We exhibit a bridge between the theory of cellular categories, used in algebraic topology and homological algebra, and the model-theoretic notion of stable independence. Roughly speaking, we show that the combinatorial cellular categories (those where, in a precise sense, the cellular morphisms are generated by a set) are exactly those that give rise to stable independence notions. We give two applications: on the one hand, we show that the abstract elementary classes of roots of Ext studied by Baldwin–Eklof–Trlifaj are stable (...) and tame. On the other hand, we give a simpler proof (in a special case) that combinatorial categories are closed under 2-limits, a theorem of Makkai and Rosický. (shrink)