Technical note: A freeware, equitable approach to dental topographic analysis

Morley, Matthew; Berthaume, Michael A.

doi:10.1002/ajpa.24807

Cited by 4 publications

(7 citation statements)

References 42 publications

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“…This may make direct comparison between results obtained by using this freeware pipeline and those of proprietary protocols difficult. Morley and Berthaume (2023) also identify this downside when using Meshlab's smoothing option (Laplacian Smooth) and instead recommend using the vcgSmooth (Taubin) tool within the R package Rvcg. Ultimately, we conclude that our proposed pipeline performs equally well as previous protocols using proprietary software, as the overall classification accuracy when using multiple dental topographic metrics (as would normally be the case) was comparable between the different protocols.…”

Section: Freeware Pipeline Validationmentioning

confidence: 99%

“…Although our freeware pipeline shares steps with that of the proposed freeware workflow introduced recently by Morley and Berthaume (2023), there are some differences. We include steps regarding surface mesh deformity reconstruction in MeshMixer and orienting the surface mesh into occlusal view, steps that are not included in the protocol by Morley and Berthaume (2023) but are important for dealing with specimens not previously processed for analyses using DTMs. Morley and Berthaume (2023) compared smoothing settings of various freeware packages, but only one smoothing setting in MeshLab, whereas we compare four different smoothing settings within MeshLab only.…”

Section: Freeware Pipeline Validationmentioning

confidence: 99%

“…Although dental topographic methods represent a powerful, quantitative approach for analysing tooth shape, a number of issues currently limit their applicability. Firstly, current pipelines for dental topographic methods typically use commercial software packages that are often relatively expensive, and hence unaffordable for many researchers (but see Morley and Berthaume 2023). Secondly, studies that attempt to link tooth shape to particular diets often use dietary classification schemes that are not based on the full range of primary data available in the scientific literature.…”

Section: Introductionmentioning

confidence: 99%

“…However, until now most dental topographic protocols (e.g., Boyer 2008; Spradley et al 2017; Fulwood et al 2021; Pampush et al 2022) have used proprietary software, such as Amira/Avizo and GeoMagic, for processing of raw scan data and digital surface meshes into the correct format for calculating dental topography (i.e., all specimens are consistently simplified to the same number of polygons, oriented into occlusal view along the z-axis, smoothed, and exported as a .ply file). Although some studies have mentioned that some steps can also be performed in the freeware package MeshLab (Winchester 2016; Melstrom 2017; Spradley et al 2017; Berthaume et al 2020), to our knowledge, an only one processing pipeline that uses free software throughout has been published and validated before (Morley and Berthaume 2023). The goal of Morley and Berthaume (2023) was to replicate the decimation and smoothing steps done in Avizo as closely as possible using freeware, whereas the aim of our freeware pipeline is to yield meaningful surface meshes suitable for distinguishing different diets using DTMs.…”

Section: Introductionmentioning

confidence: 99%

“…Although some studies have mentioned that some steps can also be performed in the freeware package MeshLab (Winchester 2016; Melstrom 2017; Spradley et al 2017; Berthaume et al 2020), to our knowledge, an only one processing pipeline that uses free software throughout has been published and validated before (Morley and Berthaume 2023). The goal of Morley and Berthaume (2023) was to replicate the decimation and smoothing steps done in Avizo as closely as possible using freeware, whereas the aim of our freeware pipeline is to yield meaningful surface meshes suitable for distinguishing different diets using DTMs. To maximise the utility of this study to other researchers, we therefore present and validate a novel free pipeline for processing scan data for dental topographic analyses that uses only freeware, specifically: Slicer (Kikinis et al 2014), the SlicerMorph extension (Rolfe et al 2021), MeshLab (Cignoni et al 2008), Autodesk MeshMixer (MeshMixer RRID:SCR_015736), R (R Core Team 2022), and the R-package molaR (Pampush et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

de Vries,

Janiak,

Batista

et al. 2023

Preprint

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Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. However, comparative samples of scanned mammal teeth suitable for analysis with DTMs remain limited in size and scope, with little or no representation of some major lineages, even within well-studied clades such as primates. In addition, current DTM protocols usually rely on proprietary software, which may be unavailable to many researchers for reasons of cost. We address these issues in the context of a DTM analysis of the primate clade Platyrrhini (“New World monkeys”) by: 1) presenting a large comparative sample of scanned second lower molars (m2s) of callitrichids (marmosets and tamarins), which were previously underrepresented in publicly available platyrrhine datasets; and 2) giving full details of an entirely freeware pipeline for DTM analysis. We also present an updated discrete dietary classification scheme for extant platyrrhines, based on cluster analysis of dietary data extracted from 98 primary studies. Our freeware pipeline performs equally well in dietary classification accuracy of an existing sample of platyrrhine m2s (excluding callitrichids) as a published protocol that uses proprietary software, at least when multiple DTMs are combined. Individual DTMs however, sometimes showed very different results in classification accuracies between that of our freeware pipeline and that of the proprietary protocol, most likely due to the differences in the smoothing functions used. The addition of callitrichids still resulted in high classification accuracy in predicting diet with combined DTMs, although accuracy was considerably higher when molar size was included (90%) than excluded (73%). We conclude that our new freeware DTM pipeline is capable of accurately predicting diet in platyrrhines based on tooth shape and size, and so is suitable for inferring probable diet of taxa for which direct dietary information is unavailable, such as fossil species.

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Section: Freeware Pipeline Validationmentioning

confidence: 99%

Section: Freeware Pipeline Validationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

de Vries,

Janiak,

Batista

et al. 2023

Preprint

View full text Add to dashboard Cite

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Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

de Vries,

Janiak,

Batista

et al. 2024

J Mammal Evol

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Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. Current DTM protocols usually rely on proprietary software, which may be unavailable to researchers for reasons of cost. We address this issue in the context of a DTM analysis of the primate clade Platyrrhini (“New World monkeys”) by: 1) presenting a large comparative sample of scanned second lower molars (m2s) of callitrichids (marmosets and tamarins), previously underrepresented in publicly available datasets; and 2) giving full details of an entirely freeware pipeline for DTM analysis and its validation. We also present an updated dietary classification scheme for extant platyrrhines, based on cluster analysis of dietary data extracted from 98 primary studies. Our freeware pipeline performs equally well in dietary classification accuracy of an existing sample of platyrrhine m2s (excluding callitrichids) as a published protocol that uses proprietary software when multiple DTMs are combined. Individual DTMs, however, sometimes showed very different results in classification accuracies between protocols, most likely due to differences in smoothing functions. The addition of callitrichids resulted in high classification accuracy in predicting diet with combined DTMs, although accuracy was considerably higher when molar size was included (90%) than excluded (73%). We conclude that our new freeware DTM pipeline is capable of accurately predicting diet in platyrrhines based on tooth shape and size, and so is suitable for inferring probable diet of taxa for which direct dietary information is unavailable, such as fossil species.

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Interspecific and intraspecific variation in grasshopper (Orthoptera: Acrididea) molar form: implications for dietary ecology

Berthaume,

Morley

2024

R. Soc. Open Sci.

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Like many mammals, grasshoppers (infraorder Acrididea) chew using molariform structures. Despite decades of research on mammals, little is known about grasshopper molar form and how it relates to grasshopper feeding biomechanics, diet, dietary ecology and evolution. Here, we develop a method for quantifying molar form and apply it to two species of distantly related grasshoppers with different diets ( Phymateus saxosus , seven females; Valanga nigricornis , seven females, 11 males). We show that there are quantifiable differences in molar form, potentially related to diet. There are some differences in molar shape between left and right molars in both species and sexes, and significant differences in molar size, potentially due to scaling. Like in mammals, molar wear can cause large differences in molar shape. Species differences in molar shape did not match what was expected based on mammalian molar functional morphology. Dental topographic analysis is a promising new avenue for quantifying molar form in grasshoppers and a distinct advantage over traditional two-dimensional microscopy methods, and promises to reveal much about the biology, biomechanics and evolution of Acrididea.

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Technical note: A freeware, equitable approach to dental topographic analysis

Cited by 4 publications

References 42 publications

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

Interspecific and intraspecific variation in grasshopper (Orthoptera: Acrididea) molar form: implications for dietary ecology

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