Adding Spot Features and Penalties to TrackMate

Posted by Greg on Mar 26, 2015; 10:17am
URL: http://imagej.273.s1.nabble.com/Adding-Spot-Features-and-Penalties-to-TrackMate-tp5012186.html

Hi,

right now I use TrackMate in the following setup: I use a custom jython script to segment the images, so I do the segmentation/detection completely outside of TrackMate. Then, I construct a TrackMate Model following this nice guide here:

http://fiji.sc/Scripting_TrackMate#Manually_creating_a_model

After assembling all the Spots to the Model via model.addSpotTo(...), I initiate the automated tracking via

trackmate = TrackMate(model, settings)
trackmate.execTracking()

This works wonderfully, but I think I can improve the results by incorporating more Spot features from my custom detection.
My question is, how can I add further features to Spots besides x,y,z,radius and quality ? And how do I set the penalties for them? I know from the TrackMate gui that you can add other features like intensity and then assign factors for the link-cost computation. I can not figure out how to use the API to accomplish this. For example here http://javadoc.imagej.net/Fiji/fiji/plugin/trackmate/Spot.html
nothing is said about including other features as the default ones. Or this one here
http://fiji.sc/How_to_write_your_own_spot_feature_analyzer_algorithm_for_TrackMate#The_spot_analyzer
deals from my understanding more with the Detection than the Tracking itself ?

Any help appreciated !

Regards,
Greg