Awesome ImageJ Plugins

A curated list of awesome ImageJ plugins for biologists. Your contributions are always welcome!

• Awesome ImageJ Plugins
  • Analysis
  • Detection
  • GUI tools
  • Paper writing
  • Resolution
  • Stacking
  • Tracking
  • Transformation

Analysis

• OrientationJ - Directional Analyzer.
  

Detection

• CurveTrace - Extractor tracing curves on images.
  
• deepImageJ - Pre-trained deep learning models to detect various cells.
  

GUI tools

• ActionBar
  

Paper writing

• QuickFigures - a toolset for creating scientific figures.
  

Resolution

• deepImageJ - Pre-trained deep learning models to transform input images into super-resolved ones.
  

Stacking

• Extended Depth of Field - Plugin to merge a stack of micrographs taken at different focal positions into a single focused image
  
• Z-stack Depth Colorcode - Plugin color-coding Z/T stacks.
  

Tracking

• TrackMate - GUI-based particle tracker.
  
• TraJClassifier - Classifier of TrackMate trajectories.
  

Transformation

• Linear Stack Alignment with SIFT - Plugin to align stacking-image with SIFT-algorithm.
  
• Polar Transformer - Plugin which converts images to polar coordinates.