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A new fully automated approach for aligning and comparing shapes.

Publication ,  Journal Article
Boyer, DM; Puente, J; Gladman, JT; Glynn, C; Mukherjee, S; Yapuncich, GS; Daubechies, I
Published in: Anat Rec (Hoboken)
January 2015

Three-dimensional geometric morphometric (3DGM) methods for placing landmarks on digitized bones have become increasingly sophisticated in the last 20 years, including greater degrees of automation. One aspect shared by all 3DGM methods is that the researcher must designate initial landmarks. Thus, researcher interpretations of homology and correspondence are required for and influence representations of shape. We present an algorithm allowing fully automatic placement of correspondence points on samples of 3D digital models representing bones of different individuals/species, which can then be input into standard 3DGM software and analyzed with dimension reduction techniques. We test this algorithm against several samples, primarily a dataset of 106 primate calcanei represented by 1,024 correspondence points per bone. Results of our automated analysis of these samples are compared to a published study using a traditional 3DGM approach with 27 landmarks on each bone. Data were analyzed with morphologika(2.5) and PAST. Our analyses returned strong correlations between principal component scores, similar variance partitioning among components, and similarities between the shape spaces generated by the automatic and traditional methods. While cluster analyses of both automatically generated and traditional datasets produced broadly similar patterns, there were also differences. Overall these results suggest to us that automatic quantifications can lead to shape spaces that are as meaningful as those based on observer landmarks, thereby presenting potential to save time in data collection, increase completeness of morphological quantification, eliminate observer error, and allow comparisons of shape diversity between different types of bones. We provide an R package for implementing this analysis.

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Published In

Anat Rec (Hoboken)

DOI

EISSN

1932-8494

Publication Date

January 2015

Volume

298

Issue

1

Start / End Page

249 / 276

Location

United States

Related Subject Headings

  • Software
  • Principal Component Analysis
  • Phylogeny
  • Models, Biological
  • Mathematics
  • Imaging, Three-Dimensional
  • Humans
  • Calcaneus
  • Automation
  • Animals
 

Citation

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Chicago
ICMJE
MLA
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Boyer, D. M., Puente, J., Gladman, J. T., Glynn, C., Mukherjee, S., Yapuncich, G. S., & Daubechies, I. (2015). A new fully automated approach for aligning and comparing shapes. Anat Rec (Hoboken), 298(1), 249–276. https://doi.org/10.1002/ar.23084
Boyer, Doug M., Jesus Puente, Justin T. Gladman, Chris Glynn, Sayan Mukherjee, Gabriel S. Yapuncich, and Ingrid Daubechies. “A new fully automated approach for aligning and comparing shapes.Anat Rec (Hoboken) 298, no. 1 (January 2015): 249–76. https://doi.org/10.1002/ar.23084.
Boyer DM, Puente J, Gladman JT, Glynn C, Mukherjee S, Yapuncich GS, et al. A new fully automated approach for aligning and comparing shapes. Anat Rec (Hoboken). 2015 Jan;298(1):249–76.
Boyer, Doug M., et al. “A new fully automated approach for aligning and comparing shapes.Anat Rec (Hoboken), vol. 298, no. 1, Jan. 2015, pp. 249–76. Pubmed, doi:10.1002/ar.23084.
Boyer DM, Puente J, Gladman JT, Glynn C, Mukherjee S, Yapuncich GS, Daubechies I. A new fully automated approach for aligning and comparing shapes. Anat Rec (Hoboken). 2015 Jan;298(1):249–276.
Journal cover image

Published In

Anat Rec (Hoboken)

DOI

EISSN

1932-8494

Publication Date

January 2015

Volume

298

Issue

1

Start / End Page

249 / 276

Location

United States

Related Subject Headings

  • Software
  • Principal Component Analysis
  • Phylogeny
  • Models, Biological
  • Mathematics
  • Imaging, Three-Dimensional
  • Humans
  • Calcaneus
  • Automation
  • Animals