Groovy script to start TrackMate without the UI wizard

Run_TrackMate_Headless.groovy

#@ ImagePlus imp
#@ File (style = "directory", label = "Output folder") outputFolder
#@ String (label = "Output file name") filename
#@ double (label = "Spot radius", stepSize=0.1) radius
#@ double (label = "Quality threshold") threshold
#@ int (label = "Max frame gap") frameGap
#@ double (label = "Linking max distance") linkingMax
#@ double (label = "Gap-closing max distance") closingMax

import fiji.plugin.trackmate.Model
import fiji.plugin.trackmate.Settings
import fiji.plugin.trackmate.TrackMate

import fiji.plugin.trackmate.detection.LogDetectorFactory

import fiji.plugin.trackmate.tracking.LAPUtils
import fiji.plugin.trackmate.tracking.sparselap.SparseLAPTrackerFactory

import fiji.plugin.trackmate.action.ExportTracksToXML


// Swap Z and T dimensions if T=1
dims = imp.getDimensions() // default order: XYCZT
if (dims[4] == 1) {
	imp.setDimensions( dims[2,4,3] )
}

// Setup settings for TrackMate
settings = new Settings()
settings.setFrom(imp)
settings.dt = 0.05

settings.detectorFactory = new LogDetectorFactory()
settings.detectorSettings = settings.detectorFactory.getDefaultSettings()
println settings.detectorSettings

settings.detectorSettings['RADIUS'] = radius
settings.detectorSettings['THRESHOLD'] = threshold
println settings.detectorSettings

settings.trackerFactory = new SparseLAPTrackerFactory()
settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap()

settings.trackerSettings['MAX_FRAME_GAP']  = frameGap
settings.trackerSettings['LINKING_MAX_DISTANCE']  = linkingMax
settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE']  = closingMax

// Run TrackMate and store data into Model
model = new Model()
trackmate = new TrackMate(model, settings)

println trackmate.checkInput()
println trackmate.process()
println trackmate.getErrorMessage()

println model.getSpots().getNSpots(true)
println model.getTrackModel().nTracks(true)

// Save tracks as XML
if (!filename.endsWith(".xml")) {
	filename += ".xml"
}
outFile = new File(outputFolder, filename)
ExportTracksToXML.export(model, settings, outFile)