Fig. 1

Overview of pipeline and GUI. A Flowchart representation of the Cell-ACDC pipeline. In the first step, the raw microscopy file(s) is/are automatically converted into TIFFs, the relevant metadata is extracted, and the files are arranged in the data structure required by Cell-ACDC. Next, the user can launch any of the three main modules: (1) GUI-based data prep where the user can align time-lapse data, select a z-slice or a projection for 3D z-stacks data, and/or crop data to reduce memory usage; (2) automatic segmentation/tracking of multiple positions and/or multiple time-frames (batch-processing) using the embedded neural network models. (3) B Main user interface, where the user visualizes and corrects the result of automatic segmentation and tracking. Almost all the available functions (such as brush, eraser, edit ID or auto-separate cells) are easily accessible from a button on the top toolbar, while sliders under the left image allow quick visualization of a specific position, frame, or z-slice. To enhance visualization of the signal in the left image, the user can adjust the intensity levels with two vertical sliders on the left side of the GUI. C Example of the output table generated by cell cycle annotations. The annotations are saved in CSV format allowing for quick import into GUI- or script-based spreadsheets software. The information saved includes the frame number, the cell ID, the cell cycle stage (either “G1” or “S/G2/M”), the generation number (automatically increased when division is annotated), the relative ID of the assigned parent cell, the relationship with the relative ID (either “mother” for both mother cells and cells in G1, or “bud” for buds that did not divide yet), the frame when the cell emerged and divided, and whether the history of the cell is fully known or not. Examples of cells with history not fully known are cells already present at frame 1 and cells appearing at a specific time point from outside of the field of view. Note that “is_history_known” is also visually highlighted with a question mark on the cell (e.g. cell ID 3, which was present at frame 1)