def runTrackMate(imp, targetChannel, dt, radius, threshold, frameGap,
linkingMax, closingMax):
# Get the number of channels
nChannels = imp.getNChannels()
IJ.log("->Detection threshold used: " + str(threshold))
IJ.log("->Number of frames is: " + str(imp.getStackSize()))
IJ.log("->Target channel is: " + str(targetChannel))
IJ.log('->Number of channels to measure %d' % nChannels)
# Setup settings for TrackMate
settings = Settings()
settings.setFrom(imp)
settings.dt = dt
# Spot analyzer: we want the multi-C intensity analyzer.
settings.addSpotAnalyzerFactory(SpotMultiChannelIntensityAnalyzerFactory())
# Spot detector.
settings.detectorFactory = LogDetectorFactory()
settings.detectorSettings = settings.detectorFactory.getDefaultSettings()
settings.detectorSettings['RADIUS'] = radius
settings.detectorSettings['THRESHOLD'] = threshold
settings.detectorSettings['TARGET_CHANNEL'] = targetChannel
# Spot tracker.
#settings.trackerFactory = SparseLAPTrackerFactory()
settings.trackerFactory = LAPTrackerFactory()
settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap()
settings.trackerSettings['MAX_FRAME_GAP'] = frameGap
settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax
settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = closingMax
settings.trackerSettings['ALLOW_TRACK_MERGING'] = False
settings.trackerSettings['ALLOW_GAP_CLOSING'] = False
settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = False
settings.trackerSettings['ALLOW_TRACK_MERGING'] = False
settings.trackerSettings['ALTERNATIVE_LINKING_COST_FACTOR'] = 0.5
settings.trackerSettings['BLOCKING_VALUE'] = 1.0
settings.trackerSettings['CUTOFF_PERCENTILE'] = 1.0
#settings.trackerSettings['SPLITTING_MAX_DISTANCE'] = 16.0
# Run TrackMate and store data into Model.
model = Model()
trackmate = TrackMate(model, settings)
if not trackmate.checkInput() or not trackmate.process():
IJ.log('Could not execute TrackMate: ' +
str(trackmate.getErrorMessage()))
else:
return model, nChannels
import ij.IJ as IJ
import java.io.File as File
import java.util.ArrayList as ArrayList
# Swap Z and T dimensions if T=1
dims = imp.getDimensions() # default order: XYCZT
if (dims[4] == 1):
imp.setDimensions(dims[2, 4, 3])
# Get the number of channels
nChannels = imp.getNChannels()
# Setup settings for TrackMate
settings = Settings()
settings.setFrom(imp)
settings.dt = 0.05
# Spot analyzer: we want the multi-C intensity analyzer.
settings.addSpotAnalyzerFactory(SpotMultiChannelIntensityAnalyzerFactory())
# Spot detector.
settings.detectorFactory = LogDetectorFactory()
settings.detectorSettings = settings.detectorFactory.getDefaultSettings()
settings.detectorSettings['RADIUS'] = radius
settings.detectorSettings['THRESHOLD'] = threshold
# Spot tracker.
settings.trackerFactory = SparseLAPTrackerFactory()
settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap()
settings.trackerSettings['MAX_FRAME_GAP'] = frameGap
settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax
import ij. IJ as IJ import java.io.File as File import java.util.ArrayList as ArrayList # Swap Z and T dimensions if T=1 dims = imp.getDimensions() # default order: XYCZT if (dims[4] == 1): imp.setDimensions( dims[2,4,3] ) # Get the number of channels nChannels = imp.getNChannels() # Setup settings for TrackMate settings = Settings() settings.setFrom( imp ) settings.dt = 0.05 # Spot analyzer: we want the multi-C intensity analyzer. settings.addSpotAnalyzerFactory( SpotMultiChannelIntensityAnalyzerFactory() ) # Spot detector. settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = settings.detectorFactory.getDefaultSettings() settings.detectorSettings['RADIUS'] = radius settings.detectorSettings['THRESHOLD'] = threshold # Spot tracker. settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['MAX_FRAME_GAP'] = frameGap settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax
