David B. Baier

X-ray reconstruction of moving morphology (XROMM): precision, accuracy and applications in comparative biomechanics research

X-Ray Reconstruction of Moving Morphology (XROMM) comprises a set of 3D X-ray motion analysis techniques that merge motion data from in vivo X-ray videos with skeletal morphology data from bone scans into precise and accurate animations of 3D bones moving in 3D space. XROMM methods include: (1) manual alignment (registration) of bone models to video sequences, i.e., Scientific Rotoscoping; (2) computer vision-based autoregistration of bone models to biplanar X-ray videos; and (3) marker-based registration of bone models to biplanar X-ray videos. Here, we describe a novel set of X-ray hardware, software, and workflows for marker-based XROMM. Refurbished C-arm fluoroscopes retrofitted with high-speed video cameras offer a relatively inexpensive X-ray hardware solution for comparative biomechanics research. Precision for our biplanar C-arm hardware and analysis software, measured as the standard deviation of pairwise distances between 1 mm tantalum markers embedded in rigid objects, was found to be +/-0.046 mm under optimal conditions and +/-0.084 mm under actual in vivo recording conditions. Mean error in measurement of a known distance between two beads was within the 0.01 mm fabrication tolerance of the test object, and mean absolute error was 0.037 mm. Animating 3D bone models from sets of marker positions (XROMM animation) makes it possible to study skeletal kinematics in the context of detailed bone morphology. The biplanar fluoroscopy hardware and computational methods described here should make XROMM an accessible and useful addition to the available technologies for studying the form, function, and evolution of vertebrate animals.

Scientific rotoscoping: a morphology-based method of 3-D motion analysis and visualization.

Three-dimensional skeletal movement is often impossible to accurately quantify from external markers. X-ray imaging more directly visualizes moving bones, but extracting 3-D kinematic data is notoriously difficult from a single perspective. Stereophotogrammetry is extremely powerful if bi-planar fluoroscopy is available, yet implantation of three radio-opaque markers in each segment of interest may be impractical. Herein we introduce scientific rotoscoping (SR), a new method of motion analysis that uses articulated bone models to simultaneously animate and quantify moving skeletons without markers. The three-step process is described using examples from our work on pigeon flight and alligator walking. First, the experimental scene is reconstructed in 3-D using commercial animation software so that frames of undistorted fluoroscopic and standard video can be viewed in their correct spatial context through calibrated virtual cameras. Second, polygonal models of relevant bones are created from CT or laser scans and rearticulated into a hierarchical marionette controlled by virtual joints. Third, the marionette is registered to video images by adjusting each of its degrees of freedom over a sequence of frames. SR outputs high-resolution 3-D kinematic data for multiple, unmarked bones and anatomically accurate animations that can be rendered from any perspective. Rather than generating moving stick figures abstracted from the coordinates of independent surface points, SR is a morphology-based method of motion analysis deeply rooted in osteological and arthrological data.

A critical ligamentous mechanism in the evolution of avian flight

Despite recent advances in aerodynamic, neuromuscular and kinematic aspects of avian flight and dozens of relevant fossil discoveries, the origin of aerial locomotion and the transition from limbs to wings continue to be debated. Interpreting this transition depends on understanding the mechanical interplay of forces in living birds, particularly at the shoulder where most wing motion takes place. Shoulder function depends on a balance of forces from muscles, ligaments and articular cartilages, as well as inertial, gravitational and aerodynamic loads on the wing. Here we show that the force balance system of the shoulder evolved from a primarily muscular mechanism to one in which the acrocoracohumeral ligament has a critical role. Features of the shoulder of Mesozoic birds and closely related theropod dinosaurs indicate that the evolution of flight preceded the acquisition of the ligament-based force balance system and that some basal birds are intermediate in shoulder morphology.

Kinematics of the quadrate bone during feeding in mallard ducks

SUMMARY Avian cranial kinesis, in which mobility of the quadrate, pterygoid and palatine bones contribute to upper bill elevation, is believed to occur in all extant birds. The most widely accepted model for upper bill elevation is that the quadrate rotates rostrally and medially towards the pterygoid, transferring force to the mobile pterygoid–palatine complex, which pushes on the upper bill. Until now, however, it has not been possible to test this hypothesis in vivo because quadrate motions are rapid, three-dimensionally complex and not visible externally. Here we use a new in vivo X-ray motion analysis technique, X-ray reconstruction of moving morphology (XROMM), to create precise (±0.06 mm) 3-D animations of the quadrate, braincase, upper bill and mandible of three mallard ducks, Anas platyrhynchos. We defined a joint coordinate system (JCS) for the quadrato-squamosal joint with the axes aligned to the anatomical planes of the skull. In this coordinate system, the quadrates 3-D rotations produce an elliptical path of pterygoid process motion, with medial and rostrodorsal then lateral and rostrodorsal motion as the upper bill elevates. As the upper bill depresses, the pterygoid process continues along the ellipsoidal path, with lateral and caudoventral then medial and caudoventral motion. We also found that the mandibular rami bow outwards (streptognathy) during mandibular depression, which may cause the lateral component of quadrate rotation that we observed. Relative to the JCS aligned with the anatomical planes of the skull, a second JCS aligned with quadrato-squamosal joint anatomy did not produce a simpler description of quadrate kinematics.

The origin of the avian flight stroke: a kinematic and kinetic perspective

Abstract Flying birds flap their wings to generate aerodynamic forces large enough to overcome weight and drag. During this behavior, the forelimbs are displaced and deformed in a complex, coordinated sequence of movements collectively known as the “flight stroke.” Despite an influx of relevant fossil material and new functional insights from extant birds, the historical origin of the avian flight stroke remains poorly resolved. Potential behavioral precursors have been identified primarily on the basis of kinematic resemblance—similarity of movement irrespective of underlying mechanisms. We discuss fundamental issues of motion analysis that are frequently overlooked by paleontologists, and conclude that a purely kinematic approach is insufficient. Consideration of kinetics, the forces responsible for motion, offers a more complete picture of flight stroke evolution. We introduce six kinetic components that interact to determine a limbs trajectory. Phylogenetic mapping reveals that forelimb loading patterns have undergone at least two major transitions on the line from basal archosaur to modern bird. Using this kinematic and kinetic perspective, we offer four specific criteria to help constrain and evaluate competing scenarios for the origin of the avian flight stroke.

Three-dimensional, high-resolution skeletal kinematics of the avian wing and shoulder during ascending flapping flight and uphill flap-running.

Past studies have shown that birds use their wings not only for flight, but also when ascending steep inclines. Uphill flap-running or wing-assisted incline running (WAIR) is used by both flight-incapable fledglings and flight-capable adults to retreat to an elevated refuge. Despite the broadly varying direction of travel during WAIR, level, and descending flight, recent studies have found that the basic wing path remains relatively invariant with reference to gravity. If so, joints undergo disparate motions to maintain a consistent wing path during those specific flapping modes. The underlying skeletal motions, however, are masked by feathers and skin. To improve our understanding of the form-functional relationship of the skeletal apparatus and joint morphology with a corresponding locomotor behavior, we used XROMM (X-ray Reconstruction of Moving Morphology) to quantify 3-D skeletal kinematics in chukars (Alectoris chukar) during WAIR (ascending with legs and wings) and ascending flight (AF, ascending with wings only) along comparable trajectories. Evidence here from the wing joints demonstrates that the glenohumeral joint controls the vast majority of wing movements. More distal joints are primarily involved in modifying wing shape. All bones are in relatively similar orientations at the top of upstroke during both behaviors, but then diverge through downstroke. Total excursion of the wing is much smaller during WAIR and the tip of the manus follows a more vertical path. The WAIR stroke appears “truncated” relative to ascending flight, primarily stemming from ca. 50% reduction in humeral depression. Additionally, the elbow and wrist exhibit reduced ranges of angular excursions during WAIR. The glenohumeral joint moves in a pattern congruent with being constrained by the acrocoracohumeral ligament. Finally, we found pronounced lateral bending of the furcula during the wingbeat cycle during ascending flight only, though the phasic pattern in chukars is opposite of that observed in starlings (Sturnus vulgaris).

Validation of XMALab software for marker-based XROMM

ABSTRACT Marker-based XROMM requires software tools for: (1) correcting fluoroscope distortion; (2) calibrating X-ray cameras; (3) tracking radio-opaque markers; and (4) calculating rigid body motion. In this paper we describe and validate XMALab, a new open-source software package for marker-based XROMM (C++ source and compiled versions on Bitbucket). Most marker-based XROMM studies to date have used XrayProject in MATLAB. XrayProject can produce results with excellent accuracy and precision, but it is somewhat cumbersome to use and requires a MATLAB license. We have designed XMALab to accelerate the XROMM process and to make it more accessible to new users. Features include the four XROMM steps (listed above) in one cohesive user interface, real-time plot windows for detecting errors, and integration with an online data management system, XMAPortal. Accuracy and precision of XMALab when tracking markers in a machined object are ±0.010 and ±0.043 mm, respectively. Mean precision for nine users tracking markers in a tutorial dataset of minipig feeding was ±0.062 mm in XMALab and ±0.14 mm in XrayProject. Reproducibility of 3D point locations across nine users was 10-fold greater in XMALab than in XrayProject, and six degree-of-freedom bone motions calculated with a joint coordinate system were 3- to 6-fold more reproducible in XMALab. XMALab is also suitable for tracking white or black markers in standard light videos with optional checkerboard calibration. We expect XMALab to increase both the quality and quantity of animal motion data available for comparative biomechanics research. Summary: New motion analysis software offers greater precision and reproducibility than existing tools for tracking markers in videos, yielding greater sensitivity for measuring 3D motions with XROMM animations.

Three‐dimensional skeletal kinematics of the shoulder girdle and forelimb in walking Alligator

Crocodylians occupy a key phylogenetic position for investigations of archosaur locomotor evolution. Compared to the well‐studied hindlimb, relatively little is known about the skeletal movements and mechanics of the forelimb. In this study, we employed manual markerless XROMM (X‐ray Reconstruction Of Moving Morphology) to measure detailed 3‐D kinematics of the shoulder girdle and forelimb bones of American alligators (Alligator mississippiensis) walking on a treadmill. Digital models of the interclavicle, scapulocoracoid, humerus, radius and ulna were created using a 3‐D laser scanner. Models were articulated and aligned to simultaneously recorded frames of fluoroscopic and standard light video to reconstruct and measure joint motion. Joint coordinate systems were established for the coracosternal, glenohumeral and elbow joints. Our analysis revealed that the limb joints only account for about half of fore/aft limb excursion; the remaining excursion results from shoulder girdle movements and lateral bending of the vertebral column. Considerable motion of each scapulocoracoid relative to the vertebral column is consistent with coracosternal mobility. The hemisellar design of the glenohumeral joint permits some additional translation, or sliding in the fore‐aft plane, but this movement does not have much of an effect on the distal excursion of the bone.

Exploratory visualization of animal kinematics using instantaneous helical axes

We present novel visual and interactive techniques for exploratory visualization of animal kinematics using instantaneous helical axes (IHAs). The helical axis has been used in orthopedics, biomechanics, and structural mechanics as a construct for describing rigid body motion. Within biomechanics, recent imaging advances have made possible accurate high‐speed measurements of individual bone positions and orientations during experiments. From this high‐speed data, instantaneous helical axes of motion may be calculated. We address questions of effective interactive, exploratory visualization of this high‐speed 3D motion data. A 3D glyph that encodes all parameters of the IHA in visual form is presented. Interactive controls are used to examine the change in the IHA over time and relate the IHA to anatomical features of interest selected by a user. The techniques developed are applied to a stereoscopic, interactive visualization of the mechanics of pig mastication and assessed by a team of evolutionary biologists who found interactive IHA‐based analysis a useful addition to more traditional motion analysis techniques.

Flapping before Flight: High Resolution, Three-Dimensional Skeletal Kinematics of Wings and Legs during Avian Development.

Some of the greatest transformations in vertebrate history involve developmental and evolutionary origins of avian flight. Flight is the most power-demanding mode of locomotion, and volant adult birds have many anatomical features that presumably help meet these demands. However, juvenile birds, like the first winged dinosaurs, lack many hallmarks of advanced flight capacity. Instead of large wings they have small “protowings”, and instead of robust, interlocking forelimb skeletons their limbs are more gracile and their joints less constrained. Such traits are often thought to preclude extinct theropods from powered flight, yet young birds with similarly rudimentary anatomies flap-run up slopes and even briefly fly, thereby challenging longstanding ideas on skeletal and feather function in the theropod-avian lineage. Though skeletons and feathers are the common link between extinct and extant theropods and figure prominently in discussions on flight performance (extant birds) and flight origins (extinct theropods), skeletal inter-workings are hidden from view and their functional relationship with aerodynamically active wings is not known. For the first time, we use X-ray Reconstruction of Moving Morphology to visualize skeletal movement in developing birds, and explore how development of the avian flight apparatus corresponds with ontogenetic trajectories in skeletal kinematics, aerodynamic performance, and the locomotor transition from pre-flight flapping behaviors to full flight capacity. Our findings reveal that developing chukars (Alectoris chukar) with rudimentary flight apparatuses acquire an “avian” flight stroke early in ontogeny, initially by using their wings and legs cooperatively and, as they acquire flight capacity, counteracting ontogenetic increases in aerodynamic output with greater skeletal channelization. In conjunction with previous work, juvenile birds thereby demonstrate that the initial function of developing wings is to enhance leg performance, and that aerodynamically active, flapping wings might better be viewed as adaptations or exaptations for enhancing leg performance.