Predicting 3D and 2D surface area of corals from simple field measurements

Background:
This study presents morphotaxon-specific conversion metrics to estimate total 3D surface area and projected 2D surface area of coral colonies from simple field measurements of colony maximum diameter. Underwater photogrammetry techniques were used to quantify surface area and estimate conversion metrics. This study presents a highly resolved and efficient method for obtaining critical surface area assessments of corals for any scale of study, including assessments of biotic surface area, tissue biomass, calcification rates, colony growth and reef restoration monitoring.
This data set contains:
1 MS Excel file (.xlsx) (also available in .ods) containing data on 159 coral colonies modelled during this study. Data on 'field measurement' and 'genus' for each colony were collected in the field by identifying corals to genus in situ and measuring each colony's maximum diameter using a tape measurement. Associated '2D surface area' and '3D surface area' data was extracted after 3D photogrammetry models were built (structure from motion photogrammetry) in Agisoft Metashape software and surface area data was extracted using Tools. This raw data was later analysed in R to produce conversion metrics, full details are described in the manuscript.
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Software/equipment used to create/collect the data: Coral colonies were measured in situ with tape measure to collect 'Field measurement'. Corals were identified to taxa and later grouped by 'morphotaxa'. Gopro Hero 11 Black cameras were used to collect close-range imagery of individual colonies for 3D modelling, following Structure from motion techniques (SfM) techniques described by Ferrari et al (2017) but using 4k video converted to .jpeg. Custom-built scaling objects (Agisoft Metashape coded targets, 12bit, inverted, 20% of full size, target centres 60 mm apart) were incorporated into the scene. 
Software/equipment used to manipulate/analyse the data: Agisoft Metashape v 1.7.6 software was used for processing of videos and model building. Models were cropped to remove all extraneous mesh. 2D and 3D surface area metrics of the coral colonies were extracted from model software using Tools.All statistical models were performed in R version 4.3.1 42 via the ‘brms’ package. Other R packages used in this project include: 'emmeans' package, 'tidybayes' package, 'DHARMa' package.

研究背景：
本研究提出了针对特定形态分类单元（morphotaxon）的转换参数，可通过测量珊瑚群体最大直径的简易野外手段，估算珊瑚群体的总三维表面积与投影二维表面积。本研究采用水下摄影测量技术量化表面积并推导转换参数，为任意尺度的珊瑚研究提供了高精准、高效的关键表面积评估方法，涵盖生物表面积、组织生物量、钙化速率、群体生长及珊瑚礁修复监测等相关评估场景。

本数据集包含：
1份Microsoft Excel（.xlsx）格式文件（同时提供.ods格式版本），收录了本研究中完成建模的159个珊瑚群体的相关数据。每个珊瑚群体的「野外测量数据」与「属级分类数据」均通过野外原位鉴定珊瑚至属级、并用卷尺测量其最大直径的方式采集；配套的「二维表面积」与「三维表面积」数据则通过以下流程获取：先采用运动恢复结构（Structure from Motion，SfM）摄影测量技术，在Agisoft Metashape软件中构建三维摄影测量模型，再通过软件内置工具提取表面积数据。后续通过R语言对该原始数据进行分析以生成转换参数，完整细节已在论文手稿中详述。

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数据采集与构建所用软件/设备：
采用卷尺原位测量珊瑚群体以获取「野外测量」数据；珊瑚先被鉴定至类群水平，后续再按「形态分类单元」进行分组。使用GoPro Hero 11 Black相机采集单个珊瑚群体的近景影像用于三维建模，参照Ferrari等人（2017）提出的运动恢复结构技术流程，将采集的4K视频转换为.jpeg格式影像后使用。拍摄场景中纳入了自定义尺度参照物：Agisoft Metashape编码标记点，参数为12位色、反色显示、尺寸为标准尺寸的20%、标记点中心间距为60mm。

数据处理与分析所用软件/设备：
使用Agisoft Metashape v1.7.6软件完成视频处理与模型构建；对模型进行裁剪以移除所有多余网格；通过软件内置工具提取珊瑚群体的二维与三维表面积参数。所有统计模型均通过R 4.3.1版本中的‘brms’包完成，本项目使用的其他R包包括：‘emmeans’包、‘tidybayes’包及‘DHARMa’包。