A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.
Different methods for intensity computation are provided:
intensity is considered in a circular region around the center of mass of the detection at each frame. Works also in 3D for a sphere. The radius is user-defined.
Several indicators are available: Mean, max, min, median, sum and variance of the intensity are computed along time.
same as above but every time a larger-radius (user-defined) disk is used for background estimation around each detection. The background pixels are those that fall within the large radius distance from the detection, while exceeding the small radius distance.
a gaussian shape is fitted at each detection location. The spatial position of the profile is fixed but the its optimal amplitude, as well as the background level, are estimated. The standard deviation of the Gaussian shape is user-defined and must be carefully chosen.
when the 'Spot Detector' and the 'Probabilistic particle tracker' plugins are used in combination to generate some tracks, it is possible to use the mask provided by the spot detector to evaluate locally the target intensity.
Here, several indicators are available based on the particle mask: Mean, max, min, median, sum and variance of the intensity are computed along time.
For each method, multiple channels are handled separately.Results can be visualized directly in the plugin user interface and exported to Microsoft Excel format (xls) are in a text file (.txt). In the latter case two files are generated: one that contains the intensity values as a list, and the second that contains the line numbers corresponding to the start of a new track in the first file.
The plugin is accessible through the TrackManager plugin.