Across animals, the capacity to generate complex body plans from a single cell relies on the early generation of gene expression asymmetries in development. Organoids derived from stem cells are valuable models to study human development, but they present challenges in controlling and studying spatiotemporal patterns of gene expression. To reproduce and study neural tissue patterning - particularly the role of morphogens - in vitro, we generated tens of mutant cell lines and a new organoid model of neural tube patterning, where we combine optogenetics and gene perturbation technologies with single-cell and spatial tramscriptomic readouts.