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 Structure from Motion (SfM) photogrammetry has been growing rapidly in use over the last 5 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 structure and perform 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 large‐scale 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 standardized protocol will help researchers apply this technology and inspire new avenues of ecological research.

中文翻译：

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使用运动摄影测量结构对珊瑚礁进行大规模分析的协议

1. 底物的复杂性是珊瑚礁健康的一项重要指标，并且是与珊瑚礁相关的若干生态过程（包括干扰，复原力以及相关的社区丰度和多样性）的有力预测指标。
2. 由于计算能力的提高，水下数码相机成本的降低以及对可复制数据的推动，过去五年来，运动摄影水下结构（SfM）摄影技术一直在迅速增长。这导致原始的地面勘测技术适应了海洋领域，现在可以在栖息地范围内应用。
3. 这项技术使研究人员可以对礁石表面进行详细的3D重建，以对礁石的物理结构进行形态计量分析，并执行大规模的图像马赛克映射。SfM对于珊瑚礁规模和殖民地规模的评估都是有用的，在这种评估中，视觉或听觉方法不可行或不够详细。
4. 在这里，我们提供了一个用于收集，分析和显示3D珊瑚礁数据的协议，着重于主要使用开放源代码软件对珊瑚礁进行的大规模栖息地评估。我们进一步建议将其用于其他水下环境和评估规模，并希望该标准化协议能够帮助研究人员应用该技术并激发生态研究的新途径。