Annotated snapshot of the GiA Roots GUI. The GiA Roots GUI is a standalone application that provides a user interface to manage input images, define a processing pipeline and manage output. It features a main window with several task windows that can be accessed through the left sidebar. Sequential access to each window page accomplishes major tasks: managing data; selecting traits to measure; tweaking parameters; performing processing; reviewing the results. This linear design helps users to keep track of progress and proceed intuitively with processing of the data. Main computational steps are described in greater detail in Implementation.