fiji.plugin.trackmate.tracking.jaqaman

Class SegmentTracker

java.lang.Object

fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker

All Implemented Interfaces:

SpotTracker, Algorithm, Benchmark, MultiThreaded, OutputAlgorithm<org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge>>

public class SegmentTracker
extends Object
implements SpotTracker, Benchmark

This class tracks deals with the second step of tracking according to the LAP tracking framework formulated by Jaqaman, K. et al. "Robust single-particle tracking in live-cell time-lapse sequences." Nature Methods, 2008.

In this tracking framework, tracking is divided into two steps:

1. Identify individual track segments
2. Gap closing, merging and splitting

and this class does the second step.

It first extract track segment from a specified graph, and create a cost matrix corresponding to the following events: Track segments can be:

• Linked end-to-tail (gap closing)
• Split (the start of one track is linked to the middle of another track)
• Merged (the end of one track is linked to the middle of another track
• Terminated (track ends)
• Initiated (track starts)

The cost matrix for this step is illustrated in Figure 1c in the paper. However, there is some important deviations from the paper: The alternative costs that specify the cost for track termination or initiation are all equals to the same fixed value.

The class itself uses a sparse version of the cost matrix and a solver that can exploit it. Therefore it is optimized for memory usage rather than speed.

Constructor Summary

Constructors

Constructor and Description
SegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph, Map<String,Object> settings)
SegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph, Map<String,Object> fullsettings, Logger logger)

Method Summary

Modifier and Type	Method and Description
boolean	checkInput()
String	getErrorMessage()
int	getNumThreads()
long	getProcessingTime()
org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge>	getResult()
boolean	process()
void	setLogger(Logger logger) Sets the Logger instance that will receive messages from this SpotTracker.
void	setNumThreads()
void	setNumThreads(int numThreads)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SegmentTracker

public SegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
                      Map<String,Object> settings)

SegmentTracker

public SegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
                      Map<String,Object> fullsettings,
                      Logger logger)

Method Detail

getResult

public org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> getResult()

Specified by:

getResult in interface OutputAlgorithm<org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge>>

checkInput

public boolean checkInput()

Specified by:

checkInput in interface Algorithm

process

public boolean process()

Specified by:

process in interface Algorithm

getErrorMessage

public String getErrorMessage()

Specified by:

getErrorMessage in interface Algorithm

getProcessingTime

public long getProcessingTime()

Specified by:

getProcessingTime in interface Benchmark

setLogger

public void setLogger(Logger logger)

Description copied from interface: SpotTracker

Sets the Logger instance that will receive messages from this SpotTracker.

Specified by:

setLogger in interface SpotTracker

Parameters:

logger - the logger to echo messages to.

setNumThreads

public void setNumThreads()

Specified by:

setNumThreads in interface MultiThreaded

setNumThreads

public void setNumThreads(int numThreads)

Specified by:

setNumThreads in interface MultiThreaded

getNumThreads

public int getNumThreads()

Specified by:

getNumThreads in interface MultiThreaded