Extended Data Fig. 8: Performance on different system: blastocyst.

(a) Lineages color-coded by error-rates for a blastocyst developing from the 16 to 64-cell stage (BlastoSPIM 1.0 dataset), as obtained by tracking without manual curation. Many cells can be tracked from the beginning to the end without any potential mistakes. b) Blastocyst cells undergoing large movements, with subsequent timepoints shown in green and magenta. Green square and red circles indicate the current and subsequent detected centroid position, respectively. The red line connects these positions, while the blue line connects to the centroid position in the previous time point. When either marker is not present, then the corresponding positions are >4 μm away from the z-slice shown. Our method tracks cells even for displacements larger than the typical nucleus size. c) Histogram of potential cell displacements in a single frame, for all potential links, with the correctness of each link established by manual curation. Many true links represent fast-moving cells, corresponding to displacements between timesteps of >1 cell radius, or ~6 μm, large compared to cell movements in intestinal organoids both in absolute and relative terms. d) Precision, recall and accuracy versus displacement between timesteps, for the optimal tracking solution before manual curation. Even fast-moving cells are tracked with high accuracy. e, f) Top: measured link likelihood versus likelihoods predicted by marginalization, either without (e) or with (f) recalibration on newly corrected data. 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 2 different blastocysts, corresponding to the data in (c) and (d). Shaded region is S.D.M. Without recalibration (c) predicted likelihoods are overconfident. Using a recalibrated threshold does not majorly increase the number of links to be checked (d, bottom histogram), as the bulk of links in the tracking solution remains above the 99% probability threshold (black vertical line).