This is a 7 sessions workshop about bioimage informatics with Fiji/ImageJ.
For each session, a pdf describes the background required to understand the session topic and methods to address it. Video tutorials are available to see how to use Fiji/ImageJ to process images with the presented methods. The images used in the tutorials are available in the ImageExamples folders. A doc file in the same folders gives their location on the Internet.
Introduction to Fiji - Download
Introduction to Fiji - Image Format
Introduction to Fiji - Image Visualization
Introduction to Fiji - A First Pipeline
Image Filtering - Mathematical Operations Applied to Images
Image Filtering - Mathematical Operations Applied between Images
Image Filtering - Linear Filtering
Image Filtering - Non Linear Filtering
Image Filtering - Fourier Transform
Segmentation - A Tour of Segmentation Approaches
Segmentation - A Case Example
Quantification - Line
Quantification - Region of Interest (ROI)
Quantification - Operations between ROIs - ROIs from segmentations
Quantification - Area
Quantification - Batch Processing
Automatization 1: CLIJ assistant
Automatization 2: Macro recorder - batch processing
Colocalization - Colocalization with Fiji
Colocalization - Colocalization with Icy
Tracking with TrackMate