Fluorescence handbook

In the years immediately before creating QuPath, I worked mostly with fluorescence microscopy images using ImageJ and Fiji.

During that time, I wrote a handbook to try to help explain the basic principles involved:

While intended primarily for biologists wanting help with fluorescence microscopy image analysis, many of the concepts and techniques describing the handbook (e.g. filtering, thresholds) are generally applicable across a wide range of image analysis applications - and are the basis for how some of QuPath's algorithms (e.g. for cell detection) are implemented.