![]() TrackMate relies on several different libraries and plugins for data manipulation, analysis and visualization. If they are not enough, functions are provided to export the whole results to other analysis software such as MATLAB. Various plots can be made directly from the plugin and for instance used to derive numerical results from the tracks. Some tools for track and spot analysis are included. But you are also offered to edit the results manually, or even to completely skip the automatic steps, and perform fully manual segmentation and/or linking. Several automated segmentation and linking algorithms are provided. The visualization tools are the one shipped with Fiji and interact nicely with others plugin. The segmentation / filtering / particle-linking processes and results are visualized immediately in 2D or 3D, allowing to judge their efficiency and adjust their control parameters. It privileges tracking schemes where the segmentation step is decoupled from the particle-linking step. The tracking process is divided in a series of steps, through which you will be guided thanks to a wizard-like GUI. TrackMate aims at offering a generic solution that works out of the box, through a simple and sensible user interface. Its development focuses on achieving two concomitant goals: For instance, the mean, max, min and median intensity will be computed, as well as the estimated radius and orientation for each spot, allowing to follow how these feature evolves over time for one object. Though these objects are solely represented by a X,Y,Z,T coordinates array, TrackMate can compute numerical features for each spot, given its coordinates and a radius. Examples include sub-resolution fluorescent spots, labelled traffic vesicles, nuclei or cells imaged at low resolution. They are bright objects over a dark background for which the object contour shape is not important, but for which the main information can be extracted from the X,Y,Z coordinates over time. TrackMate can deal with single particles, or spot-like objects. These tracks can then be either visualized or yield further analysis results such as velocity, total displacement, diffusion characteristics, division events, etc. Each spot is segmented in multiple frames and its trajectory is reconstructed by assigning it an identity over these frames, in the shape of a track. SPT is an image analysis challenge where the goal is to segment and follow over time some labelled, spot-like structures. TrackMate provides the tools to perform single particle tracking (SPT).
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