Using TSOAX is very similar to SOAX so we refer users to the detailed instructions in the SOAX Manual.  

The TSOAX output file contains a characteristic ID for each detected snake in the image sequence. The snake and junction coordinates are recorded sequentially according to the frame number. The junction locations are at the end of the snake coordinates for each frame. The snake tracks are saved as a sequence of snake IDs at the end of the output file. 

The two main new parameters in TSOAX are:

(1) Parameter c controlling the weight by which snakes detected at nearby locations in space are assigned to the same track, as a function of the number of time frames separating them. The value of 1/c is the number of frames beyond which the probability of assigning snakes to the same track decreases exponentially with frame number separation. This parameter should be increased (up to order 1) to improve track continuity over successive frames.

 (2) Option "Grouping,'' which enables the grouping process of snakes at detected junctions prior to tracking. This option can be enabled for tracking of intersecting elongating filaments and disabled for tracking the movement of filament segments in between junction points.

In TSOAX v.0.1.8 and later, the Initialize, Deform Snakes, and Track Snakes Process functions have to be executed in sequential manner by the user. "Track Snakes" solves the global correspondence part of the algorithm (this last step could be skipped if only multi-frame detection without tracking information is desired). Local correspondence is solved in "Deform Snakes" if the "Grouping" option is enabled. Grouping without solving local correspondence is not supported.

Please see the manuscript for examples of TSOAX usage.