Extended Data Fig. 3: Lightsheet imaging and lumen segmentations to track tissue morphodynamics in organoid development.

a) 2D cross sections from a time course lightsheet movie showing lumen development. Organoids were generated from 100% single label iPSC lines (histone2B-mEGFP mEGFP-beta-actin, mTagRFP–T–CAAX, mTagRFP–T-tubulin-alpha1b and mTagRFP–T-laminB1). Scale, 100 micrometers. Time is in hours. Three organoids were imaged for each label (n = 3). b) 2D cross sections from 3D imaged and segmented organoids shown in a, with organoid epithelium (gray) and segmented lumen (red) on day 9. Scale Bar is 100 micrometers. c) Violin plots showing 3D lumen volumes of organoids shown in a, over time. d) Violin plots showing lumen volumes on day 9, with horizontal bars indicating pairwise Wilcoxon rank sum test corrected for multiple testing using the Bonferroni method. P-values were > 0.5 for all comparisons. n.s. = not significant. e) Violin plots showing the major axis lengths of lumen over time. f) Violin plots showing the major axis lengths of lumen on day 9, with horizontal bars indicating Wilcoxon rank sum test corrected for multiple testing using the Bonferroni method. P-values were > 0.5 for all comparisons. n.s. = not significant. For p-values (d,f) see Supplementary Table 13. (c-f) The boxes of the violin plots show the interquartile range, the line at the center is the median and the whiskers extend to the data range excluding outliers.