Extended Data Fig. 6: Tracking performance on organoids with perturbed dynamics.

(a) The number of detected cells in the imaging volume for two organoids treated with palbociclib, which blocks cell division. After ~10 h of Palbociclib exposure, cell death dominates over cell division, leading to decreased cell numbers. (b) Distribution of cell cycle lengths (0 h is cell cycle start) plotted for the same two organoids. Cells divide either slowly (>25 h) or not at all, consistent with Palbociclib action. (c) Thirty randomly selected lineages show tracking with very low potential error rates. Cells generally divide only once, or not at all. (d) Top: measured link likelihood versus likelihoods predicted by the neural network. Data is shown for all possible links (black) or links that are either in the global solution (blue). Dotted line is perfect calibration. Data is for the 2 different organoids in (a) and (b). Shaded region is S.D.M. Predictions for Palbociclib-treated organoids remain well-calibrated, indicating that perturbation of cell dynamics does not affect the quality of error predictions. Bottom: histogram of the predictions. Almost all links in the tracking solution (blue) are above the 99% probability threshold (vertical line) indicating highly confident tracking.