Error in geometric morphometric data collection: Combining data from multiple sources

Robinson, Chris; Terhune, Claire

doi:10.1002/ajpa.23257

Cited by 82 publications

(148 citation statements)

References 36 publications

(79 reference statements)

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“…() reported no significant difference when comparing landmark data acquired from surfaces of a CT scan and of three different surface scanners. Robinson & Terhune (), in contrast, observed small, yet significant differences between sets of linear distances directly measured from the specimens (caliper measurements and digitization of landmarks) and from digital representations of them (landmarks from surfaces of CT and laser scanner). With regard to observer error, Shearer et al.…”

Section: Introductionmentioning

confidence: 99%

“…). The variability within repeated measurements performed by the same observer and the variability between different observers can also contribute significantly to measurement error (Ross & Williams, ; Robinson & Terhune, ; reports of relatively large observer error without tests for statistical significance: Curth et al. ; Fruciano et al.…”

Section: Introductionmentioning

confidence: 99%

“…The presence of such artefactual variance in landmark data has recently been noted to have been overlooked in many geometric morphometric studies (Fruciano, 2016), and different studies have stressed the importance of measurement error assessment (e.g. Klingenberg, 2015;Fruciano, 2016;Robinson & Terhune, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…The preservation and preparation of specimens can induce artefactual variance by altering the natural form of the structures of interest (Lee, 1982 [linear measurements]; Bonneau et al 2012). The variability within repeated measurements performed by the same observer and the variability between different observers can also contribute significantly to measurement error (Ross & Williams, 2008;Robinson & Terhune, 2017; reports of relatively large observer error without tests for statistical significance: Curth et al 2017;Fruciano et al 2017;Daboul et al 2018). Nevertheless, the magnitude of observer error often has been considered small or negligible compared with true biological variability (Richtsmeier et al 1995;O'Higgins & Jones, 1998;Lockwood et al 2002;Pujol et al 2014;Barbeito-Andr es et al 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Studies on the effect of the choice of a method (including the choice of a device) for 3D landmark data acquisition have reported contradictory results on the significance of measurement error caused by method choice and on the effect of choice of method on observer error (e.g. Hale et al 2014;Fruciano et al 2017;Robinson & Terhune, 2017;Shearer et al 2017;Marcy et al 2018). Hale et al (2014), for example, found significant differences between landmark data directly digitized from the specimens and landmark data derived from computed tomography (CT) scans of the same specimens.…”

Section: Introductionmentioning

confidence: 99%

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Measurement error in μCT‐based three‐dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

et al. 2019

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Computed‐tomography‐derived (CT‐derived) polymesh surfaces are widely used in geometric morphometric studies. This approach is inevitably associated with decisions on scanning parameters, resolution, and segmentation strategies. Although the underlying processing steps have been shown to potentially contribute artefactual variance to three‐dimensional landmark coordinates, their effects on measurement error have rarely been assessed systematically in CT‐based geometric morphometric studies. The present study systematically assessed artefactual variance in landmark data introduced by the use of different voxel sizes, segmentation strategies, surface simplification degrees, and by inter‐ and intra‐observer differences, and compared their magnitude to true biological variation. Multiple CT‐derived surface variants of the anuran (Amphibia: Anura) pectoral girdle were generated by systematic changes in the factors that potentially influence the surface geometries. Twenty‐four landmarks were repeatedly acquired by different observers. The contribution of all factors to the total variance in the landmark data was assessed using random‐factor nested permanovas. Selected sets of Euclidean distances between landmark sets served further to compare the variance among factor levels. Landmark precision was assessed by landmark standard deviation and compared among observers and days. Results showed that all factors, except for voxel size, significantly contributed to measurement error in at least some of the analyses performed. In total, 6.75% of the variance in landmark data that mimicked a realistic biological study was caused by measurement error. In this landmark dataset, intra‐observer error was the major source of artefactual variance followed by inter‐observer error; the factor segmentation contributed < 1% and slight surface simplification had no significant effect. Inter‐observer error clearly exceeded intra‐observer error in a different landmark dataset acquired by six partly inexperienced observers. The results suggest that intra‐observer error can potentially be reduced by including a training period prior to the actual landmark acquisition task and by acquiring landmarks in as few sessions as possible. Additionally, the application of moderate and careful surface simplification and, potentially, also the use of case‐specific optimal combinations of automatic local thresholding algorithms and parameters for segmentation can help reduce intra‐observer error. If landmark data are to be acquired by several observers, it is important to ensure that all observers are consistent in landmark identification. Despite the significant amount of artefactual variance, we have shown that landmark data acquired from microCT‐derived surfaces are precise enough to study the shape of anuran pectoral girdles. Yet, a systematic assessment of measurement error is advisable for all geometric morphometric studies.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Measurement error in μCT‐based three‐dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

et al. 2019

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Developmental stability and environmental stress: A geometric morphometrics analysis of asymmetry in the human femur

Mopin

Chaumoître

Signoli

et al. 2018

American J Phys Anthropol

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Basicranial ontogeny comparison in Pan troglodytes and Homo sapiens and its use for developmental stage definition of KNM‐ER 42700

Mori

Harvati

2019

American J Phys Anthropol

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Objective: This study aims to develop a comparative basis for assessing the developmental stage of KNM-ER 42700 based on the ontogenetic pattern of the ectocranial surface of the basicranium in modern humans and chimpanzees.Materials and methods: A total of 33 landmarks were collected from an ontogenetic sample of modern humans (80), chimpanzees (51), and 12 individuals classified as Homo erectus s.l. Ontogenetic trajectories were analyzed, and common aspects were extracted for the purpose of discriminating age groups. A regression of size on the extracted shape variables was used to investigate common ontogenetic allometry.

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Error in geometric morphometric data collection: Combining data from multiple sources

Cited by 82 publications

References 36 publications

Measurement error in μCT‐based three‐dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

Measurement error in μCT‐based three‐dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

Developmental stability and environmental stress: A geometric morphometrics analysis of asymmetry in the human femur

Basicranial ontogeny comparison in Pan troglodytes and Homo sapiens and its use for developmental stage definition of KNM‐ER 42700

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