3D shape analysis for morphometrics - Based on structured light optical scanning

Geometric morphometrics is a powerful approach to capture and quantify morphological shape variation. Morphological differences, for example, can be used to distinguish between distinct species. To analyse morphology, one has to describe shape, which is commonly done by means of landmarks. All over the world, natural history museums are digitizing their collections of biological objects, as having digital 3D models of physical specimens comes with substantial benefits.

In recent times, collecting landmarks digitally from a 3D scanned model has become a viable and widely accepted practice. This PhD thesis focuses on investigating 3D structured light scanning-based methods for geometric morphometrics. Assessing and quantifying multiple sources of measurement error was an integral part of my PhD project, since measurement error can, for example, obscure the biological signal in geometric morphometric analyses.

At the same time, the goal of this PhD project was to use digital landmarks to address a relevant biological question. We conducted a case study on grey seals together with the Natural History Museum of Denmark, Globe Institute and Aarhus University, which involved the digitization of grey seal (Halichoerus grypus) skull collections.

This thesis is composed of an introductory part, and the research contributions consisting of three published datasets on grey seal skull specimens, three journal papers (Papers A, B and C), and a technical report. Our first contribution was the creation of 116 3D surface models of grey seal skulls using a 3D structure light scanning setup.

These 3D models provided the foundation for the collection of different sets of landmark data used for the analyses in Papers A, B and C. However, the digitization of physical specimens is introducing measurement error. Thus, we investigated whether landmarks measured on 3D surface models provide an equivalent or better alternative to landmarks measured directly on the biological specimens by analysing measurement error due to various sources (Paper A).

Another source of measurement error comes from using a desktop software to digitally place landmarks, which is limited due to the flat 2D display. This was leading to the next investigation on whether using virtual reality provides an equivalent or better alternative to placing landmarks on the computer screen.

We analysed both performance and measurement error due to multiple sources (Paper B). Our findings are validating the use of 3D surface models for answering shape-related biological questions by means of geometric morphometrics, and are revealing that virtual reality is in fact a promising alternative to desktop annotation.

Together with our biologist collaborators, we investigated what the analysis of variation in grey seal skull shape can contribute to our understanding of grey seal foraging adaptations and current subspecies and populations delineations (Paper C). While the data does support the existence of at least three different grey seal populations, our geometric morphometric analyses did not warrant subspecies status for any of these.

In conclusion, this thesis has demonstrated that 3D structured light surface scanning can be used to obtain accurate digital 3D models of bone specimens, and that geometric morphometric analyses based on landmarks collected on digital specimens will give the same results as when collected on physical specimens.

However, the use of digital specimens allows for making use of the rich shape information contained in the 3D models. The findings in this PhD thesis open a plethora of new usage of digital specimens. Working in a 3D virtual environment, for example, gives the option to interact with a specimen as if you were holding it in your hand. used to obtain accurate digital 3D models of bone specimens, and that geometric morphometric analyses based on landmarks collected on digital specimens will give the same results as when collected on physical specimens.

However, the use of digital specimens allows for making use of the rich shape information contained in the 3D models. The findings in this PhD thesis open a plethora of new usage of digital specimens. Working in a 3D virtual environment, for example, gives the option to interact with a specimen as if you were holding it in your hand.