What is ImageJ?

• Opensource image analysis software
• Provides a base set of tools and libraries for interactive and programmatic image analysis
• Powerful plugin system for extending ImageJ's functionality

What is Fiji?

Short version: Fiji Is Just ImageJ

Long version: Fiji is an extension of the ImageJ core/base and it comes bundled with a whole bunch of useful plugins and goodies. It's a really good place to start with ImageJ.

Opening & Interacting with multi-dimensional images

ImageJ/Fiji Hyperstacks let you to view multi-dimensional images:

• X, Y
• Z
• Channels (Colours)
• Time

Tools

All the usaul suspect and more:

• Navigation (Zoom, Pan)
• Transformations (Duplicate, Crop, Scale, Rotate)
• Regions Of Interest (ROI)

Image Calibration

Relating image units to physical units i.e., what size does each pixel represent in metric units. Depends on the optical path that projects photons onto the detector or sensor.

Calibration are usually encoded in the image metadata in modern microscopes, but images for older microscopes need to be calibrated.