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      Evaluating causes of error in landmark-based data collection using scanners

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          Abstract

          In this study, we assess the precision, accuracy, and repeatability of craniodental landmarks (Types I, II, and III, plus curves of semilandmarks) on a single macaque cranium digitally reconstructed with three different surface scanners and a microCT scanner. Nine researchers with varying degrees of osteological and geometric morphometric knowledge landmarked ten iterations of each scan (40 total) to test the effects of scan quality, researcher experience, and landmark type on levels of intra- and interobserver error. Two researchers additionally landmarked ten specimens from seven different macaque species using the same landmark protocol to test the effects of the previously listed variables relative to species-level morphological differences (i.e., observer variance versus real biological variance). Error rates within and among researchers by scan type were calculated to determine whether or not data collected by different individuals or on different digitally rendered crania are consistent enough to be used in a single dataset. Results indicate that scan type does not impact rate of intra- or interobserver error. Interobserver error is far greater than intraobserver error among all individuals, and is similar in variance to that found among different macaque species. Additionally, experience with osteology and morphometrics both positively contribute to precision in multiple landmarking sessions, even where less experienced researchers have been trained in point acquisition. Individual training increases precision (although not necessarily accuracy), and is highly recommended in any situation where multiple researchers will be collecting data for a single project.

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          Most cited references25

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          PAST: Paleontological Statistics Software Package for Education and Data Analysis

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            Differences between sliding semi-landmark methods in geometric morphometrics, with an application to human craniofacial and dental variation.

            Over the last decade, geometric morphometric methods have been applied increasingly to the study of human form. When too few landmarks are available, outlines can be digitized as series of discrete points. The individual points must be slid along a tangential direction so as to remove tangential variation, because contours should be homologous from subject to subject whereas their individual points need not. This variation can be removed by minimizing either bending energy (BE) or Procrustes distance (D) with respect to a mean reference form. Because these two criteria make different assumptions, it becomes necessary to study how these differences modify the results obtained. We performed bootstrapped-based Goodall's F-test, Foote's measurement, principal component (PC) and discriminant function analyses on human molars and craniometric data to compare the results obtained by the two criteria. Results show that: (1) F-scores and P-values were similar for both criteria; (2) results of Foote's measurement show that both criteria yield different estimates of within- and between-sample variation; (3) there is low correlation between the first PC axes obtained by D and BE; (4) the percentage of correct classification is similar for BE and D, but the ordination of groups along discriminant scores differs between them. The differences between criteria can alter the results when morphological variation in the sample is small, as in the analysis of modern human populations.
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              Semilandmarks: a method for quantifying curves and surfaces

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: Investigation
                Role: Formal analysisRole: Investigation
                Role: ConceptualizationRole: Funding acquisitionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 November 2017
                2017
                : 12
                : 11
                : e0187452
                Affiliations
                [1 ] Ph.D. Program in Anthropology, The Graduate Center (CUNY), New York, New York, United States of America
                [2 ] New York Consortium in Evolutionary Primatology, New York, New York, United States of America
                [3 ] NYCEP Morphometrics Group, New York, New York, United States of America
                [4 ] Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
                [5 ] Department of Biology, Farmingdale State College (SUNY), Farmingdale, New York, United States of America
                [6 ] School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
                [7 ] Department of Archaeology, University of Sheffield, South Yorkshire, United Kingdom
                [8 ] Division of Vertebrate Paleontology, American Museum of Natural History, New York, New York, United States of America
                [9 ] Department of Anthropology, Lehman College (CUNY), Bronx, New York, United States of America
                [10 ] Department of Biomedical Sciences, Grand Valley State University, Grand Valley, Michigan, United States of America
                Max Planck Institute for Evolutionary Anthropology, GERMANY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0003-3747-5600
                Article
                PONE-D-17-08680
                10.1371/journal.pone.0187452
                5669428
                29099867
                e01d5121-9287-4ecc-8762-3108c0e79253
                © 2017 Shearer et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 March 2017
                : 19 October 2017
                Page count
                Figures: 12, Tables: 20, Pages: 37
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 99-82351
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 05-13660
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 11-16921
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 03-33415
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 09-66166
                Award Recipient :
                Funded by: Lehman College
                Award Recipient :
                Funded by: New York State GRTI
                Award Recipient :
                Supported in part by funds from Lehman College, New York State (Graduate Research Training Initiative), National Science Foundation awards 99-82351, 05-13660, and 11-16921, and National Science Foundation Integrative Graduate Education and Research Traineeship grants to New York Consortium in Evolutionary Primatology (03-33415 and 09-66166), all to PI E.D. and colleagues. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Primates
                Monkeys
                Old World monkeys
                Macaque
                Research and Analysis Methods
                Imaging Techniques
                Neuroimaging
                Computed Axial Tomography
                Biology and Life Sciences
                Neuroscience
                Neuroimaging
                Computed Axial Tomography
                Medicine and Health Sciences
                Diagnostic Medicine
                Diagnostic Radiology
                Tomography
                Computed Axial Tomography
                Research and Analysis Methods
                Imaging Techniques
                Diagnostic Radiology
                Tomography
                Computed Axial Tomography
                Medicine and Health Sciences
                Radiology and Imaging
                Diagnostic Radiology
                Tomography
                Computed Axial Tomography
                Biology and Life Sciences
                Anatomy
                Osteology
                Medicine and Health Sciences
                Anatomy
                Osteology
                Biology and Life Sciences
                Anatomy
                Musculoskeletal System
                Skeleton
                Skull
                Cranium
                Medicine and Health Sciences
                Anatomy
                Musculoskeletal System
                Skeleton
                Skull
                Cranium
                Research and Analysis Methods
                Imaging Techniques
                Morphometry
                Engineering and Technology
                Equipment
                Optical Equipment
                Lasers
                Social Sciences
                Anthropology
                Physical Anthropology
                Biology and Life Sciences
                Physical Anthropology
                People and Places
                Population Groupings
                Educational Status
                Undergraduates
                Custom metadata
                All landmark data files are available from Figshare ( https://doi.org/10.6084/m9.figshare.4724767.v1). Three dimensional models can be downloaded from figshare and morphosource.org ( https://doi.org/10.6084/m9.figshare.4989656.v1).

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