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

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< Month-Day-Year>_<sensor>_<software>_<clipped_img>/`

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

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

PNG images clipped from the orthomosaic of 2020 SVREC location using 256x64 image size.

    /e._ClipPlots_BN_512_128

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

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< Month-Day-Year>_<location>_<sensor>_<clipped_img>/`

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

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

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

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

PNG images clipped from the orthomosaic of 2021 SVREC location using 256x64 image size.

    /e._ClipPlots_BN_512_128

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

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< Month-Day-Year>_<location>_<sensor>_<clipped_img>/`

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

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

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:

1. 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

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

PNG images clipped from the orthomosaic of 2022 SVREC location using 256x64 image size.

    /e._ClipPlots_BN_512_128

1. Image naming structure: `Location-Experiment-PlotID<Location>_<Experiment-name>_<Plot-ID>`

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< Month-Day-Year>_<sensor>_<software>_<clipped_img>/`

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< Month-Day-Year>_<sensor>_<software>_<clipped_img>/`

Orthomosaic (TIFF image) collected throughout maturity growth stage containing readable EXIF headers with image metadata in 2022 at SVREC location.