Using point clouds to investigate the relationship between trabecular bone phenotype and behavior: An example utilizing the human calcaneus

DeMars, Lily J.D.; Stephens, Nicholas B.; Saers, Jaap P. P.; Gordon, Adam D.; Stock, Jay T.; Ryan, Timothy M.

doi:10.1002/ajhb.23468

Cited by 23 publications

(40 citation statements)

References 68 publications

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“…Inference of function from trabecular bone architecture is complicated by genetic, ontogenetic 10 , and systemic 11 factors that also influence bone form. However, numerous studies have found trabecular architectures that reflect assumed habitually and significantly loaded joint postures 12 – 24 , regardless of whether this load is gravitational, muscular, or a combination of both 25 , 26 . Thus, analysis of trabecular architecture provides additional information that can be combined with studies of internal and external cortical bone morphology, to provide a more holistic understanding of how bone reflects behaviour.…”

Section: Introductionmentioning

confidence: 99%

“…It was successfully applied to a variety of bones, including carpals, metacarpals and phalanges 12 – 16 , 36 , proximal femora 17 – 19 , distal femora 20 , distal tibiae 17 , proximal humeri 17 , distal radii 21 , and first metatarsals 22 . However, HMA is not yet able to compare the site-specific morphometry, below the sector level, for different individuals quantitatively in homologous regions 23 , 24 , 27 .…”

Section: Introductionmentioning

confidence: 99%

“…However, both of these approaches are necessarily limited to analyse the edge of the trabecular network. Volumetric sliding semi-landmarks 40 and coherent point drift 41 allow for volumetric quantitative comparisons between samples using HMA 24 .…”

Section: Introductionmentioning

confidence: 99%

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A computational framework for canonical holistic morphometric analysis of trabecular bone

Bachmann

Dunmore

Skinner

et al. 2022

Sci Rep

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Bone is a remarkable, living tissue that functionally adapts to external loading. Therefore, bone shape and internal structure carry information relevant to many disciplines, including medicine, forensic science, and anthropology. However, morphometric comparisons of homologous regions across different individuals or groups are still challenging. In this study, two methods were combined to quantify such differences: (1) Holistic morphometric analysis (HMA) was used to quantify morphometric values in each bone, (2) which could then be mapped to a volumetric mesh of a canonical bone created by a statistical free-form deformation model (SDM). Required parameters for this canonical holistic morphometric analysis (cHMA) method were identified and the robustness of the method was evaluated. The robustness studies showed that the SDM converged after one to two iterations, had only a marginal bias towards the chosen starting image, and could handle large shape differences seen in bones of different species. Case studies were performed on metacarpal bones and proximal femora of different primate species to confirm prior study results. The differences between species could be visualised and statistically analysed in both case studies. cHMA provides a framework for performing quantitative comparisons of different morphometric quantities across individuals or groups. These comparisons facilitate investigation of the relationship between spatial morphometric variations and function or pathology, or both.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A computational framework for canonical holistic morphometric analysis of trabecular bone

Bachmann

Dunmore

Skinner

et al. 2022

Sci Rep

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“…The method has even been employed for analysis of non-anatomical data [54,55]. However, it can still be powerful and preferable in certain monospecific samples [56]. A key point that users should consider is that the automatic pseudo-landmarks generated by auto3dgm cannot be expected to preserve intuitive notions of “homology” between shapes with very different proportions.…”

Section: Morphometric Data Collectionmentioning

confidence: 99%

SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology

Rolfe¹,

Pieper

Porto³

et al. 2020

Preprint

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Large scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. MorphoSource currently hosts tens of thousands of 3D scans of eukaryotes. Along with the data from similarly scoped projects such as 10kPhenomes, DigiMorph and many others, soon hundreds of thousands of specimens that represent biodiversity of extinct and extant organisms will be conveniently available to researchers. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyze them.Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration, and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. Another relevant concern is that ultimate derivative data from individual research projects (e.g., 3D models of segmentation) are shared in formats that do not preserve the correct spatial scale of the data.In this paper, we present our effort to tackle challenges biologists face when conducting 3D specimen-based research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python-scriptable open-source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open-access 3D models or import users own 3D volumes, to annotate 3D curve and patch-based landmarks, generate canonical templates, conduct geometric morphometric analyses of 3D organismal form using both landmark-driven and landmark-free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology, and extensive links to the existing tutorials are provided as supplemental material.Our goal is to establish a community of organismal biologists centered around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.

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“…Indeed, alterations to ontogenetic trajectories are the principal ways in which evolutionary changes in life history and morphology occur (Gould, 1977;Hallgŕmsson and Hall, 2005;Kardong, 2018;Woronowicz and Schneider, 2019). Recent methodological and technological advances in the analysis of trabecular bone structure have opened new possibilities for studying the development of trabecular bone structure (Gross et al, 2014;DeMars et al, 2020). Here we apply these new techniques to analyse the ontogeny of trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata).…”

Section: Introductionmentioning

confidence: 99%

Growth and development of trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata) reflects locomotor behavior, life-history, and neuromuscular development

Saers

Gordon

Ryan

et al. 2021

Preprint

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We aim to broaden the analysis of bone structure by suggesting a new way to incorporate the interactions between behavior, neuromuscular development, and life-history. We examine the associations between these variables and age-related variation in trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata). If skeletal markers linking these variables can be established, our inferences of the biology and behavior of fossil species would be significantly improved. We μCT scanned the calcaneus in a cross-sectional sample of 36 juveniles aged between 0 and 7 years old and 5 adults at the Primate Research Institute, Japan. We calculated whole bone averages of standard trabecular properties and generated whole-bone morphometric maps of bone volume fraction and Youngs modulus. Trabecular structure is increasingly heterogeneous in older individuals. BV/TV decreases during the first month of life and increases afterwards, coinciding with the onset of independent locomotion. At birth, primary Youngs modulus is oriented orthogonal to the ossification center, but after locomotor onset bone structure becomes stiffest in the direction of joint surfaces and muscle attachments. Age-related variation in bone volume fraction is best predicted by an interaction between neuromaturation, body mass, and locomotor independence. Results support the common assumption that trabecular structure dynamically adapts to novel joint loading conditions during ontogeny. The timing of independent locomotion, body size, and neuromuscular development, are all correlated to age-related variation in the trabecular structure of the macaque calcaneus. The causal mechanisms behind the observed patterns cannot be directly inferred from our cross-sectional study. If the model presented in this paper holds up under longitudinal experimental conditions, trabecular structure can be used both to infer behavior from fossil morphology and to serve as a valuable proxy for neuromuscular maturation and life history events like locomotor onset and the achievement of an adult-like gait.

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Using point clouds to investigate the relationship between trabecular bone phenotype and behavior: An example utilizing the human calcaneus

Cited by 23 publications

References 68 publications

A computational framework for canonical holistic morphometric analysis of trabecular bone

A computational framework for canonical holistic morphometric analysis of trabecular bone

SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology

Growth and development of trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata) reflects locomotor behavior, life-history, and neuromuscular development

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