Skip to content

particle_analysis

ParticleAnalysis is an open-source Python application for detecting, tracking, and analyzing fluorescent particles in microscopy image sequences. It provides a user-friendly graphical interface for analyzing single-particle dynamics, with particular emphasis on robust particle detection, reliable tr

View on GitHub →

Overview

Languages: Python

Documentation

ParticleAnalysis: A Python Tool for Single-Particle Tracking in Fluorescence Microscopy

Overview

ParticleAnalysis is an open-source Python application for detecting, tracking, and analyzing fluorescent particles in microscopy image sequences. It provides a user-friendly graphical interface for analyzing single-particle dynamics, with particular emphasis on robust particle detection, reliable tracking, and comprehensive motion analysis.

Key Features

  • Advanced Particle Detection
  • Multi-scale Gaussian detection for varying particle sizes
  • Local background subtraction and noise estimation
  • SNR-based filtering of detections

  • Interactive ROI selection and parameter tuning

  • Robust Particle Tracking

  • Nearest-neighbor linking algorithm with gap closing
  • Support for particle disappearance and reappearance
  • Track quality control and filtering

  • Visualization of tracking results

  • Comprehensive Motion Analysis

  • Mean Square Displacement (MSD) analysis
  • Diffusion coefficient calculation
  • Motion type classification (confined, normal, directed, anomalous)

  • Track shape analysis (radius of gyration, asymmetry, fractal dimension)

  • User-Friendly Interface

  • Interactive visualization of particles and tracks
  • Real-time parameter adjustment
  • Results tables with sorting and filtering
  • Batch processing capabilities

Installation

# Create a new conda environment
conda create -n particle_analysis python=3.11
conda activate particle_analysis

# Install dependencies
pip install -r requirements.txt

# Install the package
pip install .

Quick Start

  1. Launch the application: 

    python -m particle_analysis

  2. Load data:

  3. Click "Open File" to load a TIFF stack
  4. Adjust contrast using the histogram sliders

  5. Select a region of interest (optional)

  6. Detect and track particles:

  7. Adjust detection parameters if needed
  8. Click "Detect Particles" to identify particles
  9. Click

[View full README on GitHub]