The breast tumor microenvironment is a complex ecosystem of epithelial, immune, endothelial, fibroblast and adipose cells. Cellular phenotypes and spatial localizations within the microenvironment are linked to patient prognosis and response to therapy. Our CyCIF protocol, image analysis tools and atlases of breast cancer tissues all contribute to deepening our understanding of the tumor microenvironment in order to improve patient stratification and inform therapeutic strategies.