Uses of Class
fiji.plugin.trackmate.TrackMate

Packages that use TrackMate

Package	Description
fiji.plugin.trackmate
fiji.plugin.trackmate.action
fiji.plugin.trackmate.action.autonaming
fiji.plugin.trackmate.action.closegaps
fiji.plugin.trackmate.action.fit
fiji.plugin.trackmate.gui.components
fiji.plugin.trackmate.gui.wizard
fiji.plugin.trackmate.gui.wizard.descriptors

Uses of TrackMate in fiji.plugin.trackmate

Methods in fiji.plugin.trackmate that return TrackMate

Modifier and Type	Method and Description
protected TrackMate	ManualTrackingPlugIn.createTrackMate(Model model, Settings settings)
protected TrackMate	TrackMatePlugIn.createTrackMate(Model model, Settings settings) Hook for subclassers: Creates the TrackMate instance that will be controlled in the GUI.

Methods in fiji.plugin.trackmate with parameters of type TrackMate

Modifier and Type	Method and Description
protected WizardSequence	ManualTrackingPlugIn.createSequence(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings)
protected WizardSequence	TrackMatePlugIn.createSequence(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings) Hook for subclassers: Will create and position the sequence that will be played by the wizard launched by this plugin.
protected void	LoadTrackMatePlugIn.postRead(TrackMate trackmate) Hook for subclassers: The TrackMate object is loaded and properly configured.

Uses of TrackMate in fiji.plugin.trackmate.action

Methods in fiji.plugin.trackmate.action with parameters of type TrackMate

Modifier and Type	Method and Description
static ij.ImagePlus	CaptureOverlayAction.capture(TrackMate trackmate, int first, int last, Logger logger) Generates a new ImagePlus of type RGB, 2D over time, made by capturing each time frame of the TrackMate display.
static ij.ImagePlus	LabelImgExporter.createLabelImagePlus(TrackMate trackmate, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labeIdPainting) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
static ij.ImagePlus	LabelImgExporter.createLabelImagePlus(TrackMate trackmate, boolean exportSpotsAsDots, boolean exportTracksOnly, LabelImgExporter.LabelIdPainting labelIdPainting, Logger logger) Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
void	TrackMateAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent) Executes this action within an application specified by the parameters.
void	IJRoiExporter.IJRoiExporterAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	ResetSpotTimeFeatureAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	CaptureOverlayAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame gui)
void	ISBIChallengeExporter.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	MergeFileAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	ExtractTrackStackAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	RecomputeFeatureAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	MotilityLabExporter.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	ExportStatsTablesAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	TrackBranchAnalysis.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	TrimNotVisibleAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	PlotNSpotsVsTimeAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	ComputeDistanceToRoiAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	LabelImgExporter.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame gui)
void	CTCExporterAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	ExportAllSpotsStatsAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	IcyTrackExporter.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
void	ExportTracksToXML.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)
static String	CTCExporter.exportAll(String exportRootFolder, TrackMate trackmate, CTCExporter.ExportType exportType, Logger logger)
static void	CTCExporter.exportOriginalImageData(String exportRootFolder, int saveId, TrackMate trackmate, Logger logger)
static void	CTCExporter.exportSegmentationData(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate, Logger logger) Writes the segmentation ground-truth files.
static void	CTCExporter.exportSettingsFile(String exportRootFolder, int saveId, TrackMate trackmate, Logger logger) Saves the settings part as XML for reference.
static String	CTCExporter.exportTrackingData(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate, Logger logger)
static String	CTCExporter.getExportTrackingDataPath(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate) Returns the folder in which the tracking data will be exported.
static void	RecomputeFeatureAction.recompute(TrackMate trackmate, Logger logger)
static ij.ImagePlus	ExtractTrackStackAction.trackStack(TrackMate trackmate, Spot spot, boolean do3d, Logger logger)
static ij.ImagePlus	ExtractTrackStackAction.trackStack(TrackMate trackmate, Spot start, Spot end, boolean do3d, Logger logger)

Uses of TrackMate in fiji.plugin.trackmate.action.autonaming

Methods in fiji.plugin.trackmate.action.autonaming with parameters of type TrackMate

Modifier and Type	Method and Description
void	AutoNamingAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)

Constructors in fiji.plugin.trackmate.action.autonaming with parameters of type TrackMate

Constructor and Description
AutoNamingController(TrackMate trackmate, Logger logger)

Uses of TrackMate in fiji.plugin.trackmate.action.closegaps

Methods in fiji.plugin.trackmate.action.closegaps with parameters of type TrackMate

Modifier and Type	Method and Description
void	CloseGapsByLinearInterpolation.execute(TrackMate trackmate, Logger logger)
void	CloseGapsByDetection.execute(TrackMate trackmate, Logger logger)
void	GapClosingMethod.execute(TrackMate trackmate, Logger logger) Performs the gap closing.
void	CloseGapsAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)

Constructors in fiji.plugin.trackmate.action.closegaps with parameters of type TrackMate

Constructor and Description
CloseGapsController(TrackMate trackmate, Logger logger)

Uses of TrackMate in fiji.plugin.trackmate.action.fit

Methods in fiji.plugin.trackmate.action.fit with parameters of type TrackMate

Modifier and Type	Method and Description
void	SpotGaussianFittingAction.execute(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings, Frame parent)

Constructors in fiji.plugin.trackmate.action.fit with parameters of type TrackMate

Constructor and Description
SpotFitterController(TrackMate trackmate, SelectionModel selectionModel, Logger logger)

Uses of TrackMate in fiji.plugin.trackmate.gui.components

Constructors in fiji.plugin.trackmate.gui.components with parameters of type TrackMate

Constructor and Description
ActionChooserPanel(ActionProvider actionProvider, TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings)
GrapherPanel(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings)

Uses of TrackMate in fiji.plugin.trackmate.gui.wizard

Constructors in fiji.plugin.trackmate.gui.wizard with parameters of type TrackMate

Constructor and Description
TrackMateWizardSequence(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings)

Uses of TrackMate in fiji.plugin.trackmate.gui.wizard.descriptors

Constructors in fiji.plugin.trackmate.gui.wizard.descriptors with parameters of type TrackMate

Constructor and Description
ActionChooserDescriptor(ActionProvider actionProvider, TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings)
ChooseDetectorDescriptor(DetectorProvider detectorProvider, TrackMate trackmate)
ChooseTrackerDescriptor(TrackerProvider trackerProvider, TrackMate trackmate)
ExecuteDetectionDescriptor(TrackMate trackmate, LogPanel logPanel)
ExecuteTrackingDescriptor(TrackMate trackmate, LogPanel logPanel)
GrapherDescriptor(TrackMate trackmate, SelectionModel selectionModel, DisplaySettings displaySettings)
InitFilterDescriptor(TrackMate trackmate, FeatureFilter filter)
SaveDescriptor(TrackMate trackmate, DisplaySettings displaySettings, WizardSequence sequence)
SpotFilterDescriptor(TrackMate trackmate, List<FeatureFilter> filters, FeatureDisplaySelector featureSelector)
TrackFilterDescriptor(TrackMate trackmate, List<FeatureFilter> filters, FeatureDisplaySelector featureSelector)