Genomics and proteomics have evolved towards systems biology. The general goal here is the construction of complex, functional models of biological systems on the basis of molecular networks. Such models enable improved quality in interpretation and evaluation of quantitative measurements and afford a substantially deeper functional understanding. Systems pathology differs from systems biology by attaching the same importance to spatial modelling of tissue alterations as to gene regulatory modelling. In this way, systems pathology is able to deploy disease models for improved diagnosis, prognosis and therapy. In the present work a generic process for systems pathology is created, integrating gene regulatory and morphological models towards molecular disease models. For this purpose, fluorescent virtual microscopy will be essential as it delivers morphological and molecular tissue data with high spatial resolution and high throughput. Using epidermal differentiation as an example, it is shown how - using virtual microscopy - the spatiotemporal expression of biomarkers can be modelled by reconstructing protein networks from fluorescent tissue sections.