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., Vasquez, V., & Muller-Landau, H. C. (2023).Barro Colorado whole-island aerial photogrammetry products for 2018-2023. Smithsonian Tropical Research Institute. Smithsonian Figshare. 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 mbetween photos along a flight path. Coverage of the entire island required ~XX flights in each mission, which were typically spread over 2-3 days.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 format 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 on 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