Intestinal epithelium is a single layer of cells exposed to external aggressive conditions, that is renewed every 4–5 days, that makes it one of the most sensitive part of human body. Its tissue homeostasis is highly sensitive to proliferation and cell migration; events occurring in a specific microenvironment: the intestinal crypt. However, mechanical interaction within this niche may be difficult to observe in vivo and mechanical properties of this model are poorly described. Recent developments in cell imaging and culture, with the creation of artificial tissue respecting natural architecture or organoids, have opened new access for the creation of epithelial tissues models that can easily be virtualized. We propose a combination of ‘computational models’, integrating the Finite Element Method Updated and Deep Learning, and organoids humanly designed ‘biological models’, to characterize colon epithelial structures, offering a promising avenue for fully automated diagnosis analysis.