Introduction to Bioimage Analysis

This book tries explain the main ideas of image analysis in a practical and engaging way.

It’s written primarily for busy biologists who need to analyze images as part of their work – but I hope others might find it useful as well.

The core content is based on my earlier handbook Analyzing fluorescence microscopy images with ImageJ (PDF, GitBook). This has been extensively revised, generalized and expanded; the new title reflects the fact that it’s no longer entirely focussed on fluorescence images, nor on ImageJ – although both still play a big role.

The biggest change is that it now exists as an open Jupyter Book. This makes the whole thing more maintainable for me, and interactive for anyone who reads it.

It’s a work in progress, and probably always will be, but I hope you find it useful.

You can download the images used in the practical exercises here.