🌱 PhoTorch Studio

PhoTorch Studio is a web and desktop app for PhoTorch, an open-source Python library for plant ecophysiologists and crop modelers, designed to streamline the fitting and analysis of core physiological models from gas exchange and water relations data.

🌐 Web app: Try it instantly at https://photorch.streamlit.app.

🐳 Docker-based desktop app (Recommended): Install and run locally following instructions.

📄 Accompanying publications: [PhoTorch]

🔬 What does PhoTorch Studio do?

PhoTorch Studio provides an intuitive, interactive platform for fitting widely used plant physiological models, enabling rapid exploration and interpretation of experimental data.

🚀 Key Features

• Photosynthesis Model Fitting
  • Fit the full Farquhar-von Caemmerer-Berry (1980) model for:
    • V_cmax25, J_max25, TPU₂₅, and 16+ other parameters
  • Integrate CO₂ (A–Ci), light response (A–Q), and temperature response (A-T) curves
  • Recover Temperature Optima
• Stomatal Conductance Model Fitting
  • Fit multiple empirical and optimization-based models, including:
    • Ball-Woodrow-Berry (1987)
    • Medlyn et al. (2011)
    • Leuning (1995)
    • Buckley-Turnbull-Adams (2012)
• Pressure–Volume (PV) Curve Fitting
  • Analyze water relations data to extract parameters such as:
    • Osmotic potential at full turgor (π₀)
    • Bulk modulus of elasticity (ε)
    • Relative water content at turgor loss point (RWC_tlp)
• Flexible Data Input
• Accepts .csv, .txt, and .xlsx formats
• Optional rescaling with survey data
• Species-specific analysis and visualization
• Interactive and Visual
• Real-time fitting feedback
• Plotly-based visualization of fit quality
• View error metrics for model evaluation

🧪 Who is it for?

PhoTorch Studio is designed for:

• Field scientists needing a fast way to process LI-600 or LI-6800 data
• Plant ecophysiologists analyzing gas exchange and water relations
• Crop modelers calibrating parameters for predictive models
• Students and educators learning how physiological models work

📦 Installation Options

🌍 Use it in the browser

• No installation required
• Try it instantly at https://photorch.streamlit.app
• (Currently compute limited)

🖥️ Run locally via Docker

• Clone this repository and run via Docker for full offline functionality
• See Installation Instructions below

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🛠️ Local Setup Instructions (All Platforms)

Step 0: Install Docker

macOS

1. Download Docker Desktop for Mac
2. Install it and launch Docker
3. Allow permissions when prompted

Windows

1. Download Docker Desktop for Windows
2. Follow the installation prompts (Enable WSL 2 if asked)
3. Launch Docker

Linux (Ubuntu/Debian)

Follow instructions here or try

sudo apt update
sudo apt install -y docker.io
sudo systemctl enable docker
sudo systemctl start docker
sudo usermod -aG docker $USER
newgrp docker

Step 1: Download the App

git clone https://github.com/ktrizzo/photorch-sutdio.git
cd photorch-studio

Step 2: Launch the App

chmod +x launch.sh
./launch.sh

If not opened in a web browser tab automatically, go to https://localhost:8501.

Step 3: Enjoy

Fit lots of models!

Step 4: Close the App

docker stop photorch-studio
docker rm photorch-studio