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 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