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User Guides


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