Raw Data - A Freeware, Equitable Approach to Dental Topographic Analysis

Dataset

Morley, M. and Berthaume, M. (2023). Raw Data - A Freeware, Equitable Approach to Dental Topographic Analysis. London South Bank University. https://doi.org/10.18744/lsbu.93322
AuthorsMorley, M. and Berthaume, M.
Abstract

Dental topographic analysis has proved a valuable tool for quantifying dental morphology. Established workflows use proprietary software for pre-processing dental surfaces, rendering the method expensive and inaccessible. This study explores the use of freeware pre-processing alternatives.
We tested 4 decimation tools and 13 smoothing tools across 7 different freeware packages. Although surfaces generated via proprietary software could not be replicated, it was possible to obtain statistically similar topographic metrics in freeware to those obtained via proprietary means. Based on this investigation, we present a freeware workflow, via which researchers may conduct dental topographic analysis equitably, and with the expectation that their data will be comparable to that obtained via established proprietary methods.

KeywordsDental Topographic Analysis, Freeware, Smoothing, Meshlab, molaR
Year2023
PublisherLondon South Bank University
Digital Object Identifier (DOI)https://doi.org/10.18744/lsbu.93322
Data files
License
File description
Surface files of 25 different platyrrhine and prosimian lower second molars, having undergone simplification and smoothing with several different tools and settings. Also contained are spreadsheets containing dental topographic metrics of these surfaces, and results of statistical analysis of these metrics.
Data type
Archive
Contents
Data
File Access Level
Open
Data collection period11 Dec 2020 to end of 20 Sep 2022
Geographic location
London, UK
Data collection method

Surface files were initially downloaded from Morphosource.org, a 3D data repository - published under a Creative Commons - Attribution license (CC-BY-NC-4.0). Files were created by Doug Boyer of Stony Brook University, New York. MicroCT scans were taken of teeth, and these scans were subsequently segmented in Avizo, generating 3D surface files.

Data preparation and processing activities

Surface files were rotated and any stray data points removed, and underwent simplification and smoothing with several different tools and settings. Surfaces were then imported to the molaR package in Rstudio, where morphological metrics were obtained. These metrics were exported to .csv format, and statistical analysis (Shapiro-Wilks, Wlicoxon Signed Rank and Student's T tests) was conducted on them.

Publication process dates
Deposited10 Feb 2023
Permalink -

https://openresearch.lsbu.ac.uk/item/93322

Download files

Data files
Freeware DTA Data.zip
License: CC BY-NC 4.0
File access level: Open

  • 213
    total views
  • 26
    total downloads
  • 18
    views this month
  • 1
    downloads this month

Export as

Related outputs

Biomechanics in anthropology
Berthaume, M. and Elton, S. (2024). Biomechanics in anthropology. Evolutionary Anthropology: Issues, News, and Reviews. p. e22019. https://doi.org/10.1002/evan.22019
Variation in enamel mechanical properties throughout the crown in catarrhine primates.
Towle, I., Loho, T., Salem, A.S., Berthaume, M.A. and Loch, C. (2023). Variation in enamel mechanical properties throughout the crown in catarrhine primates. Journal of Human Evolution. 182, p. 103413. https://doi.org/10.1016/j.jhevol.2023.103413
Technical note: A freeware, equitable approach to dental topographic analysis
Morley, M.J. and Berthaume, M. (2023). Technical note: A freeware, equitable approach to dental topographic analysis. American Journal of Biological Anthropology. https://doi.org/10.1002/ajpa.24807
Low-cost locally manufacturable unilateral imperial external fixator for low- and middle-income countries
Saeidi, M., Barnes, S.C., Berthaume, M., Holthof, S.R., Milandri, G.S., Bull, A.M.J. and Jeffers, J. (2022). Low-cost locally manufacturable unilateral imperial external fixator for low- and middle-income countries. Frontiers in Medical Technology. 4, p. 1004976. https://doi.org/10.3389/fmedt.2022.1004976
Dental macrowear reveals ecological diversity of Gorilla spp.
Harty, T., Berthaume, M.A., Bortolini, E., Evans, A.R., Galbany, J., Guy, F., Kullmer, O., Lazzari, V., Romero, A. and Fiorenza, L. (2022). Dental macrowear reveals ecological diversity of Gorilla spp. Scientific Reports. 12 (1), p. 9203. https://doi.org/10.1038/s41598-022-12488-8
Molar biomechanical function in South African hominins
Berthaume, M. and Kupczik, K. (2021). Molar biomechanical function in South African hominins . Interface Focus. 11 (5), p. 20200085. https://doi.org/10.1098/rsfs.2020.0085
Introduction to the theme issue ‘Biological anthroengineering’
Kramer, P. and Berthaume, M. (2021). Introduction to the theme issue ‘Biological anthroengineering’. Interface Focus. 11 (5), p. 20210058. https://doi.org/10.1098/rsfs.2021.0058
Anthroengineering: an independent interdisciplinary field
Berthaume, M. and Kramer, P. (2021). Anthroengineering: an independent interdisciplinary field. Interface Focus. 11 (5), p. 20200056. https://doi.org/10.1098/rsfs.2020.0056
The effects of femoral metaphyseal morphology on growth plate biomechanics in juvenile chimpanzees and humans
Stamos, P. and Berthaume, M.A. (2021). The effects of femoral metaphyseal morphology on growth plate biomechanics in juvenile chimpanzees and humans. Interface Focus. 11 (5), p. 20200092. https://doi.org/10.1098/rsfs.2020.0092
Cyamella (a popliteal sesamoid bone) prevalence: A systematic review, meta‐analysis, and proposed classification system
Berthaume, M. and Bull, A. (2021). Cyamella (a popliteal sesamoid bone) prevalence: A systematic review, meta‐analysis, and proposed classification system. Clinical anatomy. pp. 1-11. https://doi.org/10.1002/ca.23743
The landscape of tooth shape: Over 20 years of dental topography in primates
Berthaume, M., Lazzari, Vincent and Guy, Franck (2020). The landscape of tooth shape: Over 20 years of dental topography in primates. Evolutionary anthropology. 29 (5), pp. 245-262. https://doi.org/10.1002/evan.21856
Unique myological changes associated with ossified fabellae: a femorofabellar ligament and systematic review of the double-headed popliteus
Berthaume, M. A., Barnes, S., Athwal, K.K. and Willinger, L. (2020). Unique myological changes associated with ossified fabellae: a femorofabellar ligament and systematic review of the double-headed popliteus. PeerJ. 8, pp. e10028-e10028. https://doi.org/10.7717/peerj.10028
Fabella prevalence rate increases over 150 years, and rates of other sesamoid bones remain constant: a systematic review
Berthaume, M., Di Federico, E. and Bill, A. (2019). Fabella prevalence rate increases over 150 years, and rates of other sesamoid bones remain constant: a systematic review. Journal of Anatomy. 235, pp. 67-79. https://doi.org/10.1111/joa.12994
Effects of cropping, smoothing, triangle count, and mesh resolution on 6 dental topographic metrics
Berthaume, M., Winchester, J. and Kupczik, K (2019). Effects of cropping, smoothing, triangle count, and mesh resolution on 6 dental topographic metrics. PLoS ONE. 14 (5), p. e0216229. https://doi.org/10.1371/journal.pone.0216229
Ambient occlusion and PCV (portion de ciel visible): A new dental topographic metric and proxy of morphological wear resistance
Berthaume, M., Winchester, J. and Kupczik, K. (2019). Ambient occlusion and PCV (portion de ciel visible): A new dental topographic metric and proxy of morphological wear resistance. PLoS ONE. 14 (5), p. e0215436. https://doi.org/10.1371/journal.pone.0215436
Human biological variation in sesamoid bone prevalence: the curious case of the fabella
Berthaume, M. and Bull, A.M.J. (2019). Human biological variation in sesamoid bone prevalence: the curious case of the fabella. Journal of Anatomy. https://doi.org/10.1111/joa.13091
Dental topography and the diet of Homo naledi
Berthaume, M., Delezene, L. and Kupczik, K. (2018). Dental topography and the diet of Homo naledi. Journal of Human Evolution. 118, pp. 14-26. https://doi.org/10.1016/j.jhevol.2018.02.006
Extant ape dental topography and its implications for reconstructing the emergence of early Homo
Berthaume, M. and Schroer, K. (2017). Extant ape dental topography and its implications for reconstructing the emergence of early Homo. Journal of Human Evolution. 112, pp. 15-29. https://doi.org/10.1016/j.jhevol.2017.09.001
Functional and evolutionary consequences of cranial fenestration in birds
Gussekloo, S., Berthaume, M., Pulaski, D., Westbroek, I., Waarsing, J., Heinen, R., Grosse, I. and Dumont, E. (2017). Functional and evolutionary consequences of cranial fenestration in birds. Evolution. 71 (5), pp. 1327-1338. https://doi.org/10.1111/evo.13210
Skeletal Immaturity, Rostral Sparing, and Disparate Hip Morphologies as Biomechanical Causes for Legg-Calve-Perthes’ Disease
Berthaume, M., Perry, D.C., Dobson, C., Witzel, U., Clarke, N.M. and Fagan, M. (2016). Skeletal Immaturity, Rostral Sparing, and Disparate Hip Morphologies as Biomechanical Causes for Legg-Calve-Perthes’ Disease . Clinical Anatomy. https://doi.org/10.1002/ca.22690
On the relationship between tooth shape and masticatory efficiency: a finite element study
Berthaume, M. (2016). On the relationship between tooth shape and masticatory efficiency: a finite element study. The Anatomical Record. 299 (5), pp. 679-687. https://doi.org/10.1002/ar.23328
Food mechanical properties and dietary ecology
Berthaume, M. (2016). Food mechanical properties and dietary ecology. Americal Journal of Physical Anthropology. 159, pp. 79-104. https://doi.org/10.1002/ajpa.22903
What did Hadropithecus eat, and why should paleoanthropologists care?
Godfrey, L., Crowley, B., Muldoon, K., Kelley, E., King, S., Best, A. and Berthaume, M. (2016). What did Hadropithecus eat, and why should paleoanthropologists care? American Journal of Primatology. 78 (10), pp. 1098-1112. https://doi.org/10.1002/ajp.22506
Mechanical evidence that Australopithecus sediba was limited in its ability to eat hard foods
Ledogar, J., Smith, A., Benazzi, S., Weber, G., Spencer, M., Carlson, K., McNulty, K., Dechow, P., Grosse, I., Ross, C., Richmond, B., Wright, B., Wang, Q., Byron, C., Carlson, K., de Ruiter, D., Berger, L., Tamvada, K., Pryor, L., Berthaume, M. and Strait, D. (2016). Mechanical evidence that Australopithecus sediba was limited in its ability to eat hard foods. Nature Communications. 7 (1). https://doi.org/10.1038/ncomms10596
The Feeding Biomechanics and Dietary Ecology of Paranthropus boisei
Smith, A., Benazzi, S, Ledogar, J., Tamvada, K., Pryor Smith, L., Weber, G., Spencer, M., Lucas, P., Michael, S., Shekeban, A., Al-Fadhalah, K., Almusallam, A, Dechow, P., Grosse, I., Ross, C., Madden, R., Richmond, B., Wright, B., Wang, Q, Byron, C., Slice, D., Wood, S., Dzialo, C., Berthaume, M., van Casteren, A. and Strait, D. (2015). The Feeding Biomechanics and Dietary Ecology of Paranthropus boisei. The Anatomical Record. 298 (1), pp. 145-167. https://doi.org/10.1002/ar.23073
The effects of relative food item size on optimal tooth cusp sharpness during brittle food item processing
Berthaume, M., Dumont, E., Godfrey, L. and Grosse, I. (2014). The effects of relative food item size on optimal tooth cusp sharpness during brittle food item processing. Interface. 11 (101), p. 20140965. https://doi.org/10.1098/rsif.2014.0965