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: generating image data using an imaging system, the image analysis software being installed on the imaging system; identifying a first target set of image objects in the image data; identifying a second target set of image objects in the image data; defining a pair-wise user-defined target link by specifying a spatial relationship between the first target set of image objects and the second target set of image objects; selecting the first target set of image objects and the second target set of image objects based on the spatial relationship; and utilizing the pair-wise user-defined target link to combine the first target set of image objects and the second target set of image objects in the image data into a set of interrelated targets that form a linked target set, wherein each interrelated target in the linked target set includes one image object in the first target set of image objects and at least one image object in the second target set of image objects which is linked to the image object from the first target set based on the spatial relationship.