Advances in comparative physiology from high-speed imaging of animal and fluid motion

Application of a novel deep learning-based 3D videography workflow to bat flight

Studying the detailed biomechanics of flying animals requires accurate three-dimensional coordinates for key anatomical landmarks. Traditionally, this relies on manually digitizing animal videos, a labor-intensive task that scales poorly with increasing framerates and numbers of cameras. Here, we present a workflow that combines deep learning-powered automatic digitization with filtering and correction of mislabeled points using quality metrics from deep learning and 3D reconstruction. We tested our workflow using a particularly challenging scenario: bat flight. First, we documented four bats flying steadily in a 2 m3 wind tunnel test section. Wing kinematic parameters resulting from manually digitizing bats with markers applied to anatomical landmarks were not significantly different from those resulting from applying our workflow to the same bats without markers for five out of six parameters. Second, we compared coordinates from manual digitization against those yielded via our workflow for bats flying freely in a 344 m3 enclosure. Average distance between coordinates from our workflow and those from manual digitization was less than a millimeter larger than the average human-to-human coordinate distance. The improved efficiency of our workflow has the potential to increase the scalability of studies on animal flight biomechanics.

Adhesion Behavior in Fish: From Structures to Applications

In nature, some fish can adhere tightly to the surface of stones, aquatic plants, and even other fish bodies. This adhesion behavior allows these fish to fix, eat, hide, and migrate in complex and variable aquatic environments. The adhesion function is realized by the special mouth and sucker tissue of fish. Inspired by adhesion fish, extensive research has recently been carried out. Therefore, this paper presents a brief overview to better explore underwater adhesion mechanisms and provide bionic applications. Firstly, the adhesion organs and structures of biological prototypes (e.g., clingfish, remora, Garra, suckermouth catfish, hill stream loach, and goby) are presented separately, and the underwater adhesion mechanisms are analyzed. Then, based on bionics, it is explained that the adhesion structures and components are designed and created for applications (e.g., flexible gripping adhesive discs and adhesive motion devices). Furthermore, we offer our perspectives on the limitations and future directions.

Reconstruction of Flight Parameters of a Bat for Flapping Robots

The flight of bats is comparatively less documented and understood than birds and insects and may provide novel inspiration for the design of flapping flight robots. This study captured the natural flight of short-nosed fruit bats (Cynopterus sphinx) by an optical motion capture system, 'OptiTrack', with pasted markers on the wings and body to reconstruct the flight parameters. Due to the self-occlusion at some moments, points on the membrane wings cannot be captured by any cameras. To draw a smooth trajectory, it is desired to reconstruct all missing data. Therefore, an algorithm is proposed by using numerical techniques, accompanied by modern mathematical and computational tools, to envisage the missing data from the captured flight. The least-square fitted polynomial engendered the parameter equations for x-, y- and z-coordinates of marked points which were used to reconstruct the trajectory of the flight. The parameter equations of position coordinates were also used to compute the morphological and aerodynamic characteristics of the flight. The most outstanding contribution of the work is that not only the trajectory, velocity and velocity field but also the morphing areas of the membrane wings were recreated using the reconstructed data. These data and reconstructed curves of trajectory and velocity field will be used for the further aerodynamic analysis and mechanism design of the flapping robot. This method can also be generalized to reconstruct the performance parameters of any other animals for bionic design.

Direct Measurements of the Wing Kinematics of a Bat in Straight Flight

Bat is the only mammal in the nature that can fly. Compared with birds and insects, bats are quite special in that their wings are formed by an elastic membrane, which renders that the airfoil deforms greatly during downstroke and upstroke. Due to the compliant skin of a bat, the movements of its wings are three-dimensionally complex during diverse flight behaviors. To understand the maneuverability and flight performance, three-dimensional reconstruction of the flight kinematics is essential. This study focuses on the reconstruction of the wing kinematics of the bat and identifies the primary relationship of parameters of aerodynamics in straight flight. With markers pasted on the wings and body of a bat, the motions of these points are recorded by a computerized optical motion capture system. The kinematic analysis shows that the motion of wings is very intricate. The digits of the wing display the sign of coupled motion. A novel approach was developed to measure the angle of attack and flapping angle of the wing. The angle of attack of leading edge differs with the overall angle of attack of the wing. The kinematics of the bat's wing is helpful to interpret the secret of the bat's flight.

Longer development provides first-feeding fish time to escape hydrodynamic constraints

What is the functional effect of prolonged development? By controlling for size, we quantify first-feeding performance and hydrodynamics of zebrafish and guppy offspring (5 ± 0.5 mm in length), which differ fivefold in developmental time and twofold in ontogenetic state. By manipulating water viscosity, we control the hydrodynamic regime, measured as Reynolds number. We predicted that if feeding performance were strictly the result of hydrodynamics, and not development, feeding performance would scale with Reynolds number. We find that guppy offspring successfully feed at much greater distances to prey (1.0 vs. 0.2 mm) and with higher capture success (90 vs. 20%) compared with zebrafish larvae, and that feeding performance was not a result of Reynolds number alone. Flow visualization shows that zebrafish larvae produce a bow wave ~0.2 mm in length, and that the flow field produced during suction does not extend beyond this bow wave. Due to well-developed oral jaw protrusion, the similar-sized suction field generated by guppy offspring extends beyond the horizon of their bow wave, leading to successful prey capture from greater distances. These findings suggest that prolonged development and increased ontogenetic state provides first-feeding fish time to escape the pervasive hydrodynamic constraints (bow wave) of being small.

From a Flapping Bumblebee to an Evolving Sand Dune: A Reconstruction-Based Algorithm to Feature the Digitally Recorded Objects

A reconstruction-based image processing algorithm is developed to automatically extract feature points of digitalized 2D objects. This algorithm, which is introduced using a bumblebee flight case, is made up of two parts: a four-connected dot chasing rearrangement scheme and an extreme point extraction on a polarized contour. It is then applied to a dune evolution case that is simulated with a cellular automation model. The results show that the proposed algorithm is effective in characterizing individual moving objects. An additional algorithm is developed to categorize the extracted feature points of a bumblebee with translucent wings.

Advances in the study of bat flight: the wing and the wind

Bats are diverse, speciose, and inhabit most of earth’s habitats, aided by powered flapping flight. The many traits that enable flight in these mammals have long attracted popular and research interest, but recent technological and conceptual advances have provided investigators with new kinds of information concerning diverse aspects of flight biology. As a consequence of these new data, our understanding of how bats fly has begun to undergo fundamental changes. Physical and neural science approaches are now beginning to inform understanding of structural architecture of wings. High-speed videography is dramatically expanding documentation of how bats fly. Experimental fluid dynamics and innovative physiological techniques profoundly influence how we interpret the ways bats produce aerodynamic forces as they execute distinctive flight behaviors and the mechanisms that underlie flight energetics. Here, we review how recent bat flight research has provided significant new insights into several important aspects of bat flight structure and function. We suggest that information coming from novel approaches offer opportunities to interconnect studies of wing structure, aerodynamics, and physiology more effectively, and to connect flight biology to newly emerging studies of bat evolution and ecology.

Fish locomotion: recent advances and new directions

Research on fish locomotion has expanded greatly in recent years as new approaches have been brought to bear on a classical field of study. Detailed analyses of patterns of body and fin motion and the effects of these movements on water flow patterns have helped scientists understand the causes and effects of hydrodynamic patterns produced by swimming fish. Recent developments include the study of the center-of-mass motion of swimming fish and the use of volumetric imaging systems that allow three-dimensional instantaneous snapshots of wake flow patterns. The large numbers of swimming fish in the oceans and the vorticity present in fin and body wakes support the hypothesis that fish contribute significantly to the mixing of ocean waters. New developments in fish robotics have enhanced understanding of the physical principles underlying aquatic propulsion and allowed intriguing biological features, such as the structure of shark skin, to be studied in detail.

Center of mass motion in swimming fish: effects of speed and locomotor mode during undulatory propulsion

Studies of center of mass (COM) motion are fundamental to understanding the dynamics of animal movement, and have been carried out extensively for terrestrial and aerial locomotion. But despite a large amount of literature describing different body movement patterns in fishes, analyses of how the center of mass moves during undulatory propulsion are not available. These data would be valuable for understanding the dynamics of different body movement patterns and the effect of differing body shapes on locomotor force production. In the present study, we analyzed the magnitude and frequency components of COM motion in three dimensions (x: surge, y: sway, z: heave) in three fish species (eel, bluegill sunfish, and clown knifefish) swimming with four locomotor modes at three speeds using high-speed video, and used an image cross-correlation technique to estimate COM motion, thus enabling untethered and unrestrained locomotion. Anguilliform swimming by eels shows reduced COM surge oscillation magnitude relative to carangiform swimming, but not compared to knifefish using a gymnotiform locomotor style. Labriform swimming (bluegill at 0.5 body lengths/s) displays reduced COM sway oscillation relative to swimming in a carangiform style at higher speeds. Oscillation frequency of the COM in the surge direction occurs at twice the tail beat frequency for carangiform and anguilliform swimming, but at the same frequency as the tail beat for gymnotiform locomotion in clown knifefish. Scaling analysis of COM heave oscillation for terrestrial locomotion suggests that COM heave motion scales with positive allometry, and that fish have relatively low COM oscillations for their body size.

An aeroelastic instability provides a possible basis for the transition from gliding to flapping flight

The morphology, kinematics and stiffness properties of lifting surfaces play a key role in the aerodynamic performance of vertebrate flight. These surfaces, as a result of their flexible nature, may move both actively, owing to muscle contraction, and passively, in reaction to fluid forces. However, the nature and implications of this fluid-structure interaction are not well understood. Here, we study passive flight (flight with no active wing actuation) and explore a physical mechanism that leads to the emergence of a natural flapping motion. We model a vertebrate wing with a compliant shoulder and the ability to camber with an idealized physical model consisting of a cantilevered flat plate with a hinged trailing flap. We find that at low wind speed the wing is stationary, but at a critical speed the wing spontaneously flaps. The lift coefficient is significantly enhanced once the wing starts to oscillate, although this increase in lift generation is accompanied by an increase in drag. Flow visualization suggests that a strong leading edge vortex attached to the wing during downstroke is the primary mechanism responsible for the enhanced lift. The flapping instability we observe suggests a possible scenario for an evolutionary transition from gliding to powered flapping flight in animals that possess compliant wings capable of passive camber. Although the flapping state is accompanied by a lower lift-to-drag ratio, the increased lifting capability it confers might have enabled increased body mass, improved foraging performance and/or flight at lower speeds, any of which might have been selectively advantageous.

Escaping the flow: boundary layer use by the darter Etheostoma tetrazonum (Percidae) during benthic station holding

Aquatic habitats characterized by directional water flow (lotic environments) pose numerous challenges to their inhabitants, including the constant threat of dislodgement and downstream transport. As a result, many organisms exhibit morphological and/or behavioral adaptations that facilitate midwater or benthic station holding in these environments, such as the ventral sucker disc of armored catfishes. However, a few groups, including the species-rich group of small (7-8 cm long and 1-2 cm high) North American stream fishes called darters, exhibit no obvious morphological adaptations to life in lotic habitats. We therefore asked whether small size itself facilitates benthic station holding in these fish. We first used digital particle image velocimetry to quantify the fluid dynamics of flow over a variety of substrates. We then visualized the patterns of flow over the darter Etheostoma tetrazonum during benthic station holding. The thickness of the region of decreased water velocity (i.e. the boundary layer) associated with several types of rocky substrate was large enough (∼2 cm high in some cases) for E. tetrazonum and many other darter species to escape the oncoming flow. We also found that, despite the large size of its pectoral fins, E. tetrazonum is capable of producing only very weak negative lift forces with fins. These substrate-directed forces likely act in conjunction with upstream-directed frictional forces between the tail, anal and pelvic fins and the substrate to facilitate station holding. Thus, we hypothesize that, in darters, small size is an adaptation to life in the benthic boundary layer of lotic environments.

Volumetric imaging of shark tail hydrodynamics reveals a three-dimensional dual-ring vortex wake structure

Understanding how moving organisms generate locomotor forces is fundamental to the analysis of aerodynamic and hydrodynamic flow patterns that are generated during body and appendage oscillation. In the past, this has been accomplished using two-dimensional planar techniques that require reconstruction of three-dimensional flow patterns. We have applied a new, fully three-dimensional, volumetric imaging technique that allows instantaneous capture of wake flow patterns, to a classic problem in functional vertebrate biology: the function of the asymmetrical (heterocercal) tail of swimming sharks to capture the vorticity field within the volume swept by the tail. These data were used to test a previous three-dimensional reconstruction of the shark vortex wake estimated from two-dimensional flow analyses, and show that the volumetric approach reveals a different vortex wake not previously reconstructed from two-dimensional slices. The hydrodynamic wake consists of one set of dual-linked vortex rings produced per half tail beat. In addition, we use a simple passive shark-tail model under robotic control to show that the three-dimensional wake flows of the robotic tail differ from the active tail motion of a live shark, suggesting that active control of kinematics and tail stiffness plays a substantial role in the production of wake vortical patterns.

The effect of fin ray flexural rigidity on the propulsive forces generated by a biorobotic fish pectoral fin

A biorobotic pectoral fin was developed and used to study how the flexural rigidities of fin rays within a highly deformable fish fin affect the fin's propulsive forces. The design of the biorobotic fin was based on a detailed analysis of the pectoral fin of the bluegill sunfish (Lepomis macrochirus). The biorobotic fin was made to execute the kinematics used by the biological fin during steady swimming, and to have structural properties that modeled those of the biological fin. This resulted in an engineered fin that had a similar interaction with the water as the biological fin and that created close approximations of the three-dimensional motions, flows, and forces produced by the sunfish during low speed, steady swimming. Experimental trials were conducted during which biorobotic fins of seven different stiffness configurations were flapped at frequencies from 0.5 to 2.0 Hz in flows with velocities that ranged from 0 to 270 mm s(-1). During these trials, thrust and lift forces were measured, kinematics were recorded in three dimensions, and digital particle image velocimetry was used to evaluate flow hydrodynamics. The results of the trials revealed that slight changes to the fin's mechanical properties or to the operating conditions can have significant impact on the direction, magnitude and time course of the propulsive forces. In general, the magnitude of the 2-D (thrust and lift) propulsive force scaled with fin ray stiffness, and increased as the fin's flapping speed increased or as the velocity of the flow decreased.

Automated hull reconstruction motion tracking (HRMT) applied to sideways maneuvers of free-flying insects

Flying insects perform aerial maneuvers through slight manipulations of their wing motions. Because such manipulations in wing kinematics are subtle,a reliable method is needed to properly discern consistent kinematic strategies used by the insect from inconsistent variations and measurement error. Here, we introduce a novel automated method that accurately extracts full, 3D body and wing kinematics from high-resolution films of free-flying insects. This method combines visual hull reconstruction, principal components analysis, and geometric information about the insect to recover time series data of positions and orientations. The technique has small,well-characterized errors of under 3 pixels for positions and 5 deg. for orientations. To show its utility, we apply this motion tracking to the flight of fruit flies, Drosophila melanogaster. We find that fruit flies generate sideways forces during some maneuvers and that strong lateral acceleration is associated with differences between the left and right wing angles of attack. Remarkably, this asymmetry can be induced by simply altering the relative timing of flips between the right and left wings, and we observe that fruit flies employ timing differences as high as 10% of a wing beat period while accelerating sideways at 40% g.

Advances in biological structure, function, and physiology using synchrotron X-ray imaging*

Studies of the physiology and biomechanics of small ( approximately 1 cm) organisms are often limited by the inability to see inside the animal during a behavior or process of interest and by a lack of three-dimensional morphology at the submillimeter scale. These constraints can be overcome by an imaging probe that has sensitivity to soft tissue, the ability to penetrate opaque surfaces, and high spatial and temporal resolution. Synchrotron X-ray imaging has been successfully used to visualize millimeter-centimeter-sized organisms with micrometer-range spatial resolutions in fixed and living specimens. Synchrotron imaging of small organisms has been the key to recent novel insights into structure and function, particularly in the area of respiratory physiology and function of insects. X-ray imaging has been effectively used to examine the morphology of tracheal systems, the mechanisms of tracheal and air sac compression in insects, and the function of both chewing and sucking mouthparts in insects. Synchrotron X-ray imaging provides an exciting new window into the internal workings of small animals, with future promise to contribute to a range of physiological and biomechanical questions in comparative biology.

The aerodynamic signature of running spiders

Many predators display two foraging modes, an ambush strategy and a cruising mode. These foraging strategies have been classically studied in energetic, biomechanical and ecological terms, without considering the role of signals produced by predators and perceived by prey. Wolf spiders are a typical example; they hunt in leaf litter either using an ambush strategy or by moving at high speed, taking over unwary prey. Air flow upstream of running spiders is a source of information for escaping prey, such as crickets and cockroaches. However, air displacement by running arthropods has not been previously examined. Here we show, using digital particle image velocimetry, that running spiders are highly conspicuous aerodynamically, due to substantial air displacement detectable up to several centimetres in front of them. This study explains the bimodal distribution of spider's foraging modes in terms of sensory ecology and is consistent with the escape distances and speeds of cricket prey. These findings may be relevant to the large and diverse array of arthropod prey-predator interactions in leaf litter.