Repositories list

• SMART

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

  Python

  •

  GNU General Public License v3.0

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

• 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 Dec 12, 2024Dec 12, 2024

• ml_smart_docker

  Public
  Docker container for smart

  Python

  •

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

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• Microphenotyping-of-hooked-hairs

  Public
  Python

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

• pycyapi

  Public
  unofficial Python CyVerse API client

  httpclientcyverse+ 2cyverse-discovery-environmentpython

  Python

  •

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

  •2•4•2•1•Updated Nov 25, 2024Nov 25, 2024

• 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 Nov 19, 2024Nov 19, 2024

• 3D_beanroot_phenotyping_pipeline

  Public
  Makefile

  •

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

  •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• Portable_3D_Scanner

  Public
  Python

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

• 3D_model_traits_demo

  Public
  Computation of root phenes from 3D point clouds.

  rootphenotypingphenomics+ 1phenotyping-algorithms

  Python

  •1•6•2•0•Updated Sep 27, 2024Sep 27, 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•3•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•0•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

• DIRT-Pop.v1

  Public
  R

  •0•0•0•0•Updated Mar 10, 2024Mar 10, 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•2•3•Updated Oct 29, 2023Oct 29, 2023

• 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•16•2•0•Updated Aug 16, 2023Aug 16, 2023

• plantit

  Public
  hpcsingularityphenotyping+ 2science-gatewaysphenomics

  Vue

  •

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

  •5•11•48•13•Updated Apr 4, 2023Apr 4, 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

• cactice

  Public
  computing agricultural crop lattices

  pythongridprediction+ 5python3imputationlatticemcmcknn

  Jupyter Notebook

  •0•0•1•0•Updated Apr 27, 2022Apr 27, 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

• plantit-example-hello-world

  Public
  A minimal example workflow.

  bashexamplehello-world+ 1plantit

  1•1•0•0•Updated Feb 22, 2022Feb 22, 2022

• plantit-example-accessing-data

  Public
  A simple workflow mapping an input file to an output file.

  dataexamplecyverse+ 2cyverse-discovery-environmentplantit

  0•1•0•0•Updated Feb 22, 2022Feb 22, 2022

• plantit-example-parameters

  Public
  A simple workflow to demonstrate parameters.

  parametersexampleplantit

  0•0•0•0•Updated Feb 22, 2022Feb 22, 2022

• docker-icommands

  Public
  iRODS iCommands in Docker

  Shell

  •

  MIT License

  •0•0•0•0•Updated Feb 17, 2022Feb 17, 2022