

This article describes a method to quantify the movements of larval zebrafish in multiwell plates, using the open-source MATLAB applications LSRtrack and LSRanalyze. The protocol comprises four stages: generation of high-quality, flatly illuminated video recordings with exposure settings that facilitate object recognition; analysis of the resulting recordings using tools provided in LSRtrack to optimize tracking accuracy and motion detection; analysis of tracking data using LSRanalyze or custom MATLAB scripts; and implementation of validation controls. The method is reliable, automated and flexible, requires <1 h of hands-on work for completion once optimized and shows excellent signal:noise characteristics. The resulting data can be analyzed to determine the following: positional preference; displacement, velocity and acceleration; and duration and frequency of movement events and rest periods. This approach is widely applicable to the analysis of spontaneous or stimulus-evoked zebrafish larval neurobehavioral phenotypes resulting from a broad array of genetic and environmental manipulations, in a multiwell plate format suitable for high-throughput applications.

Automated image-based tracking and its application in ecology

The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers.

Zebrafish models of human motor neuron diseases: advantages and limitations

Motor neuron diseases (MNDs) are an etiologically heterogeneous group of disorders of neurodegenerative origin, which result in degeneration of lower (LMNs) and/or upper motor neurons (UMNs). Neurodegenerative MNDs include pure hereditary spastic paraplegia (HSP), which involves specific degeneration of UMNs, leading to progressive spasticity of the lower limbs. In contrast, spinal muscular atrophy (SMA) involves the specific degeneration of LMNs, with symmetrical muscle weakness and atrophy. Amyotrophic lateral sclerosis (ALS), the most common adult-onset MND, is characterized by the degeneration of both UMNs and LMNs, leading to progressive muscle weakness, atrophy, and spasticity. A review of the comparative neuroanatomy of the human and zebrafish motor systems showed that, while the zebrafish was a homologous model for LMN disorders, such as SMA, it was only partially relevant in the case of UMN disorders, due to the absence of corticospinal and rubrospinal tracts in its central nervous system. Even considering the limitation of this model to fully reproduce the human UMN disorders, zebrafish offer an excellent alternative vertebrate model for the molecular and genetic dissection of MND mechanisms. Its advantages include the conservation of genome and physiological processes and applicable in vivo tools, including easy imaging, loss or gain of function methods, behavioral tests to examine changes in motor activity, and the ease of simultaneous chemical/drug testing on large numbers of animals. This facilitates the assessment of the environmental origin of MNDs, alone or in combination with genetic traits and putative modifier genes. Positive hits obtained by phenotype-based small-molecule screening using zebrafish may potentially be effective drugs for treatment of human MNDs.

The behavioral effects of acute Δ⁹-tetrahydrocannabinol and heroin (diacetylmorphine) exposure in adult zebrafish

The use of psychotropic drugs in clinical and translational brain research continues to grow, and the need for novel experimental models and screens is becoming widely recognized. Mounting evidence supports the utility of zebrafish (Danio rerio) for studying various pharmacological manipulations, as an alternative model complementing the existing rodent paradigms in this field. Here, we explore the effects of acute 20-min exposure to two commonly abused psychotropic compounds, Δ(9)-tetrahydrocannabinol (THC) and heroin, on adult zebrafish behavior in the novel tank test. Overall, THC administration (30 and 50 mg/L) produces an anxiogenic-like reduction of top swimming, paralleled with a slower, continuous bottom swimming. In contrast, heroin exposure (15 and 25 mg/L) evoked a hyperlocomotor response (with rapid bouts of bottom swimming and frequent 'bouncing' motions) without altering anxiety-sensitive top/bottom endpoints. The behavioral effects of these two compounds in zebrafish seem to parallel the respective rodent and human findings. Collectively, this emphasizes the growing significance of novel emerging aquatic models in translational drug abuse research and small molecule screening.

Tracking zebrafish larvae in group--status and perspectives

Video processing is increasingly becoming a standard procedure in zebrafish behavior investigations as it enables higher research throughput and new or better measures. This trend, fostered by the ever increasing performance-to-price ratio of the required recording and processing equipment, should be expected to continue in the foreseeable future, with video-processing based methods permeating more and more experiments and, as a result, expanding the very role of behavioral studies in zebrafish research. To assess whether the routine video tracking of zebrafish larvae directly in the Petri dish is a capability that can be expected in the near future, the key processing concepts are discussed and illustrated on published zebrafish studies when available or other animals when not.

Real-Time Localization of Moving Dipole Sources for Tracking Multiple Free-Swimming Weakly Electric Fish

In order to survive, animals must quickly and accurately locate prey, predators, and conspecifics using the signals they generate. The signal source location can be estimated using multiple detectors and the inverse relationship between the received signal intensity (RSI) and the distance, but difficulty of the source localization increases if there is an additional dependence on the orientation of a signal source. In such cases, the signal source could be approximated as an ideal dipole for simplification. Based on a theoretical model, the RSI can be directly predicted from a known dipole location; but estimating a dipole location from RSIs has no direct analytical solution. Here, we propose an efficient solution to the dipole localization problem by using a lookup table (LUT) to store RSIs predicted by our theoretically derived dipole model at many possible dipole positions and orientations. For a given set of RSIs measured at multiple detectors, our algorithm found a dipole location having the closest matching normalized RSIs from the LUT, and further refined the location at higher resolution. Studying the natural behavior of weakly electric fish (WEF) requires efficiently computing their location and the temporal pattern of their electric signals over extended periods. Our dipole localization method was successfully applied to track single or multiple freely swimming WEF in shallow water in real-time, as each fish could be closely approximated by an ideal current dipole in two dimensions. Our optimized search algorithm found the animal’s positions, orientations, and tail-bending angles quickly and accurately under various conditions, without the need for calibrating individual-specific parameters. Our dipole localization method is directly applicable to studying the role of active sensing during spatial navigation, or social interactions between multiple WEF. Furthermore, our method could be extended to other application areas involving dipole source localization.

ZebraZoom: an automated program for high-throughput behavioral analysis and categorization

The zebrafish larva stands out as an emergent model organism for translational studies involving gene or drug screening thanks to its size, genetics, and permeability. At the larval stage, locomotion occurs in short episodes punctuated by periods of rest. Although phenotyping behavior is a key component of large-scale screens, it has not yet been automated in this model system. We developed ZebraZoom, a program to automatically track larvae and identify maneuvers for many animals performing discrete movements. Our program detects each episodic movement and extracts large-scale statistics on motor patterns to produce a quantification of the locomotor repertoire. We used ZebraZoom to identify motor defects induced by a glycinergic receptor antagonist. The analysis of the blind mutant atoh7 revealed small locomotor defects associated with the mutation. Using multiclass supervised machine learning, ZebraZoom categorized all episodes of movement for each larva into one of three possible maneuvers: slow forward swim, routine turn, and escape. ZebraZoom reached 91% accuracy for categorization of stereotypical maneuvers that four independent experimenters unanimously identified. For all maneuvers in the data set, ZebraZoom agreed with four experimenters in 73.2-82.5% of cases. We modeled the series of maneuvers performed by larvae as Markov chains and observed that larvae often repeated the same maneuvers within a group. When analyzing subsequent maneuvers performed by different larvae, we found that larva-larva interactions occurred as series of escapes. Overall, ZebraZoom reached the level of precision found in manual analysis but accomplished tasks in a high-throughput format necessary for large screens.

Visually guided gradation of prey capture movements in larval zebrafish

A mechanistic understanding of goal-directed behavior in vertebrates is hindered by the relative inaccessibility and size of their nervous systems. Here, we have studied the kinematics of prey capture behavior in a highly accessible vertebrate model organism, the transparent larval zebrafish (Danio rerio), to assess whether they use visual cues to systematically adjust their movements. We found that zebrafish larvae scale the speed and magnitude of turning movements according to the azimuth of one of their standard prey, paramecia. They also bias the direction of subsequent swimming movements based on prey azimuth and select forward or backward movements based on the prey's direction of travel. Once within striking distance, larvae generate either ram or suction capture behaviors depending on their distance from the prey. From our experimental estimations of ocular receptive fields, we ascertained that the ultimate decision to consume prey is likely a function of the progressive vergence of the eyes that places the target in a proximal binocular 'capture zone'. By repeating these experiments in the dark, we demonstrate that paramecia are only consumed if they contact the anterior extremities of larvae, which triggers ocular vergence and tail movements similar to close proximity captures in lit conditions. These observations confirm the importance of vision in the graded movements we observe leading up to capture of more distant prey in the light, and implicate somatosensation in captures in the absence of light. We discuss the implications of these findings for future work on the neural control of visually guided behavior in zebrafish.

Effects of aquarium-related stressors on the zebrafish: a comparison of behavioral, physiological, and biochemical indicators

Fishes in aquaria and aquaculture settings may experience a variety of stressors including crowding, different lighting, periods of food deprivation, and vibrations from sources including pumps and tapping of tank sides. The effects of such low-level chronic stress are poorly explored. We used replicate sets of six Zebrafish Danio rerio in four series of experiments to compare the effects of (1) stocking densities ranging from 0.13 to 1.2 fish/L, (2) cool white (6,500 K), warm white (4,100 K), and ultraviolet-enhanced (420 actinic) fluorescent lighting, (3) food deprivation for up to 9 d, and (4) random mechanical tapping on the tank side sufficient to induce a startle response on specific behaviors (fin display, body fluttering, aggression, mouth gaping, and chattering), dissolved cortisol released into aquarium water (collected on a chromatography column and analyzed with an immunoassay), and heat-shock proteins (HSPs 27, 40, 60, and 70) detected immunochemically in western blots of muscle tissue. Of all the treatments, only food deprivation resulted in significant differences between control and treatment fish; dissolved cortisol declined after 120 h of starvation and HSP40 and HSP60 in muscle tissue increased significantly after 216 h. High variability in behaviors and HSP measurements was noted within all controls and treatments, suggesting that effects of treatments were experienced unequally by individuals within a treatment. Social stressors resulting from dominance hierarchies may play a critical role in modifying the effects of aquarium and aquaculture stressors on captive fish.

Behavioral genetics in larval zebrafish: learning from the young

Deciphering the genetic code that determines how the vertebrate nervous system assembles into neural circuits that ultimately control behavior is a fascinating and challenging question in modern neurobiology. Because of the complexity of this problem, successful strategies require a simple yet focused experimental approach without limiting the scope of the discovery. Unbiased, large-scale forward genetic screens in invertebrate organisms have yielded great insight into the genetic regulation of neural circuit assembly and function. For many reasons, this highly successful approach has been difficult to recapitulate in the behavioral neuroscience field's classic vertebrate model organisms-rodents. Here, we discuss how larval zebrafish provide a promising model system to which we can apply the design of invertebrate behavior-based screens to reveal the genetic mechanisms critical for neural circuit assembly and function in vertebrates.