Computational Plant Science Lab

All

37 repositories

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 Oct 31, 2024Oct 31, 2024
3D_beanroot_phenotyping_pipeline
Public
Makefile
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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
SMART
Public
Plant phenotyping using computer vision: Compute geometrical traits and analyze plant surface colors
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Oct 3, 2024Oct 3, 2024
ml_smart_docker
Public
Docker container for smart
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Oct 3, 2024Oct 3, 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
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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
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BSD 3-Clause "New" or "Revised" License
•2•3•2•0•Updated Aug 30, 2024Aug 30, 2024
Syngenta_PhenoTOOLs
Public
Syngenta_PhenoTOOLs
Python
•0•1•0•0•Updated Aug 6, 2024Aug 6, 2024
Drone-Based-Fusarium-Wilt-Detection-in-Lettuce-Using-RGB-Imagery
Public
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Apr 25, 2024Apr 25, 2024
Image-Mosaicking-Tiling-Python-Toolkit
Public
Python
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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
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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
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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
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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.
root phenotyping phenotyping-algorithms
C
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GNU General Public License v3.0
•3•16•2•0•Updated Aug 16, 2023Aug 16, 2023
plantit
Public
hpc singularity phenotyping science-gateways phenomics
Vue
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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
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BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Mar 25, 2023Mar 25, 2023
Microphenotyping-of-hooked-hairs
Public
Python
•2•0•0•0•Updated Mar 22, 2023Mar 22, 2023
pycyapi
Public
unofficial Python CyVerse API client
http client cyverse cyverse-discovery-environment python
Python
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BSD 3-Clause "New" or "Revised" License
•2•4•2•0•Updated Dec 31, 2022Dec 31, 2022
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
plantit-example-hello-world
Public
A minimal example workflow.
bash example hello-world plantit
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.
data example cyverse cyverse-discovery-environment plantit
0•1•0•0•Updated Feb 22, 2022Feb 22, 2022
plantit-example-parameters
Public
A simple workflow to demonstrate parameters.
parameters example plantit
0•0•0•0•Updated Feb 22, 2022Feb 22, 2022
docker-icommands
Public
iRODS iCommands in Docker
Shell
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MIT License
•0•0•0•0•Updated Feb 17, 2022Feb 17, 2022