Barro Colorado whole-island aerial photogrammetry products for 2018-2023.

Title: Barro Colorado whole-island aerial photogrammetry products for 2018-2023Authors: Milton García, Vicente Vásquez, and Helene C. Muller-LandauData citation and usePlease cite this dataset as follows:Garcia, M., V. Vásquez, and H. C. Muller-Landau (2023). Barro Colorado whole-island aerial photogrammetry products for 2018-2023. (Version 4). Smithsonian Tropical Research Institute. https://doi.org/10.25573/data.24757284This data is licensed as CC BY 4.0 and is thus freely available for reuse with proper citation. We ask that data users share any resulting publications, preprints, associated analysis code, and derived data products with us by emailing [e-mail]. We are open to contributing our expert knowledge of the study site and datasets to projects that use these data; please direct queries regarding potential collaboration to Helene Muller-Landau, [e-mail] that this dataset is part of a collection of Panama UAV data on Smithsonian Figshare, which can be viewed at https://smithsonian.figshare.com/projects/Panama_Forest_Landscapes_UAV/115572Additional information about this research can be found at the Muller-Landau lab website at https://hmullerlandau.com/Data DescriptionThis dataset is part of a larger initiative monitoring forests in Panama using drones (unoccupied aerial vehicles), an initiative led by Dr. Helene Muller-Landau at the Smithsonian Tropical Research Institute. As part of this initiative, we have been collecting repeat imagery of all 1543 ha of Barro Colorado Island (BCI), Panama, since June 2015 (see Cushman et al. 2022a for data products for 2015, 2018, and 2020). The dataset published here encompasses a total of 8 flight missions between June 2018 and June 2023, including in June or July of every year, and additional missions in February and March 2023. The June-July missions were timed to capture the flowering of the canopy emergent tree species Dipteryx oleifera; the February and March missions were timed to capture flowering of the canopy tree Jacaranda copaia. Dipteryx flowers are purplish pink, and Jacaranda flowers are bluish purple.Flights were conducted using an eBee senseFly drone and a S.O.D.A camera having a resolution of 20 megapixels, at a fixed elevation of 601 meters above sea level, and thus 430-575 m above ground, and ~390-575 m above the top of the canopy (ground elevation ranges from 26 to 171 m, and canopy height ranges from 0 to 55 m). Flights were conducted with lateral overlap of 77% and along-path overlap of 77%, which translated to 170 m between flight lines and 113 m between photos along a flight path.The drone imagery was processed independently for each date using Agisoft Metashape Pro 2.0 Python API (Agisoft LLC), employing a standardized workflow (Vasquez 2023). Key parameters for this processing included highest setting for photo alignment, medium setting for point cloud construction, and aggressive point filtering; for additional details, see Vasquez (2023).The dataset comprises the following for each flight mission:• Orthomosaic: an orthorectified image with three bands and an empty alpha band in .tif format.• DSM: a digital surface model with a single band in .tif format.• Pointcloud: in ply file extension and with coordinates reference system UTM 17 N system (EPSG:32617).• Processing report: containing all processing parameters utilized in Agisoft Metashape Pro 2.0.Note that these data products have NOT been aligned across missions and contain substantial errors of alignment. Cushman et al. (2022b) employed tiling and iterative closest point algorithms to align the point clouds for 2015, 2018, and 2020 to 2009 airborne lidar data, create associated digital surface models, and then differentiate these to quantify canopy disturbance patterns. Her original R code is available at Cushman et al. (2022a); it is based on a number of packages that have since been retired. An updated version of this code is available on GitHub at https://github.com/PanamaForestGEO/DroneCodeBCIwide/tree/main/scripts.Metadata:Detailed metadata on the products and the raw images is provided in the comma separated values (.csv) files. The data products have not been altered and maintain all the metadata as they were exported from Agisoft Metashape 2.0.Orthomosaics• N-S extension: 40806 px - 46806 px• E-W extension: 45679 px - 48506 px• Bands: 4• Data type: Unsigned integer 8 bit• Cell size x: 0.138498 m - 0.143903 m• Cell size y: 0.138498 m - 0.143903 m• Format: GeoTIFF• Coordinate reference system: UTM 17 N, EPSG:32617• No data value: None• Bottom left corner x coordinate: 623278.3334646526 - 623664.4922428882• Bottom left corner y coordinate: 1015131.5292435415 - 1015660.597072851DSM’s• N-S extension: 10202 px - 11702 px• E-W extension: 11420 px - 13548 px• Bands: 1• Data type: Float 32 bit• Cell size x: 0.553992 m - 0.6 m• Cell size y: 0.553992 m - 0.6 m• Format: GeoTIFF• Coordinate reference system: UTM 17 N, EPSG:32617• No data value: -32767• Bottom left corner x coordinate: 622774.186991835 - 623664.492242888• Bottom left corner y coordinate: 1015131.57561176 - 1015754.64117185Point clouds• Number of points: 116325422 points - 130890311 points• Colors: RGB normalized 0-1.• Coordinate reference system: UTM 17 N, EPSG:32617.• Format: Polygon File Format (Stanford Triangle Format). NotesThe BCI_whole_2018_08_25_EBEE_dipteryx mission encompassed three different dates: 2018_06_14, 2018_06_21, and 2018_08_25. Distinct flight lines were conducted on each date, and the products published here are a composite of images from these flights.The BCI_whole_2019_06_27_EBEE_dipteryx mission features raw images taken on 2019_06_19, 2019_06_22, and 2019_06_24. However, according to the pilot's notes, the flight itself occurred in 2019_06_27, hence the naming convention for the flight.The BCI_whole_2023_03_18_EBEE_jacaranda mission's raw image dates spanned 2023_03_16, 2023_03_18, and 2023_03_18. In line with standard practice, we name the data product after the last date of data collection.File naming schemeWe provide a .zip file for each mission with the following naming convention: Macrosite_site_year_month_day_drone_missiontype. Each orthomosaic follow the naming convention Macrosite_site_year_month_day_orthomosaic_missiontype. Each point cloud follow the convention Macrosite_site_year_month_day_cloud_missiontype. Each DSM follow the convention Macrosite_site_year_month_day_dsm_missiontype.Author contributionsMG led the drone imagery collection. VV processed the drone imagery. HCM conceived the study, wrote the grant proposals to obtain funding, and supervised the research. VV and HCM wrote the data description.AcknowledgmentsMilton Solano assisted with drone data management. Pablo Ramos, Paulino Villareal, and others assisted with drone data collection. Funding and/or in-kind support was provided by the Smithsonian Institution Scholarly Studies grant program (HCM), the Smithsonian Institution Equipment fund (HCM), Smithsonian ForestGEO, and the Smithsonian Tropical Research Institute.ReferencesAgisoft LLC. (n.d.). Metashape Python Reference Version (release 2.0.4). agisoft.com. Agisoft LLC. https://www.agisoft.com/pdf/metashape_python_api_2_0_4.pdf.Cushman, K. C., H. C. Muller-Landau, M. Detto, and M. Garcia. 2022a. Datasets for “Soils and topography control natural disturbance rates and thereby forest structure in a lowland tropical landscape". Smithsonian Tropical Research Institute. Smithsonian Figshare. https://doi.org/10.25573/data.17102600.v1.Cushman, K. C., M. Detto, M. García, and H. C. Muller-Landau. 2022b. Soils and topography control natural disturbance rates and thereby forest structure in a lowland tropical landscape. Ecology Letters, 25: 1126-1138. https://doi.org/https://doi.org/10.1111/ele.13978Vasquez, V. (2023). P-polycephalum/ForestLandscapes: v0.0.1-beta (v0.0.1-beta). Zenodo. https://doi.org/10.5281/zenodo.10328609# 标题：2018-2023年巴拿马巴罗科罗拉多全岛航空摄影测量产品 ## 作者：Milton García、Vicente Vásquez、Helene C. Muller-Landau ## 数据引用与使用规范 请按以下格式引用本数据集： Garcia, M., V. Vásquez, 和 H. C. Muller-Landau (2023). 2018-2023年巴拿马巴罗科罗拉多全岛航空摄影测量产品. (版本4). 史密森尼热带研究所. https://doi.org/10.25573/data.24757284 本数据集采用CC BY 4.0许可协议发布，允许在正确引用的前提下自由复用。我们恳请数据使用者将由此产生的学术论文、预印本、相关分析代码及衍生数据产品通过邮件发送至[e-mail]与我们共享。我们乐于为使用本数据集的项目提供研究样地与数据集的专业知识支持；有关潜在合作的咨询请联系Helene Muller-Landau，邮箱：[e-mail]。 请注意，本数据集是史密森尼Figshare平台上巴拿马无人机数据合集的一部分，可通过以下链接查看：https://smithsonian.figshare.com/projects/Panama_Forest_Landscapes_UAV/115572 更多研究相关信息可访问Muller-Landau实验室官网：https://hmullerlandau.com ## 数据集描述 本数据集是史密森尼热带研究所Helene Muller-Landau博士主导的巴拿马森林无人机（unoccupied aerial vehicles, UAV）监测项目的组成部分。自2015年6月起，团队已对巴拿马巴罗科罗拉多岛（Barro Colorado Island, BCI）全部1543公顷区域开展重复航拍成像（2015、2018、2020年的产品详见Cushman等人2022a）。本次发布的数据集涵盖2018年6月至2023年6月间的8次飞行任务，覆盖每年6月或7月，另包含2023年2月和3月的额外飞行任务。其中6-7月的飞行旨在捕捉冠层上层树种**钟状紫檀（Dipteryx oleifera）**的花期，2-3月的任务则针对冠层树种**蓝花楹（Jacaranda copaia）**的花期。钟状紫檀的花呈粉紫色，蓝花楹的花为蓝紫色。 本次飞行采用eBee senseFly无人机与分辨率为2000万像素的S.O.D.A相机，飞行高度固定为海拔601米，因此距地面高度为430~575米，距冠层顶部高度约390~575米（地面海拔范围26~171米，冠层高度范围0~55米）。飞行旁向重叠度为77%，航向重叠度为77%，航线间距为170米，单航线内照片间距为113米。 团队针对每个飞行日期的影像，采用Agisoft Metashape Pro 2.0 Python API（Agisoft有限责任公司）进行独立处理，执行标准化工作流（Vasquez 2023）。处理的关键参数包括：照片对齐采用最高档位，点云构建采用中等档位，点过滤采用激进模式；详细参数详见Vasquez(2023)。 本数据集包含每次飞行任务对应的以下产品： - 正射影像图（Orthomosaic）：三波段带空白Alpha通道的GeoTIFF格式正射校正影像。 - 数字表面模型（DSM, Digital Surface Model）：单波段GeoTIFF格式数字表面模型。 - 点云（Pointcloud）：PLY格式文件，采用UTM 17 N坐标系（EPSG:32617）。 - 处理报告：包含Agisoft Metashape Pro 2.0中使用的所有处理参数。 ### 重要说明 本数据集的各任务数据未进行跨任务配准，存在显著的配准误差。Cushman等人(2022b)曾采用分块与迭代最近点算法，将2015、2018、2020年的点云配准至2009年的机载激光雷达数据，生成对应的数字表面模型并通过差值量化冠层扰动模式。其原始R代码可参见Cushman等人(2022a)，但该代码依赖的部分包现已停用。更新后的代码可在GitHub获取：https://github.com/PanamaForestGEO/DroneCodeBCIwide/tree/main/scripts。 ## 元数据 产品与原始影像的详细元数据存储于逗号分隔值（.csv）文件中。所有数据产品均未经过修改，完整保留了从Agisoft Metashape 2.0导出时的元数据。 ### 正射影像参数 - 南北延伸范围：40806 px - 46806 px - 东西延伸范围：45679 px - 48506 px - 波段数：4 - 数据类型：无符号8位整数 - 像元尺寸x：0.138498 m - 0.143903 m - 像元尺寸y：0.138498 m - 0.143903 m - 格式：GeoTIFF - 坐标系：UTM 17 N, EPSG:32617 - 无数据值：无 - 左下角x坐标：623278.3334646526 - 623664.4922428882 - 左下角y坐标：1015131.5292435415 - 1015660.597072851 ### 数字表面模型（DSM）参数 - 南北延伸范围：10202 px - 11702 px - 东西延伸范围：11420 px - 13548 px - 波段数：1 - 数据类型：32位浮点型 - 像元尺寸x：0.553992 m - 0.6 m - 像元尺寸y：0.553992 m - 0.6 m - 格式：GeoTIFF - 坐标系：UTM 17 N, EPSG:32617 - 无数据值：-32767 - 左下角x坐标：622774.186991835 - 623664.492242888 - 左下角y坐标：1015131.57561176 - 1015754.64117185 ### 点云参数 - 点数：116325422 - 130890311 - 颜色：RGB归一化至0~1区间 - 坐标系：UTM 17 N, EPSG:32617 - 格式：多边形文件格式（斯坦福三角格式，PLY） ## 特殊任务说明 1. `BCI_whole_2018_08_25_EBEE_dipteryx`任务包含2018年6月14日、6月21日和8月25日三次飞行数据，每次飞行均采用独立航线，本次发布的产品为三次飞行影像的合成结果。 2. `BCI_whole_2019_06_27_EBEE_dipteryx`任务的原始影像拍摄于2019年6月19日、22日和24日，但根据飞行日志，实际飞行执行于2019年6月27日，因此采用该日期作为任务命名。 3. `BCI_whole_2023_03_18_EBEE_jacaranda`任务的原始影像拍摄日期为2023年3月16日、3月18日和3月18日，按照行业惯例，以最后一次数据采集日期作为产品命名依据。 ## 文件命名规则 每个飞行任务对应一个.zip压缩包，命名格式为：`Macrosite_site_year_month_day_drone_missiontype`。正射影像的命名格式为：`Macrosite_site_year_month_day_orthomosaic_missiontype`；点云文件命名格式为：`Macrosite_site_year_month_day_cloud_missiontype`；DSM文件命名格式为：`Macrosite_site_year_month_day_dsm_missiontype`。 ## 作者贡献 MG负责无人机影像采集工作，VV负责无人机影像处理工作，HCM构思研究设计、申请资助经费并监督整个研究项目，VV和HCM共同撰写本数据集描述。 ## 致谢 Milton Solano协助无人机数据管理工作，Pablo Ramos、Paulino Villareal及其他人员协助无人机数据采集。本研究获得史密森尼学会学术研究资助计划（HCM）、史密森尼学会设备基金（HCM）、史密森尼森林动态样地计划（ForestGEO）以及史密森尼热带研究所的资助或实物支持。 ## 参考文献 1. Agisoft LLC. (n.d.). Metashape Python Reference Version (release 2.0.4). agisoft.com. https://www.agisoft.com/pdf/metashape_python_api_2_0_4.pdf. 2. Cushman, K. C., H. C. Muller-Landau, M. Detto, 和 M. Garcia. 2022a. 题为"Soils and topography control natural disturbance rates and thereby forest structure in a lowland tropical landscape"的数据集. 史密森尼热带研究所, 史密森尼Figshare. https://doi.org/10.25573/data.17102600.v1. 3. Cushman, K. C., M. Detto, M. García, 和 H. C. Muller-Landau. 2022b. 土壤与地形调控低地热带景观的自然干扰速率并进而影响森林结构. Ecology Letters, 25: 1126-1138. https://doi.org/10.1111/ele.13978 4. Vasquez, V. (2023). P-polycephalum/ForestLandscapes: v0.0.1-beta (v0.0.1-beta). Zenodo. https://doi.org/10.5281/zenodo.10328609