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User Guides

ImageJ User Guide provides a thorough description of ImageJ”s built-in functions.

Fiji Cookbook provides an analysis-oriented introduction and user guide to ImageJ.

Analyzing fluorescence microscopy images with ImageJ provides detailed information on image analysis using ImageJ.

A textbook covering many aspects of digital image processing, with code examples built with ImageJ.

A textbook for constructing bioimage analysis workflows using ImageJ macro, Matlab and R, to extract numbers out of image data.
Freely downloadable from Wiley site .

Fiji Training Notes including demo images from Monash University. Detailed screenshot and explaination steps on basic analysis through to macro code