Digital Phenotyping in Plant Breeding: Evaluating Relative Maturity, Stand Count, and Plant Height in Dry Beans via RGB Drone-Based Imagery and Deep Learning Approaches

Abstract

The datasets comprised were collected from the MSU dry bean breeding program during 2020, 2021 and 2022 planting seasons at SVREC and HURON locations. The dataset includes the orthomosaic (.tif) generated using the raw images, plot boundary delimitations (.shp), clipped plots using two image sizes, numpy data, the CNN-LSTM deep learning model, and the ground-truth (GT) notes to predict relative maturity (RM). ############################################################################# /2020/SVREC_Mat: This directory contains subfolders /a._GCPs_coodinates: 1. Gomez_Saginaw.csv Ground Control Points coordinates collected in 2020 at SVREC location /b._Orthomosaics: Temporal flights to track plant maturity 1. Image naming structure: `Date-of-flight _ _ _ /` Orthomosaic (TIFF image) collected throughout maturity growth stage containing readable EXIF headers with image metadata. /c._Shapefiles Plot boundaries files (.shp) and field area from 2020 SVREC location containing plot level information using the breeding program metadata. /d._Ground_notes 1. 2020_SVREC_BN_ground.csv Ground truth notes collected in 2020 at SVREC location for Black and Navy bean market classes. /e._ ClipPlots_BN_256_64 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2020 SVREC location using 256x64 image size. /e._ClipPlots_BN_512_128 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2020 SVREC location using 512x128 image size. /f._numpy_data Numpy data (.npy) obtained in 2020 at SVREC location using 6 flights to Black and Navy bean market classes at two image sizes (256x64 and 512x128), as well as the ground-truth data (GT) and weather data using the Growing Degree Days (GDD). ############################################################################# /2021_HURON: This directory contains subfolders /a._GCPs_coodinates: 1. Huron GCPs1_final02.csv Ground Control Points coordinates collected in 2021 at HURON location /b._Orthomosaics: Temporal flights to track plant maturity 1. Image naming structure: `Date-of-flight _ _ _ /` Orthomosaic (TIFF image) collected throughout maturity growth stage containing readable EXIF headers with image metadata. /c._Shapefiles Plot boundaries files (.shp) and field area from 2021 HURON location containing plot level information using the breeding program metadata. /d._Ground_notes 1. 2021_HUR_Ground_data.csv Ground truth notes collected in 2021 at HURON location for Black and Navy bean market classes. /e._ClipPlots_BN_256_64 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2021 HURON location using 256x64 image size. /e._ClipPlots_BN_512_128 PNG images clipped from the orthomosaic of 2021 HURON location using 512x128 image size. /f._numpy_data Numpy data (.npy) obtained in 2021 at HURON location using 9 flights to Black and Navy bean market classes at two image sizes (256x64 and 512x128), as well as the ground-truth data (GT) and weather data using the Growing Degree Days (GDD). ############################################################################# /2021_SVREC: This directory contains subfolders /a._GCPs_coodinates: 1. SVREC_GCPs_7_21_2021_UTM_WGS84.csv Ground Control Points coordinates collected in 2021 at SVREC location /c._Shapefiles Plot boundaries files (.shp) and field area from 2021 SVREC location containing plot level information using the breeding program metadata. /d._Ground_notes 1. 2021_SVREC_BN_ground_P01.csv Ground truth notes collected in 2021 at SVREC location for Black and Navy bean market classes. /e._ ClipPlots_BN_256_64 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2021 SVREC location using 256x64 image size. /e._ClipPlots_BN_512_128 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2021 SVREC location using 512x128 image size. /f._numpy_data/SVREC_P1 Numpy data (.npy) obtained in 2021 at SVREC location using 9 flights to Black and Navy bean market classes at two image sizes (256x64 and 512x128), as well as the ground-truth data (GT) and weather data using the Growing Degree Days (GDD). ############################################################################# /2022_HURON: This directory contains subfolders /a._GCPs_coodinates: 1. 2022_HUR_GCPs_points_01.csv Ground Control Points coordinates collected in 2022 at HURON location /b._Orthomosaics: Temporal flights to track plant maturity 1. Image naming structure: `Date-of-flight _ _ _ /` Orthomosaic (TIFF image) collected throughout maturity growth stage containing readable EXIF headers with image metadata. /c._Shapefiles Plot boundaries files (.shp) and field area from 2022 HURON location containing plot level information using the breeding program metadata. /d._Ground_notes 1. Ground_Notes_HUR_22_table Ground truth notes collected in 2021 at HURON location for Black and Navy bean market classes. /e._ClipPlots_BN_256_64 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2022 HURON location using 256x64 image size. /e._ClipPlots_BN_512_128 PNG images clipped from the orthomosaic of 2022 HURON location using 512x128 image size. /f._numpy_data Numpy data (.npy) obtained in 2022 at HURON location using 9 flights to Black and Navy bean market classes at two image sizes (256x64 and 512x128), as well as the ground-truth data (GT) and weather data using the Growing Degree Days (GDD). ############################################################################# /2022_SVREC: This directory contains subfolders /a._GCPs_coodinates: GCPs_SVREC_2022_UTM_WGS84_Meters_01.csv Ground Control Points coordinates collected in 2022 at SVREC location /c._Shapefiles Plot boundaries files (.shp) and field area from 2022 SVREC location containing plot level information using the breeding program metadata. /d._Ground_notes 1. 22_SVREC_BN_ground.csv Ground truth notes collected in 2022 at SVREC location for Black and Navy bean market classes. /e._ ClipPlots_BN_256_64 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2022 SVREC location using 256x64 image size. /e._ClipPlots_BN_512_128 Image naming structure: `Location-Experiment-PlotID _ _ ` PNG images clipped from the orthomosaic of 2022 SVREC location using 512x128 image size. /f._numpy_data Numpy data (.npy) obtained in 2022 at SVREC location using 6 flights to Black and Navy bean market classes at two image sizes (256x64 and 512x128), as well as the ground-truth data (GT) and weather data using the Growing Degree Days (GDD). ############################################################################# /2021_SVREC_ortho1 and /2021_SVREC_ortho2 Image naming structure: `Date-of-flight _ _ _ /` Orthomosaic (TIFF image) collected throughout maturity growth stage containing readable EXIF headers with image metadata in 2021 at SVREC location. ############################################################################# /2022_SVREC_ortho1, /2022_SVREC_ortho2 and /2022_SVREC_ortho3 Image naming structure: `Date-of-flight _ _ _ /` Orthomosaic (TIFF image) collected throughout maturity growth stage containing readable EXIF headers with image metadata in 2022 at SVREC location.

Plant phenotyping relevance

乾燥インゲンの成熟期・草丈・立株数をRGBドローン画像と深層学習で推定するデータセットおよびモデルを提供しており、植物形質の取得・推定方法が中心である。

Code and data availability

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