For several years we have been developing a software application, called Leginon, for the automated control and acquisition of images from a transmission electron microscope. One of the primary motivations in developing this software is to provide for a system that can acquire many hundreds of images under low dose conditions from a specimen embedded in vitreous ice. In order to set up and manage this system we have developed a number of simple interactive graphical tools that enable the user to design, oversee and manage protocols for controlling the microscope and collecting the images.