YouScope is a free, open-source microscope control software compatible with most present-day automatized microscopes. YouScope allows to easily automatize complex microscopy protocols using an user-friendly graphical interface. Besides a wide range of built-in configurable standard protocols, like the measurement of the wells of various types of microplates with bright-field, fluorescence and out-of-focus channels, it is easily extendible to support specific custom protocols. For this task, various scripting languages, like JavaScript and Matlab, are supported, as well as lower level plug-ins written in Java.