Computational Plant Science Lab

All

40 repositories

3D_colmap
Public
General-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline using COLMAP
Python
•0•0•0•0•Updated Feb 25, 2025Feb 25, 2025
3D_model_reconstruction_demo
Public
Implementation of the 3D reconstruction pipeline optimized for plant branching structures.
root phenotyping phenotyping-algorithms
C
•
GNU General Public License v3.0
•4•16•2•0•Updated Feb 24, 2025Feb 24, 2025
sorghum_results_analysis
Public
Python
•0•0•0•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
ml_smart_release
Public
SMART software release version
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jan 9, 2025Jan 9, 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
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
http client cyverse cyverse-discovery-environment python
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.
root phenotyping phenomics phenotyping-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•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•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-processing root phenotyping imaging computer-vis phenotyping-algorithms
Python
•
Other
•18•25•2•3•Updated Oct 29, 2023Oct 29, 2023
plantit
Public
hpc singularity phenotyping science-gateways phenomics
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
hpc containers slurm apptainer
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
python grid prediction python3 imputation lattice mcmc knn
Jupyter Notebook
•0•0•1•0•Updated Apr 27, 2022Apr 27, 2022
DIRT-storage
Public
Automatic estimation of storage root length, diameter and volume.
root phenotyping phenomics
Python
•0•1•0•0•Updated Feb 26, 2022Feb 26, 2022