Computational Plant Science Lab

DIRT

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

3D_model_reconstruction_demo

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

SMART

Monitor and analyze plant growth conditions by computing geometric and color traits from any top-view image dataset

plantit

3D_model_traits_demo

Computation of root phenes from 3D point clouds.

pycyapi

unofficial Python CyVerse API client

raspberry_pi_cluster

raspberry pi cluster MPI and step motor control

DIRTmu

Automatic root hair extraction from microscopy images

plantit-logging

Logging services for PlantIT.

3D_review_scripts

scripts for comparison 3D reconstruction pipelines

irods_python_client

Python port of the iRODS iCommands

DIRT-storage

Automatic estimation of storage root length, diameter and volume.

plantit-example-accessing-data

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

plantit-example-hello-world

A minimal example workflow.

slappt

Slurm scripts for Apptainer jobs

3D_model_descriptor

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

3D_model_reconstruction_workflow

cactice

computing agricultural crop lattices

DIRT-Pop.v1

docker-icommands

iRODS iCommands in Docker

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

hairyroots_workflow

icommands-benchmark

iRODS iCommands upload speed testing

Image-Mosaicking-Tiling-Python-Toolkit

Microphenotyping-of-hooked-hairs

plantit-example-bind-mounts

A simple workflow demonstrating bind mounts.

plantit-example-parameters

A simple workflow to demonstrate parameters.

Portable_3D_Scanner

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

Root Diameter Prediction with Residual Neural Network

Root_Image_Segmentation