Measurement error in μCT-based three-dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

Brain shapes of large-bodied, flightless ratites (Aves: Palaeognathae) emerge through distinct developmental allometries

Comparative neuroanatomical studies have long debated the role of development in the evolution of novel and disparate brain morphologies. Historically, these studies have emphasized whether evolutionary shifts along conserved or distinct developmental allometric trends cause changes in brain morphologies. However, the degree to which interspecific differences between variably sized taxa originate through modifying developmental allometry remains largely untested. Taxa with disparate brain shapes and sizes thus allow for investigation into how developmental trends contribute to neuroanatomical diversification. Here, we examine a developmental series of large-bodied ratite birds (approx. 60-140 kg). We use three-dimensional geometric morphometrics on cephalic endocasts of common ostriches, emus and southern cassowaries and compare their developmental trajectories with those of the more modestly sized domestic chicken, previously shown to be in the same allometric grade as ratites. The results suggest that ratites and chickens exhibit disparate endocranial shapes not simply accounted for by their size differences. When shape and age are examined, chickens partly exhibit more accelerated and mature brain shapes than ratites of similar size and age. Taken together, our study indicates that disparate brain shapes between these differently sized taxa have emerged from the evolution of distinct developmental allometries, rather than simply following conserved scaling trends.

Is shape in the eye of the beholder? Assessing landmarking error in geometric morphometric analyses on live fish

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon (Salmo salar L.) from two rivers. Using repeated measures tests, we found significant inter-operator differences in mean body shape, suggesting that the operators introduced a systematic error despite following the same landmarking scheme. No significant differences were detected when the landmarking process was repeated by the same operator on a random subset of photographs. Importantly, in spite of significant operator bias, small but statistically significant morphological differences between fish from the two rivers were found consistently by all operators. Pairwise tests of angles of vectors of shape change showed that these between-river differences in body shape were analogous across operator datasets, suggesting a general reproducibility of findings obtained by geometric morphometric studies. In contrast, merging landmark data when fish from each river are digitised by different operators had a significant impact on downstream analyses, highlighting an intrinsic risk of bias. Overall, we show that, even when significant inter-operator error is introduced during digitisation, following an identical landmarking scheme can identify morphological differences between populations. This study indicates that operators digitising at least a sub-set of all data groups of interest may be an effective way of mitigating inter-operator error and potentially enabling data sharing.

How does scanner choice and 3D model resolution affect data accuracy?

Researchers using digital methods often collect data from 3D models at different resolutions, obtained using different scanning techniques. Although previous research has sought to understand whether scanning method and model resolution affect data accuracy, no study has systematically evaluated the sources of error associated with scanning method, data acquisition method and model resolution with the aim of providing practical recommendations about the model resolution required to yield sufficiently accurate data for specimens of given sizes. In this study, using data taken from primate specimens of three broad size categories, we test whether 3D models obtained using five different scanners (Breuckmann SmartSCAN, DAVID/HP 3D Pro S3, NextEngine 2020i, Creaform Go!Scan 20 and microCT/clinicalCT) yield accurate measurements. We assess whether caliper measurements can be used alongside measurements collected from 3D surface models, whether scanning resolution affects measurement accuracy, and how scan resolution, estimated using each scanner's proprietary software, compares to model resolution measured in a standardized way. Each scanner produces 3D models that yield accurate measurements for each size category, however, combining caliper data with those taken from digital models can be problematic. Our results indicate that the accuracy of measurements taken from 3D models depends on both object size and model resolution. Based on our findings, we recommend that small specimens should be scanned at <0.3 mm, medium specimens at 0.3-0.7 mm, and large specimens at 0.3-0.5 mm resolutions if data taken from 3D surface models are to be combined with caliper datasets. We further show, for the first time, that discrepancies in estimated final model resolution are frequently observed across software packages. We therefore recommend that researchers ensure that final model resolutions are adequate based on specimen size and are independently verified using a software package other than the scanner's proprietary software. Finally, we consider the implications of the findings that measurements obtained from surface models are variably consistent with those obtained using calipers.

Accuracy of bone segmentation and surface generation strategies analyzed by using synthetic CT volumes

Different kinds of bone measurements are commonly derived from computed-tomography (CT) volumes to answer a multitude of questions in biology and related fields. The underlying steps of bone segmentation and, optionally, polygon surface generation are crucial to keep the measurement error small. In this study, the performance of different, easily accessible segmentation techniques (global thresholding, automatic local thresholding, weighted random walk, neural network, and watershed) and surface generation approaches (different algorithms combined with varying degrees of simplification) was analyzed and recommendations for minimizing inaccuracies were derived. The different approaches were applied to synthetic CT volumes for which the correct segmentation and surface geometry were known. The most accurate segmentations of the synthetic volumes were achieved by setting a case-specific window to the gray value histogram and subsequently applying automatic local thresholding with appropriately chosen thresholding method and radius. Surfaces generated by the Amira® module Generate Lego Surface in combination with careful surface simplification were the most accurate. Surfaces with sub-voxel accuracy were obtained even for synthetic CT volumes with low contrast-to-noise ratios. Segmentation trials with real CT volumes supported the findings. Very accurate segmentations and surfaces can be derived from CT volumes by using readily accessible software packages. The presented results and derived recommendations will help to reduce the measurement error in future studies. Furthermore, the demonstrated strategies for assessing segmentation and surface qualities can be adopted to quantify the performance of new segmentation approaches in future studies.

Ecomorphology of the pectoral girdle in anurans (Amphibia, Anura): Shape diversity and biomechanical considerations

Frogs and toads (Lissamphibia: Anura) show a diversity of locomotor modes that allow them to inhabit a wide range of habitats. The different locomotor modes are likely to be linked to anatomical specializations of the skeleton within the typical frog Bauplan. While such anatomical adaptations of the hind limbs and the pelvic girdle are comparably well understood, the pectoral girdle received much less attention in the past. We tested for locomotor-mode-related shape differences in the pectoral girdle bones of 64 anuran species by means of micro-computed-tomography-based geometric morphometrics. The pectoral girdles of selected species were analyzed with regard to the effects of shape differences on muscle moment arms across the shoulder joint and stress dissipation within the coracoid. Phylogenetic relationships, size, and locomotor behavior have an effect on the shape of the pectoral girdle in anurans, but there are differences in the relative impact of these factors between the bones of this skeletal unit. Remarkable shape diversity has been observed within locomotor groups indicating many-to-one mapping of form onto function. Significant shape differences have mainly been related to the overall pectoral girdle geometry and the shape of the coracoid. Most prominent shape differences have been found between burrowing and nonburrowing species with headfirst and backward burrowing species significantly differing from one another and from the other locomotor groups. The pectoral girdle shapes of burrowing species have generally larger moment arms for (simulated) humerus retractor muscles across the shoulder joint, which might be an adaptation to the burrowing behavior. The mechanisms of how the moment arms were enlarged differed between species and were associated with differences in the reaction of the coracoid to simulated loading by physiologically relevant forces.

Testing repeatability, measurement error and species differentiation when using geometric morphometrics on complex shapes: a case study of Patagonian lizards of the genus Liolaemus (Squamata: Liolaemini)

The repeatability of findings is the key factor behind scientific reliability, and the failure to reproduce scientific findings has been termed the ‘replication crisis’. Geometric morphometrics is an established tool in evolutionary biology. However, different operators (and/or different methods) could act as large sources of variation in the data obtained. Here, we investigated inter-operator error in geometric morphometric protocols on complex shapes of Liolaemus lizards, as well as measurement error in three taxa varying in their difficulty of digitalization. We also examined the potential for these protocols to discriminate among complex shapes in closely related species. We found a wide range of inter-operator error, contributing between 19.5% and 60% to the total variation. Moreover, measurement error increased with the complexity of the quantified shape. All protocols were able to discriminate between species, but the use of more landmarks did not imply better performance. We present evidence that complex shapes reduce repeatability, highlighting the need to explore different sources of variation that could lead to such low repeatability. Lastly, we suggest some recommendations to improve the repeatability and reliability of geometric morphometrics results.

Evaluating fidelity of CT based 3D models for Zebrafish conductive hearing system

The zebrafish Weberian apparatus is an emerging model for human conductive hearing system. Their Weberian apparatus comprises minute bones and ligamentary links, and conducts sound pressure transmission from the gas bladder to inner ear through four pairs of Weberian ossicles along the vertebral column. We herein present a methodological study using MicroCT to image the Weberian apparatus for biomechanical and morphological analysis. The aim of this work is to evaluate computational models generated from multiple MicroCT scans with different parameters, to identify the most feasible scan combination for practical (minimized scan time) yet accurate (relative to highest resolution) biomechanical simulations. We segmented and created 3D models from CT scan image stacks at 4.64 μm, 5.05 μm, 9.30 μm and 13.08 μm voxel resolutions, respectively. Then, we used geometric morphometrics analysis to quantify inter-model shape differences, as well as a series of finite element modal and harmonic analyses to simulate auditory signal vibrations. Relative to the highest resolution and most accurate model, the Model 9.30 is closest in overall geometry and biomechanical behavior of all lower resolution models. The differences in resolution and quality of the CT substantially affect the segmentation and reconstruction process of the three-dimensional model of the ossicles, and the subsequent analyses. We conclude that scan voxel resolution is a key factor influencing outcomes of biomechanical simulations of delicate and minute structures, especially when studying the harmonic response of minute ossicles connected by ligaments using finite element modeling. Furthermore, contrast variations in CT images as determined by x-ray power and scan speed, also affect fidelity in 3D models and simulation outcomes.

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis-based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis-specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.