Most learning-based algorithms developed for clinical imaging are too demanding in terms of technical expertise to be deployed routinely in clinics. Hence, the development of standard approaches to these advanced algorithms is a foundational work of obvious importance. It is also an essential first step towards the integration of patients’ images with other “-omics” data. In this project, we shall design pipelines that simplify the access to automated digital imaging tools, hence helping to further spread their use in clinical settings. In parallel, we shall carry out two concrete research projects in collaboration with several clinical partners in Western Switzerland. We shall consider applications at both the microscopic scale (digital pathology) and the macroscopic scale (MRI), hence addressing two different yet complementary clinical needs.