Abstract: Implementations discussed and claimed herein provide systems and methods for characterizing patient tissue of a patient. In one implementation, a pathological image of the patient tissue is received. Nuclei of the plurality of cells in the pathological image are simultaneously segmented and classified using a histology-based digital staining system. The nuclei of the plurality of cells are segmented according to spatial location and classified according to cell type, thereby generating one or more groups of nuclei. Each of the one or more groups of nuclei have an identified cell type. A composition and a spatial organization of a tumor microenvironment of the patient tissue is determined based on the one or more groups of nuclei. A prognostic model for the patient is generated based on the composition and the spatial organization of the tumor microenvironment.