We have built a novel computational microscopy platform that integrates image acquisition, storage, processing and analysis to study cell populations in situ. This platform allows high-content studies where multiple features are measured and linked at multiple scales. We used this approach to study the cellular composition and architecture of the mouse mammary gland by quantitatively tracking the distribution and type, position, proliferative state, and hormone receptor status of epithelial cells that incorporated bromodeoxyuridine while undergoing DNA synthesis during puberty and retained this label in the adult gland as a function of tissue structure. Immunofluorescence was used to identify label-retaining cells, as well as epithelial cells expressing the proteins progesterone receptor and P63. Only 3.6% of luminal cells were label-retaining cells, the majority of which did not express the progesterone receptor. Multi-scale in situ analysis revealed that luminal label-retaining cells have a distinct nuclear morphology, are enriched 3.4-fold in large ducts, and are distributed asymmetrically across the tissue. We postulated that LRC enriched in the ventral mammary gland represent progenitor cells. Epithelial cells isolated from the ventral versus the dorsal portion of the gland were enriched for the putative stem cell markers CD24 and CD49f as measured by fluorescence activated cell sorting. Thus, quantitative analysis of the cellular composition of the mammary epithelium across spatial scales identified a previously unrecognized architecture in which the ventral-most, large ducts contain a reservoir of undifferentiated, putative stem cells.