Low resolution scans can provide a sufficiently accurate, cost- and timeeffective alternative to high resolution scans for 3D shape analyses

Ariel E. Marcy*, Carmelo Fruciano, Matthew J. Phillips, Karine Mardon, Vera Weisbecker

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Background: Advances in 3D shape capture technology have made powerful shape analyses, such as geometric morphometrics, more feasible. While the highly accurate micro-computed tomography (μCT) scanners have been the "gold standard," recent improvements in 3D surface scanners may make this technology a faster, portable, and cost-effective alternative. Several studies have already compared the two devices but all use relatively large specimens such as human crania. Here we perform shape analyses on Australia's smallest rodent to test whether a 3D scanner produces similar results to a μCT scanner. 

Methods: We captured 19 delicate mouse (Pseudomys delicatulus) crania with a μCT scanner and a 3D scanner for geometric morphometrics. We ran multiple Procrustes ANOVAs to test how variation due to scan device compared to other sources such as biologically relevant variation and operator error. We quantified operator error as levels of variation and repeatability. Further, we tested if the two devices performed differently at classifying individuals based on sexual dimorphism. Finally, we inspected scatterplots of principal component analysis (PCA) scores for non-random patterns. 

Results: In all Procrustes ANOVAs, regardless of factors included, differences between individuals contributed the most to total variation. The PCA plots reflect this in how the individuals are dispersed. Including only the symmetric component of shape increased the biological signal relative to variation due to device and due to error. 3D scans showed a higher level of operator error as evidenced by a greater spread of their replicates on the PCA, a higher level of multivariate variation, and a lower repeatability score. However, the 3D scan and μCT scan datasets performed identically in classifying individuals based on intra-specific patterns of sexual dimorphism. 

Discussion: Compared to μCT scans, we find that even low resolution 3D scans of very small specimens are sufficiently accurate to classify intra-specific differences. We also make three recommendations for best use of low resolution data. First, we recommend that extreme caution should be taken when analyzing the asymmetric component of shape variation. Second, using 3D scans generates more random error due to increased landmarking difficulty, therefore users should be conservative in landmark choice and avoid multiple operators. Third, using 3D scans introduces a source of systematic error relative to μCT scans, therefore we recommend not combining them when possible, especially in studies expecting little biological variation. Our findings support increased use of low resolution 3D scans for most morphological studies; they are likely also applicable to low resolution scans of large specimens made in a medical CT scanner. As most vertebrates are relatively small, we anticipate our results will bolster more researchers in designing affordable large scale studies on small specimens with 3D surface scanners.

Original languageEnglish
Article numbere5032
Number of pages25
Issue number6
Publication statusPublished - 22 Jun 2018


  • Generalized procrustes analysis
  • Geometric morphometrics
  • Geomorph
  • Photogrammetry
  • Pseudomys delicatulus
  • Random error
  • Shape variation
  • Systematic error


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