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