Repositories list

• phytooracle_data

  Public
  Python

  •0•0•2•0•Updated Oct 20, 2025Oct 20, 2025

• environmental_association

  Public
  Environmental association for thermal and PS2 data from the gantry.

  Jupyter Notebook

  •1•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• 3d_landmark_selection

  Public
  3D Module: GUI for point cloud landmark selection

  Python

  •

  MIT License

  •0•0•1•0•Updated Oct 6, 2025Oct 6, 2025

• 3d_transformation_selection

  Public
  Python

  •0•0•3•0•Updated Sep 10, 2025Sep 10, 2025

• automation

  Public
  Modular, Scalable Phenomic Data Processing Pipelines

  pythonpipelinehpc+ 9distributed-computingplantphenotypinglettucephenomicssorghumworkqueue+ 2

  Python

  •

  MIT License

  •4•5•1•1•Updated Sep 4, 2025Sep 4, 2025

• 3d_neighbor_removal

  Public
  Python

  •1•0•0•0•Updated Sep 3, 2025Sep 3, 2025

• 3d_entropy_features

  Public
  Python

  •0•0•1•0•Updated Aug 26, 2025Aug 26, 2025

• SorghumPartNet

  Public
  DGCNN Segmentation of Sorghum (focal plant and leaf segmentation)

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•4•1•0•Updated May 27, 2025May 27, 2025

• flir_bin_to_tif_s17

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

• flir_bin_to_tif_s11

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Mar 20, 2025Mar 20, 2025

• flir_bin_to_tif_s10

  Public
  Conversion of FLIR bin files to geoTIFFs with calibration

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

• phenotype_extraction_update

  Public
  R

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• rgb_plant_clustering

  Public
  Clustering of plant identifications over a season for individual plant tracking

  Python

  •2•1•0•0•Updated Jun 18, 2024Jun 18, 2024

• panicle_gt_mp_association

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jun 11, 2024Jun 11, 2024

• 3d_postprocessing

  Public
  A repository for geo-correcting the ply files after they are merged and aligned and GCPs have been selected by the users manually.

  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• 3d_orthomosaic_generator

  Public
  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• 3d_preprocessing

  Public
  In this repository we preprocess the 3D data. It includes merging west and east and aligning north and south using RANSAC and finding passes that might contain lids. It paints the ply files properly and prepares them for manual selection of the lids locally.

  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• psii_fluorescence_aggregation

  Public
  Aggregate PSII fluorescence segmentation outputs to Fv/Fm

  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• psii_segmentation

  Public
  Segmentation of pixels to experimentally-determined Fv/Fm contributions

  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• psii_bin_to_tif

  Public
  Conversion of PSII fluorescence bin files to GeoTIFF images

  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• flir_plant_temp

  Public
  Extraction of mean temperatures of individual plants

  Python

  •0•0•1•0•Updated Jun 9, 2024Jun 9, 2024

• rgb_bin_to_tif

  Public
  RGB bin file conversion to geoTIFF

  Python

  •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• rgb_flir_plant_detection

  Public
  Detection of individual plants (RGB/FLIR) using a Faster R-CNN detection network

  Python

  •1•1•0•0•Updated Jun 8, 2024Jun 8, 2024

• rgb_flir_stitch_plots

  Public
  Stitching of geoTiff images (RGB/FLIR) into agricultural plots

  Python

  •0•0•0•0•Updated Jun 8, 2024Jun 8, 2024

• rgb_flir_plot_clip_geojson

  Public
  RGB/FLIR clipping to agricultural plots

  Python

  •0•0•0•0•Updated Jun 8, 2024Jun 8, 2024

• rgb_flir_edit_gps

  Public
  Edit corner coordinates of RGB/FLIR geoTIFFs

  Python

  •0•0•0•1•Updated Jun 8, 2024Jun 8, 2024

• rgb_flir_collect_gps

  Public
  Collection of corner coordinates for RGB/FLIR geoTIFFs

  Python

  •0•1•0•1•Updated Jun 8, 2024Jun 8, 2024

• uav_plot_clip

  Public
  Python

  •0•0•0•0•Updated Jun 8, 2024Jun 8, 2024

• rgb_tgi_extraction

  Public
  Python

  •0•0•0•0•Updated Jun 8, 2024Jun 8, 2024

• rgb_panicle_detection

  Public
  Python

  •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024