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