Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster

, ,
1 Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
2 School of Natural Resources and Environment, University of Florida, Gainesville, Florida, United States
3 Geomatics Program, Department of Fisheries & Aquatic Sciences, University of Florida, Gainesville, Florida, United States of America
DOI
10.7287/peerj.preprints.27596v1
Published
Accepted
Subject Areas
Biophysics, Conservation Biology, Ecology
Keywords
Structure-from-Motion photogrammetry, oyster cluster, geomorphometry, interstitial spaces, structural complexity
Copyright
© 2019 Kim et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Kim K, Lecours V, C. Frederick P. 2019. Using 3D micro-geomorphometry to quantify interstitial spaces of an oyster cluster. PeerJ Preprints 7:e27596v1

Abstract

In ecology, it is assumed that the characteristics (e.g. shape, size) of interstitial spaces found in a variety of habitats affect the colonization of species, species interactions, and species composition. However, those characteristics have traditionally been difficult to measure due to technological limitations. In this study, we used the Structure-from-Motion (SfM) photogrammetry technique to measure the physical characteristics of interstitial spaces in a small oyster cluster. The point cloud (and mesh) of the oyster cluster derived from SfM photogrammetry was found to be accurate enough (mean error of 0.654 mm) to conduct 3D geomorphometric analyses. We present an example of measures of curvature, roughness, interstitial volume, surface area, and openness for three 3D interstitial spaces. The interpretation of those measures enabled establishing which interstitial spaces were the most likely to be used as a shelter for an average crab. Those spaces are characterized by smaller openness and higher roughness and curvature measures. This initial quantitative 3D characterization of an oyster cluster is the first step in establishing empirical relationships between structural complexity of biological structures like oyster clusters and their ecological role for instance in predator-prey interactions. Overall, this study demonstrates the feasibility of combining SfM photogrammetry with geomorphometry for fine-scale ecological studies.

Author Comment

Part of the Geomorphometry 2018 collection.

Supplemental Information

Mesh of three interstitial spaces used in analyses

These are mesh (*obj) files. You can import them in CloudCompare and subsample to create point clouds. You can then conduct morphological analyses.

DOI: 10.7287/peerj.preprints.27596v1/supp-1