Dataset Information

Rapid automated landmarking for morphometric analysis of three-dimensional facial scans.

ABSTRACT: Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We validated the method using both direct comparison to manual landmarking on the same individuals and also analyses of the variation patterns and outlier patterns in a large dataset of automated and manual landmark data. Direct comparison of manual and automated landmarks reveals that automated landmark data are less variable, but more highly integrated and reproducible. Automated data produce covariation structure that closely resembles that of manual landmarks. We further find that while our method does produce some landmarking errors, they tend to be readily detectable and can be fixed by adjusting parameters used in the registration and control-point steps. Data generated using the method described here have been successfully used to study the genomic architecture of facial shape in two different genome-wide association studies of facial shape.

SUBMITTER: Li M

PROVIDER: S-EPMC5345630 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Rapid automated landmarking for morphometric analysis of three-dimensional facial scans.

Li Mao M Cole Joanne B JB Manyama Mange M Larson Jacinda R JR Liberton Denise K DK Riccardi Sheri L SL Ferrara Tracey M TM Santorico Stephanie A SA Bannister Jordan J JJ Forkert Nils D ND Spritz Richard A RA Mio Washington W Hallgrimsson Benedikt B

Journal of anatomy 20170112 4

Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We valida ...[more]

PMID: 28078731

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Project description:Landmark-based geometric morphometrics has emerged as an essential discipline for the quantitative analysis of size and shape in ecology and evolution. With the ever-increasing density of digitized landmarks, the possible development of a fully automated method of landmark placement has attracted considerable attention. Despite the recent progress in image registration techniques, which could provide a pathway to automation, three-dimensional (3D) morphometric data are still mainly gathered by trained experts. For the most part, the large infrastructure requirements necessary to perform image-based registration, together with its system specificity and its overall speed, have prevented its wide dissemination.Here, we propose and implement a general and lightweight point cloud-based approach to automatically collect high-dimensional landmark data in 3D surfaces (Automated Landmarking through Point cloud Alignment and Correspondence Analysis). Our framework possesses several advantages compared with image-based approaches. First, it presents comparable landmarking accuracy, despite relying on a single, random reference specimen and much sparser sampling of the structure's surface. Second, it can be efficiently run on consumer-grade personal computers. Finally, it is general and can be applied at the intraspecific level to any biological structure of interest, regardless of whether anatomical atlases are available.Our validation procedures indicate that the method can recover intraspecific patterns of morphological variation that are largely comparable to those obtained by manual digitization, indicating that the use of an automated landmarking approach should not result in different conclusions regarding the nature of multivariate patterns of morphological variation.The proposed point cloud-based approach has the potential to increase the scale and reproducibility of morphometrics research. To allow ALPACA to be used out-of-the-box by users with no prior programming experience, we implemented it as a SlicerMorph module. SlicerMorph is an extension that enables geometric morphometrics data collection and 3D specimen analysis within the open-source 3D Slicer biomedical visualization ecosystem. We expect that convenient access to this platform will make ALPACA broadly applicable within ecology and evolution.

Project description:In some dentofacial deformity patients, especially patients undergoing surgical orthodontic treatments, Computed Tomography (CT) scans are useful to assess complex asymmetry or to plan orthognathic surgery. This assessment would be made easier for orthodontists and surgeons with a three-dimensional (3D) cephalometric analysis, which would require the localization of landmarks and the construction of reference planes. The objectives of this study were to assess manual landmarking repeatability and reproducibility (R&R) of a set of 3D landmarks and to evaluate R&R of vertical cephalometric measurements using two Frankfort Horizontal (FH) planes as references for horizontal 3D imaging reorientation. Thirty-three landmarks, divided into "conventional", "foraminal" and "dental", were manually located twice by three experienced operators on 20 randomly-selected CT scans of orthognathic surgery patients. R&R confidence intervals (CI) of each landmark in the -x, -y and -z directions were computed according to the ISO 5725 standard. These landmarks were then used to construct 2 FH planes: a conventional FH plane (orbitale left, porion right and left) and a newly proposed FH plane (midinternal acoustic foramen, orbitale right and left). R&R of vertical cephalometric measurements were computed using these 2 FH planes as horizontal references for CT reorientation. Landmarks showing a 95% CI of repeatability and/or reproducibility > 2 mm were found exclusively in the "conventional" landmarks group. Vertical measurements showed excellent R&R (95% CI < 1 mm) with either FH plane as horizontal reference. However, the 2 FH planes were not found to be parallel (absolute angular difference of 2.41°, SD 1.27°). Overall, "dental" and "foraminal" landmarks were more reliable than the "conventional" landmarks. Despite the poor reliability of the landmarks orbitale and porion, the construction of the conventional FH plane provided a reliable horizontal reference for 3D craniofacial CT scan reorientation.

Dataset Information

Rapid automated landmarking for morphometric analysis of three-dimensional facial scans.

Publications

Rapid automated landmarking for morphometric analysis of three-dimensional facial scans.

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