1. A computer-based method for the development of an image analysis protocol for analyzing image data, the image data containing images including image objects, the image analysis protocol being operable in an image analysis software system to report on one or more measurements conducted on selected ones of said image objects, the method comprising providing functions for selecting predetermined image analysis procedures, said functions allowing a user to define: at least one first target identification setting for identifying a first target set of image objects in said image data; at least one second target identification setting for identifying a second target set of image objects in said image data; a relationship between said first and second set of image objects; and one or more measurements which are to be reported for said image data, said measurements being conducted using said defined relationship.