We thank F. Maurer for organoid preparation, E. Tagliavini for IT support, G. de Medeiros for help in light-sheet imaging, A. Peters for light-sheet, L. Gelman for assistance and training, H. Kohler for sorting, S. Smallwood and S. Thiry for sequencing, R. Cuttat and S. Schuierer for scRNA-seq analysis, L. Pelkmans, J. Betschinger, D. Gilmour, L. Giorgetti, C. Tsiairis and laboratory members for reading the manuscript. Funding: SNSF (POOP3_157531 to P.L.). This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617).

Reviewer information

Nature thanks Anne Rios and the other anonymous reviewer(s) for their contribution to the peer review of this work.