Fig. 2: Analysis of laminar structure enables trajectory reconstruction and illuminates spatiotemporal dynamics of retinal organoid formation.

a, Schematic overview of the Laminator algorithm developed for laminar window segmentation, vertical orientation and trajectory inference. Laminar windows measure 16.25 × 1.625 μm and are oriented on the tissue contour by maximizing the Euclidean distance transform of the masked organoid for each window. b, Force-directed graph embedding of laminar window clusters (numbered) colored by timepoint. Node size represents the fraction of laminar windows within a timepoint. Insets colored by timepoints show representative oriented laminar windows per cluster. c, Graph with laminar window clusters colored based on pseudotime from diffusion analysis. d, Density plot showing laminar window proportion along the pseudotime, grouped by timepoint. e, Heat map showing fluorescence intensity measurements (Hoechst and CTBP2) or MTU intensity profiles (MTU 20, MTU 25 and MTU 3) along the inner–outer laminar axis across oriented laminar windows ordered by pseudotime. f, Representative oriented laminar windows from multiple positions along the pseudotime course showing nuclei location (Hoechst, white), proliferating cells (MTU 20, blue) and plexiform layers (MTU 25, red) along the inner–outer laminar axis. g, Scatter plot showing signal similarity of each laminar window to adult laminar windows over pseudotime. Dots are colored by timepoint. c, cluster; Wk, week.