🌱 GxExMINI Phenotyping App

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🔗 Overview

GxExMINI is a web-based phenotyping platform designed to accelerate the development of nutritious, stress-resistant staple crops in low- and middle-income countries. The application features a React.js frontend and a Flask backend, offering a seamless interface for breeders, researchers, and data scientists.

We aim to improve the speed and quality of crop breeding by using affordable, multi-modal sensors and machine learning to rapidly collect high-resolution phenotypic data.

For more information about the project and our partners: https://projectgemini.ucdavis.edu/

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📚 Resources

• 📝 Full Documentation
• 📂 Example Data

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⚙️ Installation

Docker install (recommended)

git clone git@github.com:GEMINI-Breeding/GEMINI-App.git
cd GEMINI-App

# CPU version
docker compose up
# GPU version (if nvidia-smi works on host)
docker compose -f docker-compose-gpu.yml up

If you want to rebuild the image

# Run docker-compose up
docker-compose up --build

Build docker image

docker build -t gemini-breeding:latest .

Docker Configuration

The docker-compose.yml file contains important configuration parameters that you can customize:

ports:
    - "3000:3000"  # React frontend (external:internal)
    - "5000:5000"  # Flask backend (external:internal)
    - "8091:8091"  # Tile server (external:internal)
volumes:
    - /var/run/docker.sock:/var/run/docker.sock  # Allow Docker-in-Docker
    - /mnt/d/GEMINI-App-Data:/root/GEMINI-App-Data  # Mount host data to container data directory

For more detailed configuration options, see the docker-compose.yml file.

Native install for development

# Step 1: Initialize submodules
git submodule update --init --recursive

# Step 2: Set up Flask backend
cd GEMINI-Flask-Server
./install_flask_server.sh
cd ../

# Step 3: Install Node Version Manager (NVM)
curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash
source ~/.bashrc

# Step 4: Install Node 18 and switch to it
nvm install 18
nvm use 18

# Step 5: Install frontend dependencies
cd gemini-app
npm install --legacy-peer-deps  # Fixes upstream dependency conflict

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🔍 Pipeline Overview

• File Management System – Easily organize and access raw and processed data.
• Codeless Image Orthomosaic Process – Generate field-scale mosaics without writing code.
• Linked Data Visualization – Visualize data with direct links to field design layouts.
• AI-Enabled Model Creation – Train and deploy machine learning models for trait analysis.
• Trait Extraction & Export – Extract key traits and export results for downstream use.