Medical imaging offers the possibility of achieving anatomical and functional descriptions of human body, improving the development of pathophysiological models. A major goal of biomedical research is to integrate the plurality of information that can be achieved at different spatiotemporal scales, at cellular, tissue, organ and system levels. In this paper a description of imaging modalities used to explore human functions at different levels will be given. The relevance of analysis methods based on models, i.e. on a priori information, as well as data driven ones will be outlined. Examples related to the study of heart and brain function will be described.