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trajectory_analysis

A comprehensive, modular application for analyzing particle trajectories from TIRF microscopy recordings and other single-molecule imaging data.

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Overview

Languages: Python

Documentation

Particle Tracking Application

A comprehensive, modular application for analyzing particle trajectories from TIRF microscopy recordings and other single-molecule imaging data.

Features

🔬 Multi-Method Particle Detection

  • Threshold-based detection
  • Laplacian of Gaussian (LoG) blob detection
  • Trackpy integration
  • Background subtraction and filtering

🔗 Advanced Trajectory Linking

  • Nearest neighbor linking
  • Trackpy-based linking with gap filling
  • Adaptive search parameters
  • Minimum track length filtering

📊 Comprehensive Feature Analysis

  • Radius of gyration (simple and tensor methods)
  • Asymmetry, skewness, kurtosis
  • Fractal dimension
  • Mean squared displacement (MSD)
  • Velocity and diffusion analysis
  • Nearest neighbor distances

🤖 Machine Learning Classification

  • SVM-based trajectory classification
  • Threshold-based mobility classification
  • Custom feature selection
  • Training data import

📈 Interactive Visualization

  • Real-time image display with overlays
  • Track visualization with customizable colors
  • Feature-based coloring schemes
  • Playback controls for time series
  • Export capabilities

💼 Project Management

  • Save and load analysis projects
  • Parameter persistence
  • Data file management
  • Analysis result tracking

Installation

Prerequisites

  • Python 3.8 or higher
  • pip package manager

Install from PyPI (when available)

pip install particle-tracker

Install from Source

git clone https://github.com/yourusername/particle-tracker.git
cd particle-tracker
pip install -e .

Development Installation

git clone https://github.com/yourusername/particle-tracker.git
cd particle-tracker
pip install -e ".[dev,docs,optional]"

Quick Start

GUI Application

```bash

Start the application

particle-tracker

Or run directly

python main.py

With debug logging

python main.py --debug

Load a project on startup

python main.py --project my_analysis.ptpr

[View full README on GitHub]