Creation of accurate 3D models of harbor porpoises (Phocoena phocoena) using 3D photogrammetry

Abstract

Creating accurate 3D models of marine mammals is valuable for assessment of body condition, computational fluids dynamics models of locomotion, and for education. However, the methods for creating 3D models are not well-developed.We used photography and video to create 3D photogrammetry models of harbor porpoises (Phocoena phocoena). We accessed one live adult female (155.5 cm total length), and two dead animals, one juvenile (110 cm total length) and one calf (88 cm total length). We accessed the two dead individuals through a stranding network in Germany, and the live individual through the Fjord and Baelt research center in Denmark. For all porpoises, we used still photographs from handheld cameras, drone video, and synchronized GoPro videos to create 3D photogrammetric models. We used Blender software, and other 3D reconstruction software, to recreate the 3D body meshes, and confirmed the accuracy of each of the 3D body meshes by comparing digital measures on the 3D models to original measures taken on the specimens. We also provide a colored, animated version of the live harbor porpoise for educational purposes. These open-access 3D models can be used to develop methods to study body morphometrics and condition, and to study bioenergetics and locomotion costs.

3D visualization processes for recreating and studying organismal form

“…Indeed, there are exciting new opportunities for combining data from different scanning methods. On the hardware end, dramatic improvements in computers, camera, video, and laser and white-light scanning systems now provide an unparalleled set of tools that can be used to create 3D models (Baqersad et al, 2017;Chiari et al, 2008;Egels and Kasser, 2003;Falkingham, 2012;Irschick et al, 2020aIrschick et al, , 2020bPostma et al, 2015;Szaflik, 2007). Three frequently used techniques are computed tomography (CT) scanning, laser/white-light scanning, and 3D photogrammetry.…”

“…In some cases, a combination of techniques was used to accurately recreate the body shapes of animals. For example, Irschick et al (2020a) included images from an aerial drone and multiple GoPro cameras to create 3D scans of a live harbor porpoise (Phocoena phocoena). As shown in Irschick et al (2020aIrschick et al ( , 2020bIrschick et al ( , 2020c, the 3D reconstructions were very accurate, with error rates overall less than about 1%, once the digital avatar and the original live animal were compared.…”

“…For example, Irschick et al (2020a) included images from an aerial drone and multiple GoPro cameras to create 3D scans of a live harbor porpoise (Phocoena phocoena). As shown in Irschick et al (2020aIrschick et al ( , 2020bIrschick et al ( , 2020c, the 3D reconstructions were very accurate, with error rates overall less than about 1%, once the digital avatar and the original live animal were compared. Like all digital data, 3D photogrammetry models can be conveniently shared in different ways, such as by exporting.OBJ or FBX files, which can be viewed in various Virtual Reality and Augmented Reality software and hardware because of their interest in the general public, the issues of licensing and proper data deposition for researchers are especially germane.…”

Color in motion: Generating 3-dimensional multispectral models to study dynamic visual signals in animals

“…Photogrammetric techniques, specifically Structurefrom-Motion (SfM), can be used to construct a digital 3D model that is faithful to an object's original form by combining multiple 2D images of an object taken from different angles (Chiari et al, 2008;Westoby et al, 2012;Bot and Irschick, 2019;Medina et al, 2020). Photogrammetry has been used to create 3D models from live animals (Chiari et al, 2008;Bot and Irschick, 2019;Irschick et al, 2020Irschick et al, , 2021Brown, 2022) as well as museum specimens (Chiari et al, 2008;Nguyen et al, 2014;Medina et al, 2020) to capture realistic 3D shape and color for the purpose of scientific application. Recently, Medina et al (2020) developed a rapid and cost-effective pipeline for digitizing ornithological museum specimens using 3D photogrammetry.…”

Integrating 3D models with morphometric measurements to improve volumetric estimates in marine mammals

“…Three‐dimensional (3D) models provide a promising tool for representing cetacean body forms more accurately and for estimating body volume (Adamczak et al, 2019). Using morphometric measurements, 3D models can be scaled to represent individual animals while conserving morphology, without relying on approximations from geometric shapes (Adamczak et al, 2019; Irschick et al, 2020). To date, 3D models have been developed from measurements or photographs of deceased animals to examine morphological differences between species, but integrating 3D models with drone‐based photogrammetry could provide a powerful tool for quantifying changes in the body volume and morphology of cetaceans across space and in longitudinal studies.…”