||Today’s diagnostic evaluation of cancer tumors is done by examining tissue morphology and the presence (or absence) of tumorspecific immunohistochemical protein markers. It is also of interest to include tumor heterogeneity and microenvironment variations into account. Our overall objective is to develop an analysis and visualization platform that provides and overlays genetic profiling data directly on top of histological morphology maps. This provides a scalable, multi-layered visual representation of clinically relevant information in a morphological context to the pathologist. By providing spatial distributions of molecular profiles, these can be correlated to morphological features providing new powerful information for understanding tumor heterogeneity and interactions with the tumor microenvironment. It allows pathologists to make better decisions about cancer treatment, drug resistance, and tumor regrowth.