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TrackMate Algorithms

2,267 bytes added, 09:54, 17 September 2019
Track analyzers.
[https://github.com/fiji/TrackMate/blob/master/src/main/java/fiji/plugin/trackmate/features/track/TrackSpotQualityFeatureAnalyzer.java code on github]
This feature analyzer simply takes the mean, max, min, median and standard deviation of the distribution of the '''Quality''' values of all the spots in a track. In this respect, it is similar to the previous analyzer (Track velocity) that does the same for link velocity.   === Linear track analysis.=== This feature analyzer comes from a TrackMate extra.It is available as a jar that you should download separately and drop into the jars folder of you Fiji installation.Check [[TrackMate#Extensions]] to get it. It was written to add track descriptor that would help characterize the track motility. I simply took some of the feature described in the following paper: ''Methods for cell and particle tracking.'', Meijering E, Dzyubachyk O, Smal I., Methods Enzymol. '''2012''';504:183-200. [https://www.sciencedirect.com/science/article/pii/B9780123918574000094 link to paper].  ==== Total distance traveled. ==== This feature value reports the full distance the particle traveled throughout the track. It is computed by taking the sum of the link distance (distance from the source spot to the target spot of the link, for all links).  It really report how much the particle 'walked'. For instance, if a particle travels along a equilateral triangle of size 10 µm, going back to its starting point, this feature will return 30 µm. While the '''Track displacement''' feature described above will return 0 µm. ==== Max distance traveled. ==== This feature reports the distance to the furthest point of the track, with respect to the first spot in time of the track. To get this value we simply computes the straight-line distance between each spot of the track to the first spot of the track, and returns the largest distance. This distance is a "straight-line" distance. In our example above with the particle that walks over a triangle, this feature value would be 10 µm. ==== Confinment ratio. ==== The confinment ratio tells how "efficient" was a track displacement in getting far away from its starting point.It is defined as the net-displacement divided by the total-distance. The net-displacement is given by the '''Track displacement''' feature, and the total distance is given by the '''Total distance traveled''' feature. It is a unitless value that ranges from 0 to 1. Values close to 0 indicate a confined movement, where the particle would stay close to its starting point. Values close to 1 indicate that the particle travels along a line with a constant orientation. ==== Mean straight line speed. ====
== Spot trackers ==
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