Fig. 2

Examples of Cell-ACDC functions. A Visual help: information such as the cell ID, the cell cycle stage, and the generation number, as well as the segmentation contour are conveniently displayed on the cell image. Information is colour-coded: red for newly emerged/appeared cells, white for cells already present in the previous frame, and yellow for disappeared cells. This allows for quick identification of tracking errors since often lost cells are caused by an ID misplaced due to the tracking algorithm failing. B Automatic separation: With a single click on the merged cells, the user can trigger automatic separation. With a combination of convexity defects detection and contour approximation, the algorithm separates the cells along the predicted plane. C Annotate cell as “dead”: A cell can be annotated as dead with a single click, and it is then considered dead for all future frames. The user can always annotate the cell as not dead at any point in future frames. D Annotate cell division: Cell division is often visible due to a sudden movement of the bud. The user can then click on the cell that divided to annotate it. The related information, such as generation number and cell cycle stage, is then automatically updated for both the mother and daughter cell. This annotation can be undone at any time point in past or future frames and all the information in all the involved frames is automatically updated. E Automatic mother-bud pairing: When a new cell appears, an automatic assignment algorithm is triggered. Using a cost-optimization routine, the new cell is assigned to the predicted mother. F Mother-bud pairing correction: When the automatic mother-bud pairing fails, the user can correct the assignment with a drag and drop gesture. This can be done at any time-point of the life of the new cell and the pairing is automatically corrected on all the relevant past and future frames. G Overlay fluorescent signal from tagged histone Htb1. If available, the user can overlay a fluorescent signal. This is helpful, if, for example, the tagged gene is a cell cycle marker that can aid cell cycle annotations. H Overlay fluorescent signal from tagged septin ring (Cdc10). I Representative images of murine hematopoietic stem cells segmented based on bright-field signal using Cell-ACDC (based on Cellpose, using the median z-projection). J Segmentation using Cell-ACDC (based on YeaZ) of fission yeast (S. pombe). Data from [41]