The ImageJ User Guide provides a thorough description of ImageJ’s built-in functions.
The Imaging Tutorials on this wiki offer an introduction to scientific imaging, including both image acquisition and image analysis, with a focus on ImageJ.
Analyzing fluorescence microscopy images with ImageJ provides a detailed introduction to image analysis using 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.