A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry

1.Substrate complexity is an essential metric of reef health and a strong predictor of several ecological
processes connected to the reef, including disturbance, resilience and associated community abundance and
diversity.
2. Underwater SfM photogrammetry has been growing rapidly in use over the last five years due to
advances in computing power, reduced costs of underwater digital cameras, and a push for reproducible
data. This has led to the adaptation of an originally terrestrial survey technique into the marine realm,
which can now be applied at the habitat scale.
3. This technique allows researchers to make detailed 3D reconstructions of reef surfaces for morphometric
analysis of reef physical structural and large-scale image-mosaic mapping. SfM is useful for both reef-scale
and colony-scale assessments, where visual or acoustic methods are impractical or not sufficiently detailed.
4. Here we provide a protocol for the collection, analysis and display of 3D reef data, focussing on largescale habitat assessments of coral reefs using primarily open-source software. We further suggest
applications for other underwater environments and scales of assessment, and hope this standardised
protocol will help researchers apply this technology and inspire new avenues of ecological research.