Module 1: Introduction
Learning Objectives
- Understand the differences between ImageJ, ImageJ2, and FIJI
- Successfully install and configure the software
- Configure memory settings across different platforms
- Navigate the basic user interface
Installation and Setup
ImageJ
Original ImageJ platform
Download
ImageJ2
Next generation of ImageJ
Download
FIJI
FIJI Is Just ImageJ (with batteries included)
Download
Sample Images
Download sample images for practice
Download
ImageJ, ImageJ2, and Fiji Comparison
ImageJ
Original version - lightweight and fast
Strengths
- Basic image analysis
- Small file size
- Simple interface
- Good for basic research
Limitations
- Limited to 2D/3D images
- Basic memory management
- Older plugin architecture
Best For
- Basic research needs
- Simple image processing
- Limited computing resources
- Learning image analysis
ImageJ2
Modern rebuild with improved architecture
Strengths
- N-dimensional image support
- Advanced memory management
- Modern plugin architecture
- Better reproducibility
- Improved user interface
Limitations
- Larger file size than ImageJ
- Fewer plugins than Fiji
- Learning curve for new features
Best For
- Advanced image analysis
- Large dataset processing
- Modern research workflows
- Software integration needs
Fiji
ImageJ2 + Bio-plugins bundle
Strengths
- All ImageJ2 features
- Rich bio-image plugins
- Active community
- Regular updates
- Built-in update system
Limitations
- Largest file size
- Most complex interface
- Resource intensive
Best For
- Biological research
- Advanced bio-imaging
- Complex analysis workflows
- Collaborative research
Desktop Version
Click the arrows to cycle through the different instructions.
Cheat Sheet