Abstract: Cell identification and classification is a well-known problem in the pathology domain that help identify microenvironments. In addition to the characteristic of each cell, its interactions with the neighboring regions or other cells is also important. This involves correct identification of neighboring elements and analytically representing the interactions between them. This disclosure presents a system that combines many such features, some hand engineered and some machine derived through training of Deep Learning algorithms that can be used to study the microenvironments.