Human pathology depends on the interplay between malignant cells, stroma, and the immune system, which can act both to suppress and promote various diseases, including cancer autoimmune disorders. While it is appreciated that all these players are important, we have much better understanding of individual cells than of their cumulative behavior. Our research is focused on understanding how different cells interact as a system to collectively define progression and outcome in response to treatment using novel high-dimensional imaging methods, computer vision and AI.