Extended Data Fig. 4: Lumen segmentations to track organoid and lumen morphodynamics in organoid development.

a) 2D cross sections showing organoid epithelium (gray) and segmented lumen (red) from day 4–7. Scale, 500 micrometers. Time is in hours. All 16 organoids were imaged in one experiment. b) 3D renderings of segmented lumen for the corresponding organoids shown in a. Time is in hours. c) Plot shows individual lumen volumes over time, from day 4 to day 9, of all segmented lumen from organoids shown in a and b. d) 3D renderings of lumen segmentations and tracking. Lumens from the same track show the same color. 16 organoids were imaged in one experiment with 4 different organoids in matrigel condition, 8 organoids from no-matrix condition and 4 organoids for diffusion barrier condition. Time is in hours. e-h) Graphs showing total organoid volume (e), epithelium volume (f), individual lumen volumes (g) and mean major axis length measurements (h) of all segmented lumen for all imaged organoids in d. Error bars indicate standard deviation and the center line indicates the mean (e, f, h). Total imaged organoids used for measurements: Matrigel (n = 4), no-matrix (n = 8) and Diffusion barrier (n = 4). i) 3D renderings of segmented lumen in organoids shown in Fig. 2g, color coded for lumen volume. j) 3D renderings of segmented lumen in organoids shown in Fig. 2g, showing a timecourse of lumen development in Matrigel, no-matrix and agarose conditions. Lumen were segmented and tracked overtime. Color shows the hours from the last fusion event with yellow indicating the just fused lumen.