MicroQuant: Bacterial Colony Counter

A modular Python tool for automated detection and counting of bacterial colonies in petri dish images.

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🚀 Overview

MicroQuant uses computer vision techniques (Circular Hough Transform, Canny Edge Detection, and Peak Local Maxima) to isolate petri dishes and count colonies with high accuracy.

🛠 Project Structure

MicroQuant-Bacterial_Colony/
├── core/                   # Main processing logic
│   ├── detector.py         # Image segmentation & colony counting
│   └── renderer.py         # visualization & output generation
├── docs/                   # Full technical documentation
├── jerms/                  # Input image directory (example)
├── results/                # Processed output visualizations
├── config.py               # Global settings & sensitivity parameters
├── main.py                 # CLI Batch processing entry point
└── requirements.txt        # Dependencies

📦 Installation

1. Clone the repository.
2. Create a virtual environment:

   python -m venv venv
   source venv/bin/activate  # Or `.\venv\Scripts\activate` on Windows

3. Install dependencies:

   pip install -r requirements.txt

⚡ Usage

1. Place your images in a folder (default: jerms/).
2. Run the batch processor:

   python main.py

3. Check the results/ folder for visualized counts.

🤝 Contributing

Please read docs/CONTRIBUTING.md for details on our code of conduct and the modular architecture of the project.