Quantifying Ship Shape in Archaeology: Evaluating 3D Geometric Morphometrics

Dhoop, Thomas; Stark, Sheila; Olaberria, Juan‐Pablo; Whitewright, Julian

doi:10.1111/1095-9270.12413

Cited by 7 publications

(2 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The method has even been employed for analysis of non-anatomical data [54,55]. However, it can still be powerful and preferable in certain monospecific samples [56].…”

Section: Morphometric Data Collectionmentioning

confidence: 99%

SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology

Rolfe¹,

Pieper

Porto³

et al. 2020

Preprint

View full text Add to dashboard Cite

Large scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. MorphoSource currently hosts tens of thousands of 3D scans of eukaryotes. Along with the data from similarly scoped projects such as 10kPhenomes, DigiMorph and many others, soon hundreds of thousands of specimens that represent biodiversity of extinct and extant organisms will be conveniently available to researchers. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyze them.Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration, and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. Another relevant concern is that ultimate derivative data from individual research projects (e.g., 3D models of segmentation) are shared in formats that do not preserve the correct spatial scale of the data.In this paper, we present our effort to tackle challenges biologists face when conducting 3D specimen-based research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python-scriptable open-source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open-access 3D models or import users own 3D volumes, to annotate 3D curve and patch-based landmarks, generate canonical templates, conduct geometric morphometric analyses of 3D organismal form using both landmark-driven and landmark-free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology, and extensive links to the existing tutorials are provided as supplemental material.Our goal is to establish a community of organismal biologists centered around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.

show abstract

“…The method has even been employed for analysis of non-anatomical data [54,55]. However, it can still be powerful and preferable in certain monospecific samples [56].…”

Section: Morphometric Data Collectionmentioning

confidence: 99%

SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology

Rolfe¹,

Pieper

Porto³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…GM analysis has been increasingly used in the natural sciences since the second half of the last century, proving to be a valuable set of statistical tools to better understand morphological variability and evolution within and between species [ 11 , 12 ]. Over the last decades, a vast number of studies have empirically demonstrated the advantages of GM analysis over traditional linear morphometrics beyond biological research, including the study of material culture in archaeology [e.g., 13 , 14 – 16 ]. Today, GM analysis of lithic assemblages has already outgrown its novelty status and many recent research projects make use of this approach to study shape- and form-related techno-functional aspects of tool use and edge resharpening, technological variability, as well as differences between artefact types [see among others: 1 , 9 , 17 , 18 – 37 ].…”

Section: Introductionmentioning

confidence: 99%

Practical and technical aspects for the 3D scanning of lithic artefacts using micro-computed tomography techniques and laser light scanners for subsequent geometric morphometric analysis. Introducing the StyroStone protocol

2022

View full text Add to dashboard Cite

Here, we present a new method to scan a large number of lithic artefacts using three-dimensional scanning technology. Despite the rising use of high-resolution 3D surface scanners in archaeological sciences, no virtual studies have focused on the 3D digitization and analysis of small lithic implements such as bladelets, microblades, and microflakes. This is mostly due to difficulties in creating reliable 3D meshes of these artefacts resulting from several inherent features (i.e., size, translucency, and acute edge angles), which compromise the efficiency of structured light or laser scanners and photogrammetry. Our new protocol StyroStone addresses this problem by proposing a step-by-step procedure relying on the use of micro-computed tomographic technology, which is able to capture the 3D shape of small lithic implements in high detail. We tested a system that enables us to scan hundreds of artefacts together at once within a single scanning session lasting a few hours. As also bigger lithic artefacts (i.e., blades) are present in our sample, this protocol is complemented by a short guide on how to effectively scan such artefacts using a structured light scanner (Artec Space Spider). Furthermore, we estimate the accuracy of our scanning protocol using principal component analysis of 3D Procrustes shape coordinates on a sample of meshes of bladelets obtained with both micro-computed tomography and another scanning device (i.e., Artec Micro). A comprehensive review on the use of 3D geometric morphometrics in lithic analysis and other computer-based approaches is provided in the introductory chapter to show the advantages of improving 3D scanning protocols and increasing the digitization of our prehistoric human heritage.

show abstract