Micro-Manager (http://micro-manager.org) operates motorized light microscopes and associated equipment. It runs as a plugin in ImageJ, works with virtually all scientific grade microscope equipment, and has a simple interface towards routine image acquisition strategies such as time-lapse, z- stacks, multi-channel, and multi-position acquisition. In addition, it uses a device abstraction layer available from various programming environments (such a C, Java, Python, Matlab and LabView), facilitating development of novel approaches to image acquisition.