Light sheet fluorescence microscopy and analysis

Cleared and stained embryos were glued with their yolk sack on a metal plunger and imaged using a Zeiss Z1 light sheet microscope (Carl Zeiss AG, Germany) in low-viscosity immersion oil mix (Mineral oil, Sigma M8410 and Silicon oil, Sigma 378488, 1:1). Then, 3D reconstructions were generated in Arivis (Vision4D, Zeiss Edition 3.1.4).

For lineage tracing after CFDA-SE injection, the distribution of the progeny was mapped using optical sections. In addition, for trajectory mapping, the region including most CFSE labeled cells was manually traced using the objects drawing tool in Arivis, in order to visualize the trajectory in 3D. This same tool was also used to reconstruct the eye, optic lobe, lateral lips and posterior transition zone at Stage XV.2 for Figure 1, and to reconstruct the different lobes in the central brain at hatching for Figure 6.