Repositories list

• 3D_beanroot_phenotyping_pipeline

  Public
  Python

  •

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

  •0•0•0•0•Updated Jul 2, 2025Jul 2, 2025

• ml_smart_docker

  Public
  Docker container for smart

  Python

  •

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

  •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

• cactice

  Public
  computing agricultural crop lattices

  pythongridprediction+ 5python3imputationlatticemcmcknn

  Jupyter Notebook

  •0•0•1•0•Updated May 23, 2025May 23, 2025

• pycyapi

  Public
  unofficial Python CyVerse API client

  httpclientcyverse+ 2cyverse-discovery-environmentpython

  Python

  •

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

  •2•4•2•1•Updated May 20, 2025May 20, 2025

• plantit

  Public
  hpcsingularityphenotyping+ 2science-gatewaysphenomics

  Vue

  •

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

  •5•11•48•13•Updated May 20, 2025May 20, 2025

• DIRT-Pop.v1

  Public
  R

  •0•0•0•0•Updated May 20, 2025May 20, 2025

• sorghum_results_analysis

  Public
  Python

  •0•0•0•0•Updated May 16, 2025May 16, 2025

• 3d_sorghum_segmentation

  Public
  A machine learning model U2net and opencv based color clustering method that performs object segmentation in a single shot

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated May 5, 2025May 5, 2025

• 3D_model_traits_demo

  Public
  Computation of root phenes from 3D point clouds.

  rootphenotypingphenomics+ 1phenotyping-algorithms

  Python

  •1•6•2•0•Updated Apr 30, 2025Apr 30, 2025

• ml_smart_release

  Public
  SMART software release version

  Python

  •

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

  •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• 3D_colmap

  Public
  General-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline using COLMAP

  Python

  •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

• 3D_model_reconstruction_demo

  Public
  Implementation of the 3D reconstruction pipeline optimized for plant branching structures.

  rootphenotypingphenotyping-algorithms

  C

  •

  GNU General Public License v3.0

  •4•17•2•0•Updated Feb 24, 2025Feb 24, 2025

• colmap_test_dev

  Public
  Dockerfile

  •0•0•0•0•Updated Feb 23, 2025Feb 23, 2025

• 3D_Sorghum_phenotyping_pipeline

  Public
  Pipeline: Traits computation from 3D Sorghum root models

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• SMART

  Public
  Plant phenotyping using computer vision: Compute geometrical traits and analyze plant surface colors

  Python

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Dec 17, 2024Dec 17, 2024

• Microphenotyping-of-hooked-hairs

  Public
  Python

  •2•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• Portable_3D_Scanner

  Public
  Python

  •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• AI_U2net_color_clustering

  Public
  A machine learning model U2net and opencv based color clsutering method hat performs object segmentation in a single shot

  Python

  •

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

  •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• DIRTmu

  Public
  Automatic root hair extraction from microscopy images

  Python

  •

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

  •2•4•3•0•Updated Aug 30, 2024Aug 30, 2024

• Drone-Based-Fusarium-Wilt-Detection-in-Lettuce-Using-RGB-Imagery

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Apr 25, 2024Apr 25, 2024

• Image-Mosaicking-Tiling-Python-Toolkit

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 25, 2024Apr 25, 2024

• Root-Diameter-Prediction-with-Residual-Neural-Network

  Public
  Root Diameter Prediction with Residual Neural Network

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

• Root_Image_Segmentation

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

• 3D_model_descriptor

  Public
  Building a 3D root Descriptor: To encode the maize root structure variation in genotype and interaction with environment using Quaternion representation of maize root Structure

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 8, 2024Jan 8, 2024

• raspberry_pi_cluster

  Public
  raspberry pi cluster MPI and step motor control

  Python

  •0•4•0•0•Updated Nov 9, 2023Nov 9, 2023

• DIRT

  Public
  Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.

  image-processingrootphenotyping+ 3imagingcomputer-visphenotyping-algorithms

  Python

  •

  Other

  •18•25•3•3•Updated Oct 29, 2023Oct 29, 2023

• slappt

  Public
  Slurm scripts for Apptainer jobs

  hpccontainersslurm+ 1apptainer

  Python

  •

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

  •1•2•0•0•Updated Mar 25, 2023Mar 25, 2023

• plantit-example-bind-mounts

  Public
  A simple workflow demonstrating bind mounts.

  0•0•0•0•Updated Dec 7, 2022Dec 7, 2022

• 3D_review_scripts

  Public
  scripts for comparison 3D reconstruction pipelines

  BSD 2-Clause "Simplified" License

  •1•2•0•0•Updated Oct 25, 2022Oct 25, 2022

• DIRT-storage

  Public
  Automatic estimation of storage root length, diameter and volume.

  rootphenotypingphenomics

  Python

  •0•1•0•0•Updated Feb 26, 2022Feb 26, 2022