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Getting started with TrackMate

59 bytes added, 09:17, 1 August 2013
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The first one deals with the <u>frame-to-frame linking</u>. It consists in creating small track segments by linking spots in one frame to the spots in the frame just after, not minding anything else. That is of course not enough to make us happy: there might be some spot missing, failed detection that might have caused your tracks to be broken. But let us focus on this one now.
Linking is made by minimizing a global cost (from one frame to another, yet). A short word on the linking logic: The base cost of linking a particle with another one is simply the squared distance<ref>. There is some theoretical grounds for that, if you are investigating Brownian motion. See the article [[TrackMate_algorithms#Cost_calculation_.26_Brownian_motion|page]] that details the segmenters and trackers for information.</ref> Following the proposal of Jaqaman ''et al.''<ref name="Jaqaman"/>, we also consider the possibility for a particle ''not'' to make any link, if is advantageous for the global cost. The sum of all costs are minimized to find to set of link for this pair of frame, and we move to the next one.
As for the simple tracker, the '''Max distance''' field helps preventing irrelevant linking to occur. Two spots separated by more than this distance will never be considered for linking. This also saves some computation time.
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