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The ImageJ User Guide provides a thorough description of ImageJ's built-in functions.
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The Fiji Cookbook provides an analysis-oriented introduction and user guide to ImageJ.
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Analyzing fluorescence microscopy images with ImageJ provides detailed information on image analysis using ImageJ.
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A textbook covering many aspects of digital image processing, with code examples built with ImageJ.
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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.
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Fiji Training Notes including demo images from the Australian national research and education network.