Skip to article frontmatterSkip to article content
Site not loading correctly?

This may be due to an incorrect BASE_URL configuration. See the MyST Documentation for reference.

FIJI Image Analysis Practical

This practical will guide you through essential image analysis techniques using FIJI (Fiji Is Just ImageJ). You’ll learn how to process, visualize, and quantitatively analyze microscopy images, from basic operations to AI-powered segmentation.

Tutorial Structure

This practical consists of 4 parts:

Part 1: Setup and Basic Processing

Installation, image processing fundamentals, and color adjustments

Part 2: 3D Visualization

3D projections, deconvolution, and advanced visualization

Part 3: Quantitative Analysis

Scaling, measurements, segmentation, and particle analysis

Part 4: AI-based Analysis

Using Labkit and StarDist for automated segmentation

Tutorials
Part 4: Making a publication ready figure of your images in OMERO
Tutorials
Part 1: Setup and Basic Image Processing