This readme.txt file was generated on 20240506 by Dorothy D Sweet ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Genomes to Fields Initiative Flight Data - Missouri C5B 2020 - Part 2 2. Author Information Principal Investigator Contact Information Name: Dorothy D Sweet Institution: University of Minnesota Address: 1991 Upper Buford Circle Saint Paul, MN 55108 Email: kirsc168@umn.edu ORCID: 0000-0002-9614-5436 Associate or Co-investigator Contact Information Name: Candice N Hirsch Institution: University of Minnesota Address: 1991 Upper Buford Circle Saint Paul, MN 55108 Email: cnhirsch@umn.edu ORCID: 0000-0002-8833-3023 Associate or Co-investigator Contact Information Name: Cory D Hirsch Institution: University of Minnesota Address: 1991 Upper Buford Circle Saint Paul, MN 55108 Email: cdhirsch@umn.edu ORCID: 0000-0002-3409-758X Associate or Co-investigator Contact Information Name: Sherry A Flint-Garcia Institution: University of Missouri Address: 301 Curtis Hall Columbia, MO 65211-7400 Email: flint-garcias@missouri.edu ORCID: 0000-0003-4156-5318 Associate or Co-investigator Contact Information Name: Jacob D Washburn Institution: University of Missouri USDA-ARS Address: 302-A Curtis Hall Columbia, MO 65211-7400 Email: Jacob.Washburn@usda.gov ORCID: 0000-0003-0185-7105 3. Date published or finalized for release: 20240515 4. Date of data collection (single date, range, approximate date): 20200617 - 20200914 5. Geographic location of data collection (where was data collected?): University of Missouri 6. Information about funding sources that supported the collection of the data: 7. Overview of the data (abstract): This dataset (DRUM 6 of 8) is a subset of the flight data collected through the Genomes to Fields Initiative in 2020 and 2021. In conjunction with equivalent datasets on similar material at alternate locations, this data provides a valuable resource for evaluating the performance and stability of hybrid maize across many environments. Many flights throughout the growing season were conducted at these locations (Delaware, Minnesota, Missouri, Nebraska, and Texas) and this dataset includes the orthomosaics, digital elevation models, plot shapefiles, and extracted plant height values for each of those flights following the pipeline from Anderson, Steven L., II, Seth C. Murray, Lonesome Malambo, Colby Ratcliff, Sorin Popescu, Dale Cope, Anjin Chang, Jinha Jung, and J. Alex Thomasson. 2019. “Prediction of Maize Grain Yield before Maturity Using Improved Temporal Height Estimates of Unmanned Aerial Systems.” The Plant Phenome Journal 2 (1): 1–15.. This maize experiment consisted of over 1000 maize hybrids grown in partial replication across 8 environments in 2 years. A set of common hybrids were grown in every location in order to establish a connection between environments. Within the partially replicated set, hybrids were produced by the cross of double haploids derived from the WI-SS-MAGIC population to the inbred testers PHK76, PHP02, and PHZ51 with the tester choice depending on the relative maturity zone of the location. For this location (Missouri 2020) all testers were used. A modified randomized complete block design was used for testing. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. The first part of this dataset Genomes to Fields Initiative Flight Data - Missouri C5B 2020 Part 1 is available at https://doi.org/10.13020/1ek6-jw34 3. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: YYYYMMDD-G2F-Missouri-C5A-RGB-DEMs.zip Short description: zipped folder containing Digital Elevation Models (DEMs) for the flight Folders contain: YYYYMMDD_m2pro_BradC5a.laz YYYYMMDD_m2pro_BradC5a_sort.laz YYYYMMDD_m2pro_BradC5a_sort_NREM.las YYYYMMDD_m2pro_BradC5a_sort_NREM_GRND.las YYYYMMDD_m2pro_BradC5a_sort_NREM_GRND_KP.laz YYYYMMDD_m2pro_BradC5a_sort_NREM_GRND_KP_BARE.las YYYYMMDD_m2pro_BradC5a_sort_NREM_GRND_KP_BARE_ASC.asc YYYYMMDD_m2pro_BradC5a_sort_NREM_GRND_KP_BARE_ASC_HGT.las YYYYMMDD_m2pro_BradC5a_sort_NREM_GRND_KP_BARE_DTM.dtm laz_[individual plot identifier].las (844 files) Projection: WGS 1984 UTM Zone 15N, EPSG 32615 2. Relationship between files: YYYYMMDD-G2F-Missouri-C5A-RGB-DEMs.zip are compressed formats of the digital elevation models, products of the structure from motion process of extracting plant height from 2D RGB images. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Various platforms were used for image collection with each location using their own UAV and camera combination. Guidelines for a standard operating procedure were distributed and followed by each group with standards for weather, camera settings, overlap percentages, and image resolution. Weather:Flights on cloudless, sunny days between 9 A.M and 4 P.M; Camera Settings: ISO: 100 or 200; Exposure time: < 1/1000; Aperture: f 2 to 4; Image Overlap: 70% overlap early in the season, 80% overlap after canopy fills out; and Image Resolution: Ground Sampling Distance <= 0.94 cm/pixel (0.37 in/pixel). Flights were intended to be collected at least once a week throughout the growing season until flowering. 2. Methods for processing the data: UAV images were processed following the protocol from Anderson et al. (2019). In short, structure from motion (SfM) photogrammetry algorithms from either Agisoft Software (Agisoft PhotoScan Professional, (Agisoft L L C 2019)) or Pix4Dmapper (PIX4Dmapper ) were used to identify common features (tie points) across images, triangulate, and adjust distortion to generate dense 3D point clouds, digital surface models, and orthomosaic images. Ground control points were placed throughout the study area to ensure correct scale, orientation, and geographic location. A processing pipeline using R/UAStools::plotshpcreate (Anderson ) was used to construct ESRI shapefiles (.shp) of individual research plots for plot extraction using a data frame containing the experimental design, plot dimensions, and unique plot IDs. After the shapefile is visually overlaid on the orthomosaics, some manual adjustment is needed due to subtle variances in the rows. Point clouds were clipped to the trial level and point anomalies above or below the point cloud were manually removed using CloudCompare v2.10 (Girardeau-Montaut ) and a custom batch script was run using executable functions from LAStools (Isenburg 2012; LAStools 220107 2022) and FUSION/LDV (McGaughey 2012) software (https://github.com/andersst91/UAS_Height_Pipeline) to sort data points, remove additional erroneous points, identify ground points, identify key points for digital terrain modeling (DTM), and construct the DTM. The noise-filtered point cloud was adjusted to aboveground height using the DTM and points below the DEM were removed. The plot-level ESRI shapefile was then used to clip individual plot point clouds and estimate height. 3. Instrument- or software-specific information needed to interpret the data: R is needed to visualize and extract data, but the raw data is also present. 4. Standards and calibration information, if appropriate: Ground targets (different for each location) were placed around the border of the area of interest for use as ground control points (GCPs) 5. Environmental/experimental conditions: Weather information including daily minimum and maximum temperatures (˚C) and daily total precipitation (mm.) were collected from WatchDog Weather Stations at each location. 6. Describe any quality-assurance procedures performed on the data: Quality control filtering included the removal of phenotypic records with missing data in terminal plant height, days to anthesis, days to silking, or grain yield and plots with a grain yield of more than 500 bu/acre. Plots were also removed based on stand count, stalk lodging, and root lodging if less than 30 percent of the plot germinated or more than 70 percent of the stand count lodged. Further quality control based on the temporal plant height removed plots with no growth throughout the season as well as plots with too many large dips and peaks in the growth rate throughout the season with a dip being a decrease of more than 20 percent and a peak being an increase of more than 20 percent. Lastly, whole flight days were removed based on visual inspection of the variation of height across the field for that day with some flights showing irregular, unexplainable patterns across the field. 7. People involved with sample collection, processing, analysis and/or submission: Dorothy Sweet, Alper Adak, Mustafa Arik, Jose Varela, Aaron DeSalvio, Seth Murray, Sherry Flint-Garcia, Jacob Washburn, Cory Hirsch, Candice Hirsch