Manual Operations
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
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
Button | Regime | |
---|---|---|
Independent Frames | Timelapse | |
Add | Assigns the first available free cell number in the frame and mark as newborn. | Assigns the first available free cell number in all frames and mark as newborn. |
Add+Shift | Asks for the number of the new cell. Must not be present on this frame. | Asks for the number of the new cell or (alternatively) the number of the mother cell (if the cell just divided; see also the Cell Numbering page). If the new cell is present on any of the previous frames, it will keep the birthframe of that cell, otherwise it will be marked as newborn. The mother cell must be present on any of the previous frames. |
Split | The orientation (old-new pole) is determined but is not marked as known. | The orientation (old-new pole) is determined and marked as known. If the frame is not the first one, one of the cells is marked as the daughter of the other on all subsequent frames. |
Join | The larger numbered cell dissapears, the other one keeps all its attributes. | Joining of more than two cells is not allowed. If the younger (larger numbered) cell was not present before but present in the next frame, its birthframe is updated. Otherwise the attributes remain unchanged. |
Refine | The lineage data remains unchanged. |
Top pages: Buttons and Controls, MicrobeTracker Suite.