Spots management¶

Transform spots¶

Menu Location: Plugins > Spots management > Transform spots > Mirror spots along X-axis
The command first calculates the mean x-coordinate of all spots. Then the x-coordinate of each spot is mirrored on the plane x = mean x. The ellipsoids are mirrored as well. The trackscheme is not modified.
Important: The command does not support mirroring of the image data. The spots will therefore appear to be in the wrong place.
Example:

Menu Location: Plugins > Spots management > Transform spots > Remove isolated spots
An isolated spot has no ancestors and no descendants
The command removes all isolated spots
Two refining conditions can be set:
- The spot must appear in the last time point
  - Lonely spots at the end of a video are much harder to find compared to lonely spots at the beginning.
- The spot’s label consists of numbers only
  - A label that does not only consist of numbers has likely been edited by the user. A label that consists of number only may indicate a spot that was automatically detected and not linked to a track.
Example:

Menu Location: Plugins > Spots management > Transform spots > Add center spots
Adds spots to the model at the average position of the selected spots of each time point. The new spots are connected by links in the order of the time points.
If there are time points without selected spots, no spot is added at that time point. In this case, the links span over the time points without spots.
If there are time points with multiple selected spots, the average position of the selected spots is calculated at that time point.
If no spots are selected, only a message dialog is shown.
Example:

Menu Location: Plugins > Spots management > Transform spots > Interpolate missing spots
Interpolates missing spots in the whole project.
Spots are considered missing, if there is a gap of more than one time point between two spots that are connected by a link.
Spots are interpolated by linearly interpolating their position and covariance matrix between the two spots that are connected by such a link and inserting the new spots and links between them.
Example:

Menu Location: Plugins > Spots management > Transform spots > Set radius of selected spots
Set the radius of all selected spots to the same value.
Example:

Menu Location: Plugins > Spots management > Rename spots > Label selected spots
The command opens a dialog where the user can enter a new label that will be set for all selected spots.
Example:

Menu Location: Plugins > Spots management > Rename spots > Change branch labels
The command opens a dialog where the user can enter a new label that will be set for all spots that belong to the branch that is currently focussed. Since the label of the last spot is shown is the branch label in the trackscheme branch view, this operation also changes the visible label of the branch.
Example:

Menu Location: Plugins > Spots management > Rename spots > Systematically label spots (extern-intern)
Derives the name of child cells from the name of the parent by appending a “1” or a “2” to the parent cell name.
The child cell further away from the center landmark gets “1” appended.
The child cell closer to the center landmark gets “2” appended.
The command is useful for systematically labeling cells in a lineage tree.
The renaming can be restricted to
- Selected spots
- Spots with a certain tag
- Spots that are yet labeled with a number only (indicating that they were automatically detected and not yet manually labeled)
- Spots whose names end with “1” or “2” (indicating that they were labeled with this command before)
Example: