Fig. 1

Whole-brain serial sectioning and image reconstruction pipeline. a Scanning electron microscopy (SEM) image showing a magnified view of the open brain in c, revealing big Joseph cells on the top layer (arrowhead). b SEM image showing a lateral view of an amphioxus head. c SEM image showing a dorsal image of an amphioxus head opened dorsally at the level of the brain and neural tube. Pipeline is shown as steps: (1) coronal sections taken at the level of the brain, (2) multidimensional imaging of hybridised sections, and (3) stitching of multiple images to reconstruct patterns across the entire brain. Scale bars in 3 are 125 μm, otherwise as indicated