RapidBenthos

Link to 12 3D photogrammetric models and underlying images to replicate the method presented in the publication titled “RapidBenthos – Automated segmentation and multi-view classification of coral reef communities from photogrammetric reconstruction”. These sites were selected to assess the performance of RapidBenthos in different environmental conditions and reef habitats, as they ranged from high visibility offshore reefs to turbid inshore reefs, spanned depths from 5 to 15 meters, and included a range of intra-reefal environments (i.e., reef front, flank, back, and lagoon).

All sites were imaged using a standardized diver-rig photogrammetry workflow described by Gordon et al. (2023). High-resolution benthic images (5686 x 3217 pixels) were captured using two Nikon D850 DSLR cameras with 20 mm Nikkor prime lens shooting at 0.5 second intervals (full camera settings described in (Gordon et al., 2023). Cameras were housed in Nauticam underwater housings with 8-inch dome ports and were mounted on an aluminium rig at a distance of 57 cm between lenses (60 % overlap between adjacent images, Figure 1c). Each site was imaged by a single diver on SCUBA over a period of 10-15 minutes to capture approximately 3,000 photos. Nadiral and oblique imagery was captured at an altitude of approximately 1.5 m using a “lawn-mowing” swim pattern consisting of 5 longitudinal passes and an additional 4-8 perpendicular passes. The swim pattern and speed used ensured a minimum overlap of 80 and 60 % between temporally and spatially adjacent photos, respectively (Figure 1d). Six GPCs were distributed across the depth gradient of the site prior imaging to scale resultant models in X, Y, and Z axes (details provided in(Gordon et al., 2023). Depth was also recorded for each GPC to incorporate bathymetric information into 3D model building.

The RapidBenthos workflow was applyed to each plots, segmenting and calssifying benthic constituents on the orthomosaics. This method resulted in extracting community compostion and colony-level metrics (i.e., colony planar-area and colony frequency). The significance of this research lies in devlopping a workflow that automatically extract community composition information from close-range photogrammetry in any coral reefs environment. We eveluated that our method was 195 time faster than manual segmentation and classification allowing to sustainably scale 3D photogrammetry mointoring, both in replication and size of reefs surveyed compared to manual data extraction.

Due to the large data files, the data can be accessed on request.

提供12个三维摄影测量模型（3D photogrammetric models）及配套原始图像，用于复现发表于《"RapidBenthos——基于摄影测量重建的珊瑚礁群落自动分割与多视图分类"》论文中的研究方法。
本数据集选取了不同环境条件与珊瑚礁生境下的调查区域，用于评估RapidBenthos的模型性能：这些区域涵盖了高能见度远岸礁与高浑浊度近岸礁，水深范围为5至15米，同时包含多种礁内生境（即礁前、礁侧、礁后与泻湖环境）。

所有调查区域均采用Gordon等人（2023）描述的标准化潜水搭载式摄影测量流程进行成像。使用两台搭载20毫米尼克尔定焦镜头的尼康D850数码单反相机，以0.5秒的间隔拍摄高分辨率底栖图像（分辨率为5686×3217像素），完整相机参数详见Gordon等人（2023）的研究。相机被安装于配备8英寸圆顶端口的Nauticam水下防水壳中，并固定于铝制搭载架上，两台镜头间距为57厘米，相邻图像的重叠率为60%（见图1c）。每个调查区域由一名持证水肺潜水员耗时10至15分钟完成成像，拍摄约3000张照片。以约1.5米的拍摄高度，采用“割草式”巡游路径采集天底与斜视角图像：该路径包含5条纵向航线与4至8条横向航线。该巡游路径与行进速度确保了时序相邻与空间相邻图像的最小重叠率分别为80%与60%（见图1d）。在成像前，于调查区域的深度梯度上布设6个地面控制点（Ground Control Points, GPCs），用于对生成的三维模型进行X、Y、Z三轴的尺度校正，详细布设方式详见Gordon等人（2023）的研究。同时记录每个地面控制点的水深，以将水深地形信息纳入三维模型构建流程。

将RapidBenthos流程应用于每个调查样区，对正射镶嵌图中的底栖生物组分进行分割与分类。该方法可提取珊瑚礁群落组成信息以及群体水平的形态指标（即群体平面面积与群体出现频率）。本研究的核心意义在于开发了一套可在任意珊瑚礁环境中，基于近景摄影测量技术自动提取群落组成信息的流程。经评估，本方法的处理速度比人工分割与分类快195倍，相较于人工数据提取方式，可实现三维摄影测量监测在调查样地重复度与礁体规模上的可持续扩展。

由于数据集文件体量较大，用户可通过申请获取该数据。