How does a stem cell know its position in a tissue, and how the positional information affects its properties? To address these fundamental biological question, we use fast spinning disc confocal imaging together with machine learning based segmentation algorithms to model the full cellular content of the fly intestine. Together with our newly developed computational method (Linear analysis of midguts or LAM: Viitanen et al. 2021) we are able to extract regionally defined phenotypes of genetic and/or environmental manipulations.