The manual operations tools are designed to manually split, join, or refine selected cells or add new cells. The controls for these tools are organized into a panel on the bottom of the main window of MicrobeTracker and consist of four buttons: Join, Refine, Split, and Add. There tools may or may not update the lineage data, which depends on whether the Timelapse or Independent Frames regime is selected (see below).

Buttons and their actions

• Join - In order to join at least two cells must be selected. The program will detect the closest poles of these cells and will try to make one cell by joining the poles.
• Split - The split regime operates in two modes. The first (semi-autmatic) mode is called by clicking the Split button and requires exactly one cell to be selected. This mode will determine the splitting point automatically by finding the minimum "valley" in the phase image corresponding to the cell.
• Split + Shift - The second mode is called by clicking Split while holding the keyboard Shift button. This mode requires the user to pick the splitting point. The cell does not need to be selected in advance - the clicked one will be taken. To exit this mode, click outside of the cells of press Escape. This mode currently operates only when the mesh is available.
• Refine - In order to refine cells, at least one cell must be selected. The program will run cell detection routine with the current parameters taking the current cell shape for the starting point.
• Add - Cell addition only works if algorithm 1 or 4 is selected; in case of algorithm 1 you have to click on the contour, and in case of algorithm 4 on the centerline (the width is then determined by cellwidth paramerer); to terminate double click or press Enter, to cancel press Escape.
• Add+Shift - Hold Shift while finishing cell addition to call a dialog asking for the new cell number. This number must be a positive integer and must not exist on the current or any later frame.

If any of the manual operations fails, no change is made; otherwise the program replaces the cells in memory, but does not save them to the disk. Note that the program in these modes also does not automatically integrate the signal, which has to be added to the meshes separately (for example, by running it on the selected meshes in 'Reuse meshes' mode, see below). To undo the last manual operation, press Control + Z on the kerboard.

Operation in the Individual Frames regime

This regime is activated if the cells on which the operation is performed were originally detected in the Individual Frames regime, which is determined by the timelapse attribute in the data structure corresponding to the cells being set to 0 (false). The user can force this regime by adding forceindframes = 1 line to the parameter list. In this regime the frames are treated individually, so every cell is marked as newborn and no lineage information is kept.

Operation in the Timelapse regime

This regime is activated if the cells on which the operation is performed were originally detected in the Timelapse regime, which is determined by the timelapse attribute in the data structure corresponding to the cells being set to 1 (true), and if the forceindframes parameter is simultaneously set to 0 (false) or is absent. In this regime the program will attempt to reconstruct the lineage history (i.e. their birthframe, division frame and parent/progeny numbers, see Cell Numbering page) of the modified cells and their relatives.

Comparison of the two regimes