This document discusses quantitative image analysis techniques for extracting information from 2D, 3D, time-lapse, and spectral biological images captured with microscopes. Traditional manual analysis is time-consuming and prone to bias, while high-throughput experiments generate millions of images. Quantitative image analysis software is used to automatically measure rates of cell division, protein localization, responses to drugs, lineage tracing, motility, and more from images of samples like yeast strains, tissue cultures, and tumor biopsies to aid in applications such as disease detection, survival prediction, and embryogenesis tracing.