Fig. 4: Applications.
a, Selected lineages before review, with color indicating associated error rates. **, Flagged error with a clearly erroneous lineage structure (unrealistically short cell cycle); *, Not identifiable as an error based on lineage structure alone. Error probabilities (perr) are calculated for entire lineage trees by combining underlying error rates. b, Blue lineage fragments are high confidence (<0.01 error rate). Users can identify high-confidence cell cycles (black arrow) or sister pairs (gray arrow) without manual review. c, Lineage trees after manual review. Gray lineage sections were added following curation. Compared to a, error probabilities now indicate high confidence in the lineages. d, Characterization of potential errors. Links flagged as potential errors either represent (dis)appearing cells (blue) or are low confidence (red). A substantial proportion of potential errors represented short tracks of cellular debris (gray), with no impact on lineage trees when removed and only few actual errors that required correction. e, Three-dimensional reconstruction with colors indicating cells in the same lineage. f, Automated analysis without manual review by filtering out low-confidence links and performing survival analysis on the resulting, partly censored data. g,h, Survival curve of the fraction of cells not divided at time t after birth (g) or after the sister’s division (h). Shown are manually annotated (gray) and automatically filtered (red) data for a single organoid. Vertical dashed line denotes average cell cycle duration, while the horizontal line shows the inferred fraction of cells that stop dividing. Proliferation ceases in 32% of cells (g), while 97% of sister cells divide within a 10-h window of one another (h), highlighting the dominance of symmetric divisions in intestinal organoid growth. Shaded region, 95% confidence interval of the surviving fraction estimate. i, Lineage dynamics parameters obtained by fully automated (red) or manual analysis (gray) show excellent agreement. j,k, Automatically obtained cell cycle duration and its difference between sisters (j, n = 20 organoids) and the fractions of cells that cease proliferation and of asymmetric sisters in which only one cell divides (k, n = 19 organoids). Dots represent individual organoids, and error bars are the standard deviation around the mean.
