Digital Morphology: Final Frontier

Abstract

Morphology is central to biological anthropology and its allied fields of anatomical sciences, forensics and other related disciplines. Many biological anthropology students have their first real foray into the discipline after completing a course in osteology, craniometry or vertebrate morphology. Unfortunately, the natural history collections that support this type of research and training haven't been growing. Many countries have strict rules about natural history specimen collections, and these collections seem to be concentrated in a few developed countries, regardless of where the specimens are collected from. Thus, access to comparative material can be problematic, where such collections are not readily available. Even in the case of availability of such collections, as the prolonged pandemic showed us, access to them can be severely restricted due circumstances. Luckily, a new field, Digital Morphology, has been emerging in the last decade, changing the landscape of specimen-based research and training. The concerted 2D and 3D digitization efforts, emergence of aggregate specimen repositories, and availability of comprehensive open-source software tools (such as 3D Slicer) to utilize these resources conveniently is causing a transformation in study of quantitative and comparative morphology. In this brief review, I will focus explicitly on the 3D Slicer ecosystem and how it can be leveraged as part of a curriculum or a research program in digital morphology. In a nutshell, the primary differentiator of the 3D Slicer is not that it is just free, but it is open-source and extensible, making access to such digital data more equitable for everyone. I will particularly focus on SlicerMorph extension of the 3D Slicer, which facilitates 3D geometric morphometric data collection and analysis within the Slicer ecosystem, so all the step of digital morphology workflow from import to visualization to data collection to visualization of morphospace can be achieved in a single, well-documented environment.

Keywords

• digital morphology
• quantitative morphology
• geometric morphometrics
• 3D imaging
• segmentation
• visualization
• Digital morphology
• Quantitative morphology
• Geometric morphometrics
• 3D imaging
• Segmentation
• Visualization

Digital Morphology: The Final Frontier

Abstract

Morphology is central to biological anthropology and its allied fields of anatomical sciences, forensics, and other related disciplines. Many biological anthropology students have their first real foray into the discipline after completing a course in osteology, craniometry, or vertebrate morphology. Unfortunately, the natural history collections that support this type of research and training have not grown. Many countries have strict rules about natural history specimen collections, and these collections seem to be concentrated in a few developed countries, regardless of where the specimens had been collected. Thus, access to comparative material can be problematic where such collections are not readily available. Even if collections are available, accessing them can be severely restricted due to external circumstances, as the prolonged pandemic has shown. Luckily, digital morphology has emerged over the last decade as a new field that stands to change the landscape of specimenbased research and training. Concerted 2D and 3D digitization efforts, the emergence of online aggregate specimen repositories, and availability of comprehensive open-source software tools (such as 3D Slicer) for utilizing these resources has conveniently transformed the field of quantitative and comparative morphology. In this brief review, I will focus explicitly on the 3D Slicer ecosystem and how it can be leveraged as part of a curriculum or research program on digital morphology. In a nutshell, the primary differentiator of the 3D Slicer is not that it is just free but that it is open-source and extensible, making access to digital data more equitable for everyone. I will particularly focus on the 3D Slicer’s SlicerMorph extension, which facilitates 3D geometric morphometric data collection and analysis within the Slicer ecosystem, so all the steps in the digital morphology workflow from import, visualization, and data collection to visualizing the morpho-space can be achieved in a single, well-documented environment.

Keywords

• Digital morphology
• Quantitative morphology
• Geometric morphometrics
• 3D imaging
• Segmentation
• Visualization

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