Fig. 5: Clonal N-cad loss induces localised shift towards crystalline archetype.

a–c N-cad knockout (KO) reduces amorphous organisation frequency at 12 hpf. a Representative renderings of control and N-cad KO embryos (nuclei segmented and coloured by archetype). KO via Cas9 + sgRNAs injection at the 1-cell stage. b Fraction of amorphously organised cells drops ~30% in KO. c Total cell number remains unchanged between conditions. d Mosaic KO (mKO) of N-cad generated via Cas9 + sgRNAs injection into a single cell at the 8-cell stage. CNS cells co-express NBT and N-cad under WT conditions; mKO cells lack N-cad but express NBT, enabling identification. e mKO is efficient, reducing N-cad+ fraction among NBT+ cells from ~98 to ~34%. f Whole-brain light sheet microscopy confirms mKO phenotype and organisational changes mKO clones (overview scale bar: 200 µm; zoom-in: 15 µm; N = 12 control, 15 mKO). g NBT+N-cad- cells from mKO embryos show a shift toward crystalline organisation in feature space, not observed in N-cad+ cells. Organisation quantified per sample and mapped onto the in toto organisational feature space (N: samples; n: total cells). h Crystalline fraction is significantly higher in mKO cells than N-cad+ cells, which are comparable to control. i N-cad-deficient cells organise crystalline only when neighbouring cells are also N-cad-deficient. Spatial correlation function g(r) shows distance-dependent likelihood of finding specific local organisation over uniform, random expectation. j Shift towards crystalline organisation is associated with reduced cell density and increased regularity. All p-values via Welch’s t-test, two-sided. Dots in bar/box plots: individual embryos (N = 3 WT or 4 KO in (b, c); N = 12 WT or 15 mKO in (e, h)). Error bars/bands: s.d. of mean. Box plots show median (centre), interquartile range (box), and 1.5× IQR (whiskers). Source data are provided as a Source Data file.