With the advent of digital cameras and motorization of mechanical components, computer control of microscopes has become increasingly important. Software for microscope image acquisition should not only be easy to use, but also enable and encourage novel approaches. The open‐source software package µManager aims to fulfill those goals. This unit provides step‐by‐step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software. Curr. Protoc. Mol. Biol. 92:14.20.1‐14.20.17. © 2010 by John Wiley & Sons, Inc.