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For the intestinal epithelium, a population of rapidly proliferating stem cells (ISCs) help regenerate the epithelial tissue. Although these cells can be monitored by isolating with FACS or introducing fluorescent transgenes, this can mask clonal and heterogeneity effects. The CellRaft arrays can be used to culture single ISCs and monitor their growth and progression to organoid formation with time-lapse microscopy. Additionally, the CellRaft-grown intestinal organoids and single ISCs can be treated with exogenous factors and/or isolated for gene expression analysis to identify micro-niches derived from clonal ISC dynamics.