A software package for control of automated microscopes. Together with the image processing application ImageJ, μManager provides a comprehensive, freely available, imaging solution. μManager has a simple and clean user interface, through which it lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging.