Researchers often examine samples by eye on the microscope — qualitatively scoring each sample for a particular feature of interest. This approach, while suitable for many experiments, sacrifices quantitative results and a permanent record of the experiment. By contrast, if digital images are collected of each sample, software can be used to quantify features of interest. For small experiments, quantitative analysis is often done manually using interactive programs like Adobe Photoshop©. For the large number of images that can be easily collected with automated microscopes, this approach is tedious and time-consuming. NIH Image/ImageJ (http://rsb.info.nih.gov/ij) allows users comfortable writing in a macro language to automate quantitative image analysis. We have developed Cell- Profiler, a free, open-source software package, designed to enable scientists without prior programming experience to quantify relevant features of samples in large numbers of images automatically, in a modular system suitable for processing hundreds of thousands of images.