Fig. 2: Collagen-grown organoids go through different phases of development.

Development phases are denoted by color bars which follow the color code presented in Fig. 1. Blue: onset, orange: extension, green: thickening, pink: lumen formation. Organoids shown here are grown in collagen. a Cellular motion patterns observed with live confocal imaging for each development phase (n = 66 organoids). Cell nuclei are stained with SiRDNA (white). Scale bars: 100 µm. From left to right: Day 4 SUM projection, and Day 7, Day 10, Day 13 maximum projections. b Top, time-projections of fluorescent beads (green, maximum projections) trajectories at different time points, indicating the deformation field around the organoids. Organoids are outlined in white and white arrows denote the direction of bead motion. From left to right: Day 4–5, Day 7–8, Day 8–9, Day 13–14. Scale bars: 100 µm. Bottom, corresponding representative squared displacement of a branch tip (solid black) and the motion of beads (dashed green) in front of it, for each development phase. c Immunostainings of Ki67 (green) and DAPI staining (blue) in organoids at different time points. Top scale bars, from left to right: 80 µm first picture, 200 µm second picture, 200 µm for the rest. Bottom (zoom-in of the top row images) scale bars: 50 µm. Confocal slices. d Cell number evolution in organoids, estimated based on maximum projections of DAPI stainings (n = 56 organoids). Blue line indicates the mean tendency. Error bars: 95% confidence interval (CI). e Ratio of Ki67- over DAPI-positive cells (n = 24 organoids). Blue line indicates the median. Error bars: standard deviation.