Index (TrackMate 7.14.0 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.GrapherDescriptor
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseDetectorDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseTrackerDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.InitFilterDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotDetectorDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotFilterDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotTrackerDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.TrackFilterDescriptor
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
AbstractAnimator - Class in fiji.plugin.trackmate.gui.wizard: Mother abstract class for animators that can animatethings.
AbstractAnimator(long) - Constructor for class fiji.plugin.trackmate.gui.wizard.AbstractAnimator: Create new animator with the given duration.
AbstractEdgeAnalyzer - Class in fiji.plugin.trackmate.features.edges: Abstract class for edge analyzers that are local and not manual.
AbstractEdgeAnalyzer(String, String, List<String>, Map<String, String>, Map<String, String>, Map<String, Dimension>, Map<String, Boolean>) - Constructor for class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
AbstractFeatureGrapher - Class in fiji.plugin.trackmate.features
AbstractFeatureGrapher(String, List<String>, Dimension, Map<String, Dimension>, Map<String, String>, String, String) - Constructor for class fiji.plugin.trackmate.features.AbstractFeatureGrapher
AbstractProvider<K extends TrackMateModule> - Class in fiji.plugin.trackmate.providers
AbstractProvider(Class<K>) - Constructor for class fiji.plugin.trackmate.providers.AbstractProvider
AbstractSemiAutoTracker<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection.semiauto: A class made to perform semi-automated tracking of spots in TrackMate & friends
AbstractSemiAutoTracker(Model, SelectionModel, Logger) - Constructor for class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
AbstractSemiAutoTracker.SearchRegion<R> - Class in fiji.plugin.trackmate.detection.semiauto: A utility class made to return the information on a neighborhood generated from a source around a Spot.
AbstractSpotFeatureAnalyzer<T extends RealType<T>> - Class in fiji.plugin.trackmate.features.spot
AbstractSpotFeatureAnalyzer() - Constructor for class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
AbstractSpotFitter - Class in fiji.plugin.trackmate.action.fit
AbstractSpotFitter(ImagePlus, int) - Constructor for class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
AbstractSpotFitter.Observation - Class in fiji.plugin.trackmate.action.fit
AbstractStringArgument() - Constructor for class fiji.plugin.trackmate.util.cli.CLIConfigurator.AbstractStringArgument
AbstractTMAction - Class in fiji.plugin.trackmate.action
AbstractTMAction() - Constructor for class fiji.plugin.trackmate.action.AbstractTMAction
AbstractTrackAnalyzer - Class in fiji.plugin.trackmate.features.track: Abstract class for track analyzers that are local and not manual.
AbstractTrackAnalyzer(String, String, List<String>, Map<String, String>, Map<String, String>, Map<String, Dimension>, Map<String, Boolean>) - Constructor for class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
AbstractTrackMateModelView - Class in fiji.plugin.trackmate.visualization: An abstract class for spot displayers, that can overlay detected spots and tracks on top of the image data.
AbstractTrackMateModelView(Model, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.LabelElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.Separator
accept(StyleElements.StyleElementVisitor) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
accept(StyleElements.StyleElementVisitor) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElement
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.DoubleArgument
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Flag
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.IntArgument
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.PathArgument
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.StringArgument
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator.ExecutablePath
accept(CLIConfigurator.ArgumentVisitor) - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator.CondaEnvironmentCommand
accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter: Returns true if file is a directory or ends with the specified extension.
accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter: Returns true if the file is a directory or has a .xml or .xml.gz extension.
accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter: Returns true if the file is a directory or ends with a known image extension.
ActionChooserDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
ActionChooserDescriptor(ActionProvider, TrackMate, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.ActionChooserDescriptor
ActionChooserPanel - Class in fiji.plugin.trackmate.gui.components
ActionChooserPanel(ActionProvider, TrackMate, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.components.ActionChooserPanel
actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SaveAction
actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions.EditAction
ActionProvider - Class in fiji.plugin.trackmate.providers
ActionProvider() - Constructor for class fiji.plugin.trackmate.providers.ActionProvider
add(double, Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.Colormap: Add a color to the color list of this paint scale, at the position given by value.
add(Spot, Integer) - Method in class fiji.plugin.trackmate.SpotCollection: Adds the given spot to this collection, at the specified frame, and mark it as visible.
add(double) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
add(CLIConfigurator.Argument<?, ?>) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
ADD_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
addAllAnalyzers() - Method in class fiji.plugin.trackmate.Settings: All the spot analyzers, edge analyzers and track analyzers discovered at runtime.
addAllEdges(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
addAllSpots(Collection<Spot>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel: Add an ChangeListener to this panel.
addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.components.FilterPanel: Add an ChangeListener to this panel.
addChoice(String) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceAdder
addChoiceAll(Collection<String>) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceAdder
addChoiceArgument() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
addDoubleArgument() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
addEdge(Spot, Spot, double) - Method in class fiji.plugin.trackmate.Model: Creates a new edge between two spots, with the specified weight.
addEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.ModelChangeEvent
addEdgeAnalyzer(EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings: Adds a EdgeAnalyzer to the List of edge analyzers configured.
addEdgeAnalyzer(int, EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings: Adds a EdgeAnalyzer to the List of edge analyzers configured, at the specified index.
addEdgeManually(mxCell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: This method is called when the user has created manually an edge in the graph, by dragging a link between two spot cells.
addEdgeToSelection(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.SelectionModel
addEdgeToSelection(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.SelectionModel
addEnvironment(String) - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator.CondaEnvironmentCommand
addExtraArgument(T) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator: Adds an extra argument, defined by other means than the adder methods.
addFeaturePenaltyToSettings(Map<?, ?>, Object, Object, Object, StringBuilder) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils: Utility method to put a value in a map, contained in a mother map.
addFilterPanel() - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
addFilterPanel(String) - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
addFilterPanel(FeatureFilter) - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
addFlag() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
addIntArgument() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
addJGraphTEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
addJGraphTVertex(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
addModelChangeListener(ModelChangeListener) - Method in class fiji.plugin.trackmate.Model
addOnClosingEvent(JComponent, Runnable) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
addOverlay(Roi) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
addPathArgument() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
addSelectableArguments() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator: Creates a 'one or the other' relationships.
addSelectionChangeListener(SelectionChangeListener) - Method in class fiji.plugin.trackmate.SelectionModel
addSpot(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent
addSpot(boolean) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
addSpotAnalyzerFactory(SpotAnalyzerFactoryBase<?>) - Method in class fiji.plugin.trackmate.Settings: Adds a SpotAnalyzerFactory to the List of spot analyzers configured.
addSpotAnalyzerFactory(int, SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings: Adds a SpotAnalyzerFactory to the List of spot analyzers configured, at the specified index.
addSpotFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings: Add a filter to the list of spot filters.
addSpotTo(Spot, Integer) - Method in class fiji.plugin.trackmate.Model: Adds a single spot to the collections managed by this model, mark it as visible, then update its features.
addSpotToSelection(Spot) - Method in class fiji.plugin.trackmate.SelectionModel
addSpotToSelection(Collection<Spot>) - Method in class fiji.plugin.trackmate.SelectionModel
addStringArgument() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
addTrackAnalyzer(TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings: Adds a TrackAnalyzer to the List of track analyzers configured.
addTrackAnalyzer(int, TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings: Adds a TrackAnalyzer to the List of track analyzers configured, at the specified index.
addTrackFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings: Add a filter to the list of track filters.
addUnseenChildrenOf(V) - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator: This is where we add the multiple children in proper sorted order.
addUnseenChildrenOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedDepthFirstIterator
addUnseenChildrenOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedSortedDepthFirstIterator
AdvancedKalmanTracker - Class in fiji.plugin.trackmate.tracking.kalman: Kalman tracker factory with features cost addition and segment splitting / merging.
AdvancedKalmanTracker(SpotCollection, Map<String, Object>) - Constructor for class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
AdvancedKalmanTrackerFactory - Class in fiji.plugin.trackmate.tracking.kalman: Kalman tracker factory with features cost addition and segment splitting / merging.
AdvancedKalmanTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
AdvancedKalmanTrackerSettingsPanel - Class in fiji.plugin.trackmate.gui.components.tracker
AdvancedKalmanTrackerSettingsPanel(String, String, Collection<String>, Map<String, String>) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.AdvancedKalmanTrackerSettingsPanel
AllSpotsTableView - Class in fiji.plugin.trackmate.visualization.table
AllSpotsTableView(Model, SelectionModel, DisplaySettings, String) - Constructor for class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
AlphanumComparator - Class in fiji.plugin.trackmate.util: Alpha-numerical comparator.
ANALYSER_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
ANALYSER_KEY_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
analyze(DefaultWeightedEdge, Model) - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
analyze(DefaultWeightedEdge, Model) - Method in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
analyze(DefaultWeightedEdge, Model) - Method in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
analyze(DefaultWeightedEdge, Model) - Method in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
analyze(DefaultWeightedEdge, Model) - Method in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
analyze(Integer, Model) - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
analyze(Integer, Model) - Method in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
analyze(Integer, Model) - Method in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
analyze(Integer, Model) - Method in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
analyze(Integer, Model) - Method in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
analyze(Integer, Model) - Method in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
ANALYZER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
appendDisplaySettings(DisplaySettings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
appendGUIState(String) - Method in class fiji.plugin.trackmate.io.TmXmlWriter: Appends the current GUI state as a state string to the document.
appendLog(String) - Method in class fiji.plugin.trackmate.io.TmXmlWriter: Appends the log content to the document.
appendModel(Model) - Method in class fiji.plugin.trackmate.io.TmXmlWriter: Appends the content of a Model to the file generated by this writer.
appendSettings(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter: Appends the content of a Settings object to the document.
apply(V) - Method in class fiji.plugin.trackmate.graph.RecursiveCumSum
apply(K) - Method in interface fiji.plugin.trackmate.visualization.FeatureColorGenerator
APPLY_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
applyMedianFilter(RandomAccessibleInterval<R>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Apply a simple 3x3 median filter to the target image.
AREA - Static variable in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
area() - Method in class fiji.plugin.trackmate.SpotRoi
Argument() - Constructor for class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
arguments - Variable in class fiji.plugin.trackmate.util.cli.CLIConfigurator
ARROW_DOWN_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_DOWNLEFT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_DOWNRIGHT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_LEFT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_RIGHT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_UP_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_UPLEFT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ARROW_UPRIGHT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
askForFileForLoading(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils: Prompts the user for a xml file to load from.
askForFileForSaving(File, Frame) - Static method in class fiji.plugin.trackmate.io.IOUtils: Prompts the user for a xml file to save to.
askForFolder(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils: Prompts the user for a target folder.
ASPECTRATIO - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
Assignment(int, int, double) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
autoMinMax(Model, DisplaySettings.TrackMateObject, String) - Static method in class fiji.plugin.trackmate.features.FeatureUtils
autoNameSpots(Model, AutoNamingRule) - Static method in class fiji.plugin.trackmate.action.autonaming.AutoNamingPerformer
AutoNamingAction - Class in fiji.plugin.trackmate.action.autonaming
AutoNamingAction() - Constructor for class fiji.plugin.trackmate.action.autonaming.AutoNamingAction
AutoNamingAction.Factory - Class in fiji.plugin.trackmate.action.autonaming
AutoNamingController - Class in fiji.plugin.trackmate.action.autonaming
AutoNamingController(TrackMate, Logger) - Constructor for class fiji.plugin.trackmate.action.autonaming.AutoNamingController
AutoNamingPanel - Class in fiji.plugin.trackmate.action.autonaming
AutoNamingPanel(Collection<AutoNamingRule>) - Constructor for class fiji.plugin.trackmate.action.autonaming.AutoNamingPanel
AutoNamingPerformer - Class in fiji.plugin.trackmate.action.autonaming
AutoNamingPerformer() - Constructor for class fiji.plugin.trackmate.action.autonaming.AutoNamingPerformer
AutoNamingRule - Interface in fiji.plugin.trackmate.action.autonaming
average(DoubleArray) - Static method in class fiji.plugin.trackmate.util.TMUtils
axisLabel(String) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the axis label to appear on the histogram.

B

BASE_ERROR_MESSAGE - Static variable in class fiji.plugin.trackmate.detection.DogDetector
BASE_ERROR_MESSAGE - Static variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
baseErrorMessage - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector
baseErrorMessage - Variable in class fiji.plugin.trackmate.detection.LogDetector
baseErrorMessage - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector
bck(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
beginUpdate() - Method in class fiji.plugin.trackmate.Model
bestPoint - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
bestSquDistance - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
BIG_FONT - Static variable in class fiji.plugin.trackmate.gui.Fonts
BIG_FONT - Static variable in class fiji.plugin.trackmate.gui.wizard.WizardPanel
BIN_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
BLUE_COLOR - Static variable in class fiji.plugin.trackmate.Logger
booleanElement(String, BooleanSupplier, Consumer<Boolean>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
BooleanElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
BOTTOM_TO_TOP - Static variable in class fiji.plugin.trackmate.util.ImageHelper
boundedDoubleElement(String, double, double, DoubleSupplier, Consumer<Double>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
BoundedDoubleElement(String, double, double) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
BoundedValue - Class in fiji.plugin.trackmate.gui.displaysettings: A int variable that can take any value in a given range.
BoundedValue(int, int, int) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
BoundedValue.UpdateListener - Interface in fiji.plugin.trackmate.gui.displaysettings
BoundedValueDouble - Class in fiji.plugin.trackmate.gui.displaysettings: A double variable that can take any value in a given range.
BoundedValueDouble(double, double, double) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
BoundedValueDouble.UpdateListener - Interface in fiji.plugin.trackmate.gui.displaysettings
Branch() - Constructor for class fiji.plugin.trackmate.visualization.table.BranchTableView.Branch
BRANCH_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
BRANCH_ICON_16x16 - Static variable in class fiji.plugin.trackmate.gui.Icons
branches - Variable in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition.TrackBranchDecomposition: Branches are returned as list of spot.
BranchTableView - Class in fiji.plugin.trackmate.visualization.table
BranchTableView(Model, SelectionModel, String) - Constructor for class fiji.plugin.trackmate.visualization.table.BranchTableView
BranchTableView.Branch - Class in fiji.plugin.trackmate.visualization.table: A class to describe a branch.
btnAutoThreshold - Variable in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
build(CLIConfigurator) - Static method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
build(CLIConfigurator) - Static method in class fiji.plugin.trackmate.util.cli.CommandBuilder
buildBranchGraph(ConvexBranchesDecomposition.TrackBranchDecomposition) - Static method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Builds a directed graph made of a convex branch decomposition.
buildMainDataSet(List<String>) - Method in class fiji.plugin.trackmate.features.AbstractFeatureGrapher
buildMainDataSet(List<String>) - Method in class fiji.plugin.trackmate.features.EdgeFeatureGrapher
buildMainDataSet(List<String>) - Method in class fiji.plugin.trackmate.features.SpotFeatureGrapher
buildMainDataSet(List<String>) - Method in class fiji.plugin.trackmate.features.TrackFeatureGrapher

C

cache - Variable in class fiji.plugin.trackmate.io.TmXmlReader: A map of all spots loaded.
CALCULATOR_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
calibration - Variable in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
calibration - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector
calibration - Variable in class fiji.plugin.trackmate.detection.LogDetector
calibration - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker.SearchRegion: The source image calibration.
calibration - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector
calibration - Variable in class fiji.plugin.trackmate.util.SpotNeighborhood
calibration - Variable in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
calibration - Variable in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
calibration - Variable in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
CAMERA_EXPORT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
CAMERA_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
cancel(String) - Method in class fiji.plugin.trackmate.features.EdgeFeatureCalculator
cancel(String) - Method in class fiji.plugin.trackmate.features.SpotFeatureCalculator
cancel(String) - Method in class fiji.plugin.trackmate.features.TrackFeatureCalculator
cancel() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
cancel(String) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
cancel(String) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
cancel(String) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
cancel(String) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
cancel(String) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
cancel(String) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
cancel(String) - Method in class fiji.plugin.trackmate.TrackMate
CANCEL_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
canReadFile(String, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
capture(TrackMate, int, int, Logger) - Static method in class fiji.plugin.trackmate.action.CaptureOverlayAction: Generates a new ImagePlus of type RGB, 2D over time, made by capturing each time frame of the TrackMate display.
capture(ImagePlus, int, int, Logger) - Static method in class fiji.plugin.trackmate.action.CaptureOverlayAction: Generates a new ImagePlus of type RGB, 2D over time, made by capturing each time frame of the specified ImagePlus.
CAPTURE_DECORATED_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
CAPTURE_UNDECORATED_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
captureComponent(Component) - Static method in class fiji.plugin.trackmate.util.ImageHelper: Capture a Swing Component and return as a BufferedImage
captureDecorated() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
CaptureOverlayAction - Class in fiji.plugin.trackmate.action
CaptureOverlayAction() - Constructor for class fiji.plugin.trackmate.action.CaptureOverlayAction
CaptureOverlayAction.Factory - Class in fiji.plugin.trackmate.action
CaptureOverlayPanel - Class in fiji.plugin.trackmate.action
CaptureOverlayPanel(int, int, boolean, boolean) - Constructor for class fiji.plugin.trackmate.action.CaptureOverlayPanel
captureUndecorated() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
CategoryJComboBox<K,V> - Class in fiji.plugin.trackmate.gui.components: A JcomboBox that displays categories, and return the category the selected item belong to.
CategoryJComboBox(Map<K, Collection<V>>, Map<V, String>, Map<K, String>) - Constructor for class fiji.plugin.trackmate.gui.components.CategoryJComboBox
cellLabelChanged(Object, Object, boolean) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter: Overridden method so that when a label is changed, we change the target spot's name.
center - Variable in class fiji.plugin.trackmate.util.SpotNeighborhood
center - Variable in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
centerViewOn(Spot) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
centerViewOn(Spot) - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
centerViewOn(Spot) - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
centerViewOn(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
centerViewOn(Spot) - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
centerViewOn(Spot) - Method in interface fiji.plugin.trackmate.visualization.TrackMateModelView: Centers the view on the given spot.
centerViewOn(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
centerViewOn(mxICell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFrame
changeSpotRadius(boolean, boolean) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
channel - Variable in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
ChartExporter - Class in fiji.plugin.trackmate.util: A collection of static utilities made to export a JPanel to various scalable file format.
ChartExporter() - Constructor for class fiji.plugin.trackmate.util.ChartExporter
check() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
check() - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator
checkExecutable() - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator
checkFeatureMap(Map<String, Object>, String, StringBuilder) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils: Check the validity of a feature penalty map in a settings map.
checkInput() - Method in class fiji.plugin.trackmate.detection.HessianDetector
checkInput() - Method in class fiji.plugin.trackmate.detection.LabelImageDetector
checkInput() - Method in class fiji.plugin.trackmate.detection.LogDetector
checkInput() - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
checkInput() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
checkInput() - Method in class fiji.plugin.trackmate.detection.util.MedianFilter2D
checkInput() - Method in class fiji.plugin.trackmate.features.EdgeFeatureCalculator
checkInput() - Method in class fiji.plugin.trackmate.features.SpotFeatureCalculator
checkInput() - Method in class fiji.plugin.trackmate.features.TrackFeatureCalculator
checkInput() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition
checkInput() - Method in class fiji.plugin.trackmate.graph.FromContinuousBranches
checkInput() - Method in class fiji.plugin.trackmate.io.IcyTrackFormatWriter
checkInput() - Method in class fiji.plugin.trackmate.io.TGMMImporter
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
checkInput() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
checkInput() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
checkInput() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
checkInput() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
checkInput(Map<String, Object>, StringBuilder) - Static method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
checkInput() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
checkInput() - Method in class fiji.plugin.trackmate.TrackMate
checkMapKeys(Map<T, ?>, Collection<T>, Collection<T>, StringBuilder) - Static method in class fiji.plugin.trackmate.util.TMUtils: Check that the given map has all some keys.
checkParameter(Map<String, Object>, String, Class<?>, StringBuilder) - Static method in class fiji.plugin.trackmate.util.TMUtils: Check the presence and the validity of a key in a map, and test it is of the desired class.
checkSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
checkSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
checkSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
checkSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
checkSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
checkSettings(Map<String, Object>) - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Check that the given settings map is suitable for target detector.
checkSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
checkSettingsValidity(Map<String, Object>, StringBuilder, boolean) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
checkSettingsValidity(Map<String, Object>, StringBuilder) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
checkSettingsValidity(Map<String, Object>, StringBuilder) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
checkSettingsValidity(Map<String, Object>, StringBuilder) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
checkSettingsValidity(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
checkSettingsValidity(Map<String, Object>) - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Checks the validity of the given settings map for the tracker.
checkValidity() - Method in class fiji.plugin.trackmate.Settings
chkboxSimplify - Variable in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
ChooseDetectorDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
ChooseDetectorDescriptor(DetectorProvider, TrackMate) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseDetectorDescriptor
chooseFile(Component, String, FileChooser.DialogType) - Static method in class fiji.plugin.trackmate.util.FileChooser
chooseFile(Component, String, FileFilter, String, FileChooser.DialogType) - Static method in class fiji.plugin.trackmate.util.FileChooser
chooseFile(Component, String, FileFilter, String, FileChooser.DialogType, FileChooser.SelectionMode) - Static method in class fiji.plugin.trackmate.util.FileChooser
chooseFile(boolean, Component, String, FileFilter, String, FileChooser.DialogType, FileChooser.SelectionMode) - Static method in class fiji.plugin.trackmate.util.FileChooser
ChooseTrackerDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
ChooseTrackerDescriptor(TrackerProvider, TrackMate) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseTrackerDescriptor
CIRCULARITY - Static variable in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
clean() - Method in class fiji.plugin.trackmate.gui.components.ConfigurationPanel: Executes any task related to cleaning the possible previews generated by this panel prior to moving to another GUI panel.
clean() - Method in class fiji.plugin.trackmate.gui.components.detector.HessianDetectorConfigurationPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.detector.ManualDetectorConfigurationPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.tracker.AdvancedKalmanTrackerSettingsPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.tracker.KalmanTrackerConfigPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.tracker.LAPTrackerSettingsPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.tracker.NearestNeighborTrackerSettingsPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.tracker.OverlapTrackerSettingsPanel
clean() - Method in class fiji.plugin.trackmate.gui.components.tracker.SimpleLAPTrackerSettingsPanel
clear() - Method in class fiji.plugin.trackmate.SpotCollection: Removes all the content from this collection.
clear() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
clear() - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
clear() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
clear() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
clear() - Method in interface fiji.plugin.trackmate.visualization.TrackMateModelView: Removes any overlay (for spots or tracks) from this displayer.
clear() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
clearEdgeAnalyzers() - Method in class fiji.plugin.trackmate.Settings: Remove any EdgeAnalyzer to this object.
clearEdgeSelection() - Method in class fiji.plugin.trackmate.SelectionModel
clearSelection() - Method in class fiji.plugin.trackmate.SelectionModel
clearSpotAnalyzerFactories() - Method in class fiji.plugin.trackmate.Settings: Remove any SpotAnalyzerFactory to this object.
clearSpotFilters() - Method in class fiji.plugin.trackmate.Settings: Remove all spot filters stored in this model.
clearSpots(boolean) - Method in class fiji.plugin.trackmate.Model: Removes all the spots from this model.
clearSpotSelection() - Method in class fiji.plugin.trackmate.SelectionModel
clearTrackAnalyzers() - Method in class fiji.plugin.trackmate.Settings: Remove any TrackAnalyzer to this object.
clearTrackFilters() - Method in class fiji.plugin.trackmate.Settings: Remove all track filters stored in this model.
clearTracks(boolean) - Method in class fiji.plugin.trackmate.Model: Removes all the tracks from this model.
CliConfigPanel() - Constructor for class fiji.plugin.trackmate.util.cli.CliGuiBuilder.CliConfigPanel
CLIConfigurator - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator() - Constructor for class fiji.plugin.trackmate.util.cli.CLIConfigurator
CLIConfigurator.AbstractStringArgument<T extends CLIConfigurator.AbstractStringArgument<T>> - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.Argument<T extends CLIConfigurator.Argument<T,O>,O> - Class in fiji.plugin.trackmate.util.cli: Mother class for command arguments.
CLIConfigurator.ArgumentVisitor - Interface in fiji.plugin.trackmate.util.cli
CLIConfigurator.BoundedValueArgument<T extends CLIConfigurator.BoundedValueArgument<T,O>,O> - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.ChoiceAdder - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.ChoiceArgument - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.DoubleAdder - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.DoubleArgument - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.Flag - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.FlagAdder - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.IntAdder - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.IntArgument - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.PathAdder - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.PathArgument - Class in fiji.plugin.trackmate.util.cli: Specialization of CLIConfigurator.StringArgument to be used in a GUI.
CLIConfigurator.SelectableArguments - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.StringAdder - Class in fiji.plugin.trackmate.util.cli
CLIConfigurator.StringArgument - Class in fiji.plugin.trackmate.util.cli
CliGuiBuilder - Class in fiji.plugin.trackmate.util.cli
CliGuiBuilder.CliConfigPanel - Class in fiji.plugin.trackmate.util.cli
clipBackground(AbstractSpotFitter.Observation) - Static method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
CLIUtils - Class in fiji.plugin.trackmate.util.cli
CLIUtils() - Constructor for class fiji.plugin.trackmate.util.cli.CLIUtils
CLIUtils.LoggerTailerListener - Class in fiji.plugin.trackmate.util.cli
clone() - Method in class fiji.plugin.trackmate.gui.displaysettings.Colormap
CloseGapsAction - Class in fiji.plugin.trackmate.action.closegaps
CloseGapsAction() - Constructor for class fiji.plugin.trackmate.action.closegaps.CloseGapsAction
CloseGapsAction.Factory - Class in fiji.plugin.trackmate.action.closegaps
CloseGapsByDetection - Class in fiji.plugin.trackmate.action.closegaps: This action allows to close gaps in tracks by executing detection in the vicinity of position that are linearly interpolated.
CloseGapsByDetection() - Constructor for class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
CloseGapsByLinearInterpolation - Class in fiji.plugin.trackmate.action.closegaps: This action allows to close gaps in tracks by creating new intermediate spots which are located at interpolated positions.
CloseGapsByLinearInterpolation() - Constructor for class fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation
CloseGapsController - Class in fiji.plugin.trackmate.action.closegaps
CloseGapsController(TrackMate, Logger) - Constructor for class fiji.plugin.trackmate.action.closegaps.CloseGapsController
CloseGapsPanel - Class in fiji.plugin.trackmate.action.closegaps: A basic UI to let a TrackMate user choose between several techniques for gap closing.
CloseGapsPanel(Collection<GapClosingMethod>) - Constructor for class fiji.plugin.trackmate.action.closegaps.CloseGapsPanel
COG_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
collectFeatureKeys(DisplaySettings.TrackMateObject, Model, Settings) - Static method in class fiji.plugin.trackmate.features.FeatureUtils
collectFeatureValues(String, DisplaySettings.TrackMateObject, Model, boolean) - Static method in class fiji.plugin.trackmate.features.FeatureUtils: Missing or undefined values are not included.
COLOR - Variable in class fiji.plugin.trackmate.util.cli.CLIUtils.LoggerTailerListener
color(K) - Method in interface fiji.plugin.trackmate.visualization.FeatureColorGenerator: Returns a color for the given object.
color(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator
color(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.ManualEdgePerSpotColorGenerator
color(Spot) - Method in class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator
color(Spot) - Method in class fiji.plugin.trackmate.visualization.ManualSpotPerEdgeColorGenerator
color(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.PerEdgeFeatureColorGenerator
color(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.PerSpotFeatureColorGenerator
color(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator
color(Spot) - Method in class fiji.plugin.trackmate.visualization.RandomSpotColorGenerator
color(Spot) - Method in class fiji.plugin.trackmate.visualization.SpotColorGenerator
color(Spot) - Method in class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerEdgeFeature
color(Spot) - Method in class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerTrackFeature
color(Spot) - Method in class fiji.plugin.trackmate.visualization.UniformSpotColorGenerator
color(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.UniformTrackColorGenerator
color(Integer) - Method in class fiji.plugin.trackmate.visualization.WholeTrackFeatureColorGenerator
COLOR_FEATURE_CHANGED - Variable in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
colorDistance(Color, Color) - Static method in class fiji.plugin.trackmate.gui.GuiUtils: Distance between two colors.
colorElement(String, Supplier<Color>, Consumer<Color>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
ColorElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
ColorIcon - Class in fiji.plugin.trackmate.gui.displaysettings: Adapted from http://stackoverflow.com/a/3072979/230513
ColorIcon(Color, int, int) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
ColorIcon(Color, int) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
ColorIcon(Color) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
Colormap - Class in fiji.plugin.trackmate.gui.displaysettings: This class implements a PaintScale that generate colors interpolated within a list of given color, using a linear scale.
Colormap(String, double, double, Color) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.Colormap: Create a paint scale with given lower and upper bound, and a specified default color.
Colormap(String, double, double) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.Colormap: Create a paint scale with a given lower and upper bound and a default black color.
Colormap(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.Colormap: Create a paint scale with a lower bound of 0, an upper bound of 1 and a default black color.
colormapElement(String, Supplier<Colormap>, Consumer<Colormap>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
ColormapElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
ColormapIO - Class in fiji.plugin.trackmate.gui.displaysettings: Loat LUTS for Colormap.
ColormapIO() - Constructor for class fiji.plugin.trackmate.gui.displaysettings.ColormapIO
colorOf(Integer) - Method in class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator
colors - Static variable in class fiji.plugin.trackmate.visualization.GlasbeyLut
combineImages(BufferedImage, BufferedImage, int) - Static method in class fiji.plugin.trackmate.util.ImageHelper: Helper method to combine two images, in the specified format.
CommandBuilder - Class in fiji.plugin.trackmate.util.cli
CommandBuilder(Map<CLIConfigurator.Argument<?, ?>, Function<Object, List<String>>>) - Constructor for class fiji.plugin.trackmate.util.cli.CommandBuilder
CommandCLIConfigurator - Class in fiji.plugin.trackmate.util.cli: Base class for CLI config that are based on an executable, reachable by a path.
CommandCLIConfigurator() - Constructor for class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator
CommandCLIConfigurator.ExecutablePath - Class in fiji.plugin.trackmate.util.cli
CommonTrackMateArguments - Class in fiji.plugin.trackmate.util.cli: Arguments that are commonly used by TrackMate, to add to custom CLIConfigurator.
CommonTrackMateArguments() - Constructor for class fiji.plugin.trackmate.util.cli.CommonTrackMateArguments
comparator - Variable in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
compareTo(Spot) - Method in class fiji.plugin.trackmate.Spot
compareTo(DefaultCostMatrixCreator.Assignment) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
compareTo(BranchTableView.Branch) - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView.Branch: Sort by predecessors number, then successors number, then alphabetically by first spot name.
compute(T1, T2) - Method in interface fiji.plugin.trackmate.graph.Function1: Compute a value from the data in input, and store in output.
compute(T1, T1, T2) - Method in interface fiji.plugin.trackmate.graph.Function2: Compute a value from the data in two inputs, and store in output.
compute(E, E) - Method in interface fiji.plugin.trackmate.graph.OutputFunction
computeAlternativeCosts() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
computeDistance(Model, RoiManager, double[]) - Static method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction
computeDistance(Model, Roi[], double[]) - Static method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction
ComputeDistanceToRoiAction - Class in fiji.plugin.trackmate.action
ComputeDistanceToRoiAction() - Constructor for class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction
ComputeDistanceToRoiAction.DistanceToRoiFeature<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.action
ComputeDistanceToRoiAction.Factory - Class in fiji.plugin.trackmate.action
computeEdgeFeatures(boolean) - Method in class fiji.plugin.trackmate.TrackMate: Calculate all features for all detected spots.
computeEdgesFeatures(Collection<DefaultWeightedEdge>, boolean) - Method in class fiji.plugin.trackmate.features.EdgeFeatureCalculator: Calculates all the edge features configured in the Settings object for the specified edges.
computeLinkingCostFor(Spot, Spot, double, double, Map<String, Double>) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils: Compute the cost to link two spots, in the default way for the TrackMate trackmate.
computeSpotFeatures(SpotCollection, boolean) - Method in class fiji.plugin.trackmate.features.SpotFeatureCalculator: Calculates all the spot features configured in the Settings object, but only for the spots in the specified collection.
computeSpotFeatures(boolean) - Method in class fiji.plugin.trackmate.TrackMate: Calculate all features for all detected spots.
computeTrackFeatures(Collection<Integer>, boolean) - Method in class fiji.plugin.trackmate.features.TrackFeatureCalculator: Calculates all the track features configured in the Settings object for the specified tracks.
computeTrackFeatures(boolean) - Method in class fiji.plugin.trackmate.TrackMate: Calculate all features for all tracks.
CONDA_PATH_PREF_KEY - Static variable in class fiji.plugin.trackmate.util.cli.CLIUtils
CondaCLIConfigurator - Class in fiji.plugin.trackmate.util.cli
CondaCLIConfigurator() - Constructor for class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator
CondaCLIConfigurator.CondaEnvironmentCommand - Class in fiji.plugin.trackmate.util.cli
CondaEnvironmentCommand() - Constructor for class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator.CondaEnvironmentCommand
CondaPathConfigCommand - Class in fiji.plugin.trackmate.util.cli
CondaPathConfigCommand() - Constructor for class fiji.plugin.trackmate.util.cli.CondaPathConfigCommand
configDescriptor() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
configDescriptor() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns the descriptor in charge of configure the views.
ConfigTrackMateDisplaySettings - Class in fiji.plugin.trackmate.gui.displaysettings
ConfigTrackMateDisplaySettings() - Constructor for class fiji.plugin.trackmate.gui.displaysettings.ConfigTrackMateDisplaySettings
ConfigurationPanel - Class in fiji.plugin.trackmate.gui.components: The mother class for all the configuration panels.
ConfigurationPanel() - Constructor for class fiji.plugin.trackmate.gui.components.ConfigurationPanel
ConfigureViewsDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
ConfigureViewsDescriptor(DisplaySettings, FeatureDisplaySelector, Action, Action, Action, String) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.ConfigureViewsDescriptor
ConfigureViewsPanel - Class in fiji.plugin.trackmate.gui.components: A configuration panel used to tune the aspect of spots and tracks in multiple AbstractTrackMateModelView.
ConfigureViewsPanel(DisplaySettings, FeatureDisplaySelector, String, Action, Action, Action) - Constructor for class fiji.plugin.trackmate.gui.components.ConfigureViewsPanel
containsEdge(Spot, Spot) - Method in class fiji.plugin.trackmate.TrackModel: Returns true if this model contains the specified edge.
CONTRAST - Static variable in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
ConvexBranchesDecomposition - Class in fiji.plugin.trackmate.graph: A class that can decompose the tracks of a Model in convex branches.
ConvexBranchesDecomposition(Model, boolean, boolean) - Constructor for class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Creates a new track splitter.
ConvexBranchesDecomposition(Model) - Constructor for class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Creates a new track splitter.
ConvexBranchesDecomposition.TrackBranchDecomposition - Class in fiji.plugin.trackmate.graph: A two public fields class used to return the convex branch decomposition of a track.
ConvexHull - Class in fiji.plugin.trackmate.features.spot: Adapted from a code by Kirill Artemov, https://github.com/DoctorGester/cia-stats.
ConvexHull() - Constructor for class fiji.plugin.trackmate.features.spot.ConvexHull
convexHull(SpotRoi) - Static method in class fiji.plugin.trackmate.features.spot.ConvexHull
copy() - Method in class fiji.plugin.trackmate.detection.DogDetectorFactory
copy() - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
copy() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
copy() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
copy() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
copy() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
copy() - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Returns a copy the current instance.
copy() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
copy() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
copy(String) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings: Returns a new display settings, copied from this instance.
copy() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
copy() - Method in class fiji.plugin.trackmate.Model: Returns a copy of this model.
copy() - Method in class fiji.plugin.trackmate.SpotRoi
copy() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
copy() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
copy() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
copy() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
copy() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
copy() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
copy() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
copy() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
copy() - Method in interface fiji.plugin.trackmate.tracking.SpotImageTrackerFactory
copy() - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Returns a copy the current instance.
copy(Supplier<V>, Function1<Spot, V>, Map<Spot, V>) - Method in class fiji.plugin.trackmate.TrackModel: Returns a new graph with the same structure as the one wrapped here, and with vertices generated by the given Function1.
copy() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
copyFeatures(Spot, Map<String, Double>) - Method in class fiji.plugin.trackmate.Spot: Copy the listed features of the spot src to the current spot
copyOn(ImagePlus) - Method in class fiji.plugin.trackmate.Settings: Copy a settings objects based on this instance, but configured to run on the specified image.
copyToFloatImg(RandomAccessible<T>, Interval, ImgFactory<FloatType>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Copy an interval of the specified source image on a float image.
CopyTrackNameNamingRule - Class in fiji.plugin.trackmate.action.autonaming
CopyTrackNameNamingRule() - Constructor for class fiji.plugin.trackmate.action.autonaming.CopyTrackNameNamingRule
CostFunction<K,J> - Interface in fiji.plugin.trackmate.tracking.jaqaman.costfunction: Interface representing a function that can calculate the cost to link a source object to a target object.
CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>> - Interface in fiji.plugin.trackmate.tracking.jaqaman.costmatrix: Interface for function that can generate a SparseCostMatrix from assignment candidates.
countMissingSpots(Collection<DefaultWeightedEdge>, Model) - Static method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod
countMissingSpots(DefaultWeightedEdge, Model) - Static method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod
create() - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
create() - Method in class fiji.plugin.trackmate.action.CaptureOverlayAction.Factory
create() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction.Factory
create() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.Factory
create() - Method in class fiji.plugin.trackmate.action.CTCExporterAction.Factory
create() - Method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction.Factory
create() - Method in class fiji.plugin.trackmate.action.ExportStatsTablesAction.Factory
create() - Method in class fiji.plugin.trackmate.action.ExportTracksToXML.Factory
create() - Method in class fiji.plugin.trackmate.action.ExtractTrackStackAction.ExtractTrackStackActionFactory
create() - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
create() - Method in class fiji.plugin.trackmate.action.IcyTrackExporter.Factory
create() - Method in class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterActionFactory
create() - Method in class fiji.plugin.trackmate.action.ISBIChallengeExporter.Factory
create() - Method in class fiji.plugin.trackmate.action.LabelImgExporter.Factory
create() - Method in class fiji.plugin.trackmate.action.MergeFileAction.Factory
create() - Method in class fiji.plugin.trackmate.action.MotilityLabExporter.Factory
create() - Method in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction.Factory
create() - Method in class fiji.plugin.trackmate.action.RecomputeFeatureAction.Factory
create() - Method in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction.Factory
create() - Method in class fiji.plugin.trackmate.action.TrackBranchAnalysis.Factory
create() - Method in interface fiji.plugin.trackmate.action.TrackMateActionFactory
create() - Method in class fiji.plugin.trackmate.action.TrimNotVisibleAction.Factory
create(SpotCollection, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
create(SpotCollection, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
create(SpotCollection, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
create(SpotCollection, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
create(SpotCollection, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
create(SpotCollection, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
create(SpotCollection, Map<String, Object>, ImagePlus) - Method in interface fiji.plugin.trackmate.tracking.SpotImageTrackerFactory: Instantiates and returns a new SpotTracker configured to operate on the specified SpotCollection, using the specified settins map.
create(SpotCollection, Map<String, Object>) - Method in interface fiji.plugin.trackmate.tracking.SpotImageTrackerFactory
create(SpotCollection, Map<String, Object>) - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Instantiates and returns a new SpotTracker configured to operate on the specified SpotCollection, using the specified settins map.
create() - Static method in class fiji.plugin.trackmate.util.DetectionPreview
create(Model, Settings, SelectionModel, DisplaySettings) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayerFactory
create(Model, Settings, SelectionModel, DisplaySettings) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFactory
create(Model, Settings, SelectionModel, DisplaySettings) - Method in interface fiji.plugin.trackmate.visualization.ViewFactory: Returns a new instance of the concrete view.
createActionMap() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeKeyboardHandler: Return the mapping between JTree's input map and JGraph's actions.
createBranchTable(Model, SelectionModel, String) - Static method in class fiji.plugin.trackmate.action.TrackBranchAnalysis
createBranchTable(Model, SelectionModel) - Static method in class fiji.plugin.trackmate.visualization.table.BranchTableView
createCellEditor() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent: Overridden to customize the look of the editor.
createComboBoxSelector(Model, Settings) - Static method in class fiji.plugin.trackmate.gui.components.FeatureDisplaySelector: Return a CategoryJComboBox that lets a user select among all available features in TrackMate.
createDetector(RandomAccessible<T>, Interval, double[], double, double) - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: Returns a new instance of a SpotDetector that will inspect the neighborhood.
createDisplaySettings() - Method in class fiji.plugin.trackmate.TrackMatePlugIn
createEdgeTable(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.visualization.table.TrackTableView
createFeatureModel() - Method in class fiji.plugin.trackmate.Model: Instantiates a blank FeatureModel to use whithin this model.
createGraphHandler() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent: Custom mxGraphHandler so as to avoid clearing the selection when right-clicking elsewhere than on a cell, which is reserved for aimed at displaying a popup menu.
createLabelImagePlus(TrackMate, boolean, boolean, LabelImgExporter.LabelIdPainting) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImagePlus(TrackMate, boolean, boolean, LabelImgExporter.LabelIdPainting, Logger) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImagePlus(Model, ImagePlus, boolean, boolean, LabelImgExporter.LabelIdPainting) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImagePlus(Model, ImagePlus, boolean, boolean, LabelImgExporter.LabelIdPainting, Logger) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImagePlus(Model, int[], double[], boolean, boolean, LabelImgExporter.LabelIdPainting) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImagePlus(Model, int[], double[], boolean, boolean, LabelImgExporter.LabelIdPainting, Logger) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImagePlus where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImg(Model, long[], double[], boolean, boolean, LabelImgExporter.LabelIdPainting) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with their track ID as pixel value.
createLabelImg(Model, long[], double[], boolean, boolean, LabelImgExporter.LabelIdPainting, Logger) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label Img of FloatType where the spots of the specified model are painted with their shape, with an ID pixel value.
createLabelImg(SpotCollection, long[], double[], boolean, LabelImgExporter.LabelIdPainting, T, Logger) - Static method in class fiji.plugin.trackmate.action.LabelImgExporter: Creates a new label ImgPlus of FloatType where the spots are painted with an ID.
createLoGKernel(double, int, double[]) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Creates a laplacian of gaussian (LoG) kernel tuned for blobs with a radius specified using calibrated units.
createModel() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Hook for subclassers:
Creates the instance of Model that will be built upon loading with this reader.
createModel(ImagePlus) - Method in class fiji.plugin.trackmate.TrackMatePlugIn: Hook for subclassers:
Creates the Model instance that will be used to store data in the TrackMate instance.
createPopupMenu(boolean, boolean, boolean, boolean, boolean) - Method in class fiji.plugin.trackmate.util.ExportableChartPanel
createReader(File) - Method in class fiji.plugin.trackmate.LoadTrackMatePlugIn: Hook for subclassers:
Creates the TmXmlReader instance that will be used to load the file.
createSelectorFor(DisplaySettings.TrackMateObject) - Method in class fiji.plugin.trackmate.gui.components.FeatureDisplaySelector
createSelectorForSpots() - Method in class fiji.plugin.trackmate.gui.components.FeatureDisplaySelector
createSelectorForTracks() - Method in class fiji.plugin.trackmate.gui.components.FeatureDisplaySelector
createSequence(TrackMate, SelectionModel, DisplaySettings) - Method in class fiji.plugin.trackmate.ManualTrackingPlugIn
createSequence(TrackMate, SelectionModel, DisplaySettings) - Method in class fiji.plugin.trackmate.TrackMatePlugIn: Hook for subclassers:
Will create and position the sequence that will be played by the wizard launched by this plugin.
createSettings(ImagePlus) - Method in class fiji.plugin.trackmate.ManualTrackingPlugIn
createSettings(ImagePlus) - Method in class fiji.plugin.trackmate.TrackMatePlugIn: Hook for subclassers:
Creates the Settings instance that will be used to tune the TrackMate instance.
createSpot(double[], double[], double) - Static method in class fiji.plugin.trackmate.SpotRoi
createSpotColorGenerator(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.features.FeatureUtils
createSpotOverlay(DisplaySettings) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer: Hook for subclassers.
createSpotsTable(Model, SelectionModel, DisplaySettings, String) - Static method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction
createSpotTable(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
createSpotTable(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.visualization.table.TrackTableView
createTrackColorGenerator(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.features.FeatureUtils
createTrackMate(Model, Settings) - Method in class fiji.plugin.trackmate.ManualTrackingPlugIn
createTrackMate(Model, Settings) - Method in class fiji.plugin.trackmate.TrackMatePlugIn: Hook for subclassers:
Creates the TrackMate instance that will be controlled in the GUI.
createTrackModel() - Method in class fiji.plugin.trackmate.Model: Instantiates a blank TrackModel to use whithin this model.
createTrackOverlay(DisplaySettings) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer: Hook for subclassers.
createTrackTable(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.visualization.table.TrackTableView
createTrackTables(Model, SelectionModel, DisplaySettings, String) - Static method in class fiji.plugin.trackmate.action.ExportStatsTablesAction
createURLMouseListener(JLabel, String, String) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
createWholeTrackColorGenerator(Model, DisplaySettings) - Static method in class fiji.plugin.trackmate.features.FeatureUtils
crop() - Method in class fiji.plugin.trackmate.SpotCollection: Remove all the non-visible spots of this collection.
CROP_DETECTION_CHANNEL_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_TEND_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_TSTART_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_XEND_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_XSTART_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_YEND_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_YSTART_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_ZEND_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CROP_ZSTART_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
CSV_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
CSVExporter - Class in fiji.plugin.trackmate.io
CSVExporter() - Constructor for class fiji.plugin.trackmate.io.CSVExporter
CTCExporter - Class in fiji.plugin.trackmate.action: An exporter that saves the current TrackMate session as files following the Cell-Tracking-Challenge convention.
CTCExporter() - Constructor for class fiji.plugin.trackmate.action.CTCExporter
CTCExporter.ExportType - Enum in fiji.plugin.trackmate.action
CTCExporterAction - Class in fiji.plugin.trackmate.action
CTCExporterAction() - Constructor for class fiji.plugin.trackmate.action.CTCExporterAction
CTCExporterAction.Factory - Class in fiji.plugin.trackmate.action
cumulativeBranchWidth(TrackModel) - Static method in class fiji.plugin.trackmate.graph.GraphUtils
current() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
current() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns the descriptor currently displayed.
cursor() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
cursor() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
cursor - Variable in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
CVMKalmanFilter - Class in fiji.plugin.trackmate.tracking.kalman: A Kalman filter that deals with a single particle motion in 3D with a constant velocity vector.
CVMKalmanFilter(double[], double, double, double, double) - Constructor for class fiji.plugin.trackmate.tracking.kalman.CVMKalmanFilter: Initialize a new Kalman filter with the specified initial state.

D

data - Variable in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
DEBUG - Static variable in class fiji.plugin.trackmate.io.TmXmlReader
declareEdgeFeatures(Collection<String>, Map<String, String>, Map<String, String>, Map<String, Dimension>, Map<String, Boolean>) - Method in class fiji.plugin.trackmate.FeatureModel: Declares edge features, by specifying their name, short name and dimension.
declareSpotFeatures(Collection<String>, Map<String, String>, Map<String, String>, Map<String, Dimension>, Map<String, Boolean>) - Method in class fiji.plugin.trackmate.FeatureModel: Declares spot features, by specifying their names, short name and dimension.
declareTrackFeatures(Collection<String>, Map<String, String>, Map<String, String>, Map<String, Dimension>, Map<String, Boolean>) - Method in class fiji.plugin.trackmate.FeatureModel: Declares track features, by specifying their names, short name and dimension.
DEFAULT_ALLOW_GAP_CLOSING - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "ALLOW_GAP_CLOSING" parameter.
DEFAULT_ALLOW_TRACK_MERGING - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "ALLOW_TRACK_MERGING" parameter.
DEFAULT_ALLOW_TRACK_SPLITTING - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "ALLOW_TRACK_SPLITTING" parameter.
DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "ALTERNATIVE_LINKING_COST_FACTOR" parameter.
DEFAULT_BLOCKING_VALUE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "BLOCKING_VALUE" parameter.
DEFAULT_COLOR - Static variable in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
DEFAULT_CUTOFF_PERCENTILE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "CUTOFF_PERCENTILE" parameter.
DEFAULT_DO_MEDIAN_FILTERING - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_DO_MEDIAN_FILTERING parameter.
DEFAULT_DO_SUBPIXEL_LOCALIZATION - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION parameter.
DEFAULT_DOWNSAMPLE_FACTOR - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_DOWNSAMPLE_FACTOR parameter.
DEFAULT_GAP_CLOSING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "GAP_CLOSING_FEATURE_PENALTIES" parameter.
DEFAULT_GAP_CLOSING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "GAP_CLOSING_MAX_DISTANCE" parameter.
DEFAULT_GAP_CLOSING_MAX_FRAME_GAP - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "MAX_FRAME_GAP" parameter.
DEFAULT_KALMAN_SEARCH_RADIUS - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "KALMAN_SEARCH_RADIUS" parameter.
DEFAULT_LINKING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "LINKING_FEATURE_PENALTIES" parameter.
DEFAULT_LINKING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "LINKING_MAX_DISTANCE" parameter.
DEFAULT_LOGGER - Static variable in class fiji.plugin.trackmate.Logger: This Logger simply outputs to the standard output and standard error.
DEFAULT_MERGING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "MERGING_FEATURE_PENALTIES" parameter.
DEFAULT_MERGING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "MERGING_MAX_DISTANCE" parameter.
DEFAULT_MIN_IOU - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
DEFAULT_NORMALIZE - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_NORMALIZE parameter.
DEFAULT_RADIUS - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_RADIUS parameter.
DEFAULT_RADIUS_Z - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_RADIUS_Z parameter.
DEFAULT_SCALE_FACTOR - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
DEFAULT_SPLITTING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the "SPLITTING_FEATURE_PENALTIES" parameter.
DEFAULT_SPLITTING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: A default value for the TrackerKeys.KEY_SPLITTING_MAX_DISTANCE parameter.
DEFAULT_TARGET_CHANNEL - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_TARGET_CHANNEL parameter.
DEFAULT_THRESHOLD - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: A default value for the DetectorKeys.KEY_THRESHOLD parameter.
DefaultAutoNamingRule - Class in fiji.plugin.trackmate.action.autonaming
DefaultAutoNamingRule() - Constructor for class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
DefaultAutoNamingRule(String, String, boolean) - Constructor for class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
DefaultCostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>> - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix: A CostMatrixCreator that build a cost matrix from 3 lists containing the sources, the targets and the associated costs.
DefaultCostMatrixCreator(List<K>, List<J>, double[], double, double) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
DefaultCostMatrixCreator.Assignment - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix
DefaultFileFilter - Class in fiji.plugin.trackmate.util: Filter for use in a JFileChooser.
DefaultFileFilter(String, String) - Constructor for class fiji.plugin.trackmate.util.DefaultFileFilter: Constructs a new filter for the specified extension and description.
DefaultFileFilter.EditorFileFilter - Class in fiji.plugin.trackmate.util: Utility file filter to accept editor files, namely .xml and .xml.gz extensions.
DefaultFileFilter.ImageFileFilter - Class in fiji.plugin.trackmate.util: Utility file filter to accept all image formats supported by image io.
defaultStyle() - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
defaultValue(String) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceAdder
defaultValue(int) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceAdder
deleteSpot() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
deleteSpotSelection() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
desc - Variable in class fiji.plugin.trackmate.util.DefaultFileFilter: Description of accepted files.
desc - Variable in class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter: Description of the File format
desc - Variable in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter: Description of the filter.
DESCRIPTOR - Static variable in class fiji.plugin.trackmate.gui.components.LogPanel
DetectionPreview - Class in fiji.plugin.trackmate.util
DetectionPreview(Model, Settings, SpotDetectorFactoryBase<?>, Supplier<Map<String, Object>>, Supplier<Integer>, DoubleConsumer, String, String) - Constructor for class fiji.plugin.trackmate.util.DetectionPreview
DetectionPreview.Builder - Class in fiji.plugin.trackmate.util
DetectionPreviewPanel - Class in fiji.plugin.trackmate.util
DetectionPreviewPanel(DoubleConsumer, String) - Constructor for class fiji.plugin.trackmate.util.DetectionPreviewPanel
detectionSettingsSupplier(Supplier<Map<String, Object>>) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the supplier function that will return the detector settings to use for the preview.
DetectionUtils - Class in fiji.plugin.trackmate.detection
DetectionUtils() - Constructor for class fiji.plugin.trackmate.detection.DetectionUtils
DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.HessianDetectorFactory
DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory: A string key identifying this factory.
DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.LogDetectorFactory: A string key identifying this factory.
DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.ManualDetectorFactory
DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.MaskDetectorFactory: A string key identifying this factory.
DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory: A string key identifying this factory.
DETECTOR_SETTINGS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
detectorFactory - Variable in class fiji.plugin.trackmate.Settings: The name of the detector factory to use.
detectorFactory(SpotDetectorFactoryBase<?>) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the detector factory to use for the preview.
DetectorKeys - Class in fiji.plugin.trackmate.detection: A class to store key names for parameters of the current SpotDetector s.
DetectorKeys() - Constructor for class fiji.plugin.trackmate.detection.DetectorKeys
DetectorProvider - Class in fiji.plugin.trackmate.providers
DetectorProvider() - Constructor for class fiji.plugin.trackmate.providers.DetectorProvider
detectorSettings - Variable in class fiji.plugin.trackmate.Settings: Settings map for SpotDetector.
diffTo(Spot, String) - Method in class fiji.plugin.trackmate.Spot: Returns the difference of the feature value for this spot with the one of the specified spot.
dijkstraShortestPath(Spot, Spot) - Method in class fiji.plugin.trackmate.TrackModel: Returns the shortest path between two connected spot, using Dijkstra's algorithm.
dimension(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
Dimension - Enum in fiji.plugin.trackmate
dimension(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
dimensions(long[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
dimensions(long[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
DIRECTIONAL_CHANGE_RATE - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
DirectionalChangeAnalyzer - Class in fiji.plugin.trackmate.features.edges
DirectionalChangeAnalyzer() - Constructor for class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
disable() - Method in class fiji.plugin.trackmate.util.EverythingDisablerAndReenabler: Disables everything recursively, except the excluded types.
disabled - Variable in class fiji.plugin.trackmate.providers.AbstractProvider
DISPLACEMENT - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
display(WizardPanelDescriptor) - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanel
DISPLAY_CONFIG_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
DISPLAY_DECORATIONS_ON_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
DISPLAY_SETTINGS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
displayConfig(boolean) - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
displayCostMatrix(double[][], int, int, double, int[][]) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils: Display the cost matrix solved by the Hungarian algorithm in the LAP approach.
displayHistogram(double[]) - Method in class fiji.plugin.trackmate.util.QualityHistogramChart
displayHistogram(double[], double) - Method in class fiji.plugin.trackmate.util.QualityHistogramChart
displayingPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseDetectorDescriptor
displayingPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseTrackerDescriptor
displayingPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SaveDescriptor
displayingPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotFilterDescriptor
displayingPanel() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.TrackFilterDescriptor
displayingPanel() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
displayLAPresults(int[][]) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
DisplaySettings - Class in fiji.plugin.trackmate.gui.displaysettings
DisplaySettings() - Constructor for class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
displaySettings - Variable in class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView
displaySettings - Variable in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
displaySettings - Variable in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
DisplaySettings.TrackDisplayMode - Enum in fiji.plugin.trackmate.gui.displaysettings
DisplaySettings.TrackMateObject - Enum in fiji.plugin.trackmate.gui.displaysettings
DisplaySettings.UpdateListener - Interface in fiji.plugin.trackmate.gui.displaysettings
displaySettingsChanged() - Method in interface fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.UpdateListener
DisplaySettingsIO - Class in fiji.plugin.trackmate.gui.displaysettings
DisplaySettingsIO() - Constructor for class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
DisplaySettingsPanel - Class in fiji.plugin.trackmate.gui.displaysettings
DisplaySettingsPanel(DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsPanel
distance(Spot, List<Roi>, double[]) - Static method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction
distance(Spot, Roi, double[]) - Static method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction
distanceTolerance - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: How close must be the new spot found to be accepted, in radius units.
DistanceToRoiFeature() - Constructor for class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
document - Variable in class fiji.plugin.trackmate.io.TmXmlReader
DogDetector<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
DogDetector(RandomAccessible<T>, Interval, double[], double, double, boolean, boolean) - Constructor for class fiji.plugin.trackmate.detection.DogDetector
DogDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector
DogDetectorConfigurationPanel(Settings, Model, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.detector.DogDetectorConfigurationPanel
DogDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
DogDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.DogDetectorFactory
doMedianFilter - Variable in class fiji.plugin.trackmate.detection.LogDetector
doSaveAs() - Method in class fiji.plugin.trackmate.util.ExportableChartPanel: Opens a file chooser and gives the user an opportunity to save the chart in PNG, PDF or SVG format.
doSubPixelLocalization - Variable in class fiji.plugin.trackmate.detection.LogDetector
doTrackLayout() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
doTrackStyle() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
DoubleArgument() - Constructor for class fiji.plugin.trackmate.util.cli.CLIConfigurator.DoubleArgument
doubleElement(String, DoubleSupplier, Consumer<Double>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
DoubleElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
douglasPeucker(List<double[]>, double) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Given a curve composed of line segments find a similar curve with fewer points.
doUpdate() - Method in class fiji.plugin.trackmate.util.OnRequestUpdater
draw(Graphics2D, XYPlot, Rectangle2D, ValueAxis, ValueAxis, int, PlotRenderingInfo) - Method in class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation
drawEdge(Graphics2D, Spot, Spot, int, int, double, float) - Method in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
drawEdge(Graphics2D, Spot, Spot, int, int, double) - Method in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
drawExtraLayer(Graphics2D, int) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
drawOverlay(Graphics) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
drawOverlay(Graphics) - Method in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
drawShape(int, int, int, int, Map<String, Object>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeSvgCanvas
drawSpot(Graphics2D, Spot, double, int, int, double, boolean) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
ds - Variable in class fiji.plugin.trackmate.features.ModelDataset
dt - Variable in class fiji.plugin.trackmate.Settings
DUMMY_ANALYZER - Static variable in interface fiji.plugin.trackmate.features.spot.SpotAnalyzer
DUMMY_MODEL - Static variable in class fiji.plugin.trackmate.features.FeatureUtils
dummyAnalyzer() - Static method in interface fiji.plugin.trackmate.features.spot.SpotAnalyzer: Returns a SpotAnalyzer that does nothing.
DummySpotAnalyzer() - Constructor for class fiji.plugin.trackmate.features.spot.SpotAnalyzer.DummySpotAnalyzer
dx - Variable in class fiji.plugin.trackmate.Settings
dy - Variable in class fiji.plugin.trackmate.Settings
dz - Variable in class fiji.plugin.trackmate.Settings

E

echo() - Method in class fiji.plugin.trackmate.FeatureModel: Echoes the full content of this FeatureModel.
echo() - Method in class fiji.plugin.trackmate.providers.AbstractProvider
echo() - Method in class fiji.plugin.trackmate.Spot: Return a string representation of this spot, with calculated features.
echo() - Method in class fiji.plugin.trackmate.TrackModel
echoAnalyzers(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
echoDetectorSettings(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
echoFeaturePenalties(Map<String, Double>) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
echoImageInfo(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
echoInitialSpotFilter(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
echoMap(Map<String, Object>, int) - Static method in class fiji.plugin.trackmate.util.TMUtils: Generate a string representation of a map, typically a settings map.
echoMatrix(double[][]) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
echoSolutions(int[][]) - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
echoSpotFilters(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
echoTrackerSettings(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
echoTrackFilters(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
EDGE_ANALYSERS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
EDGE_COST - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
EDGE_FEATURES_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
EDGE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
EDGE_ICON_16x16 - Static variable in class fiji.plugin.trackmate.gui.Icons
EDGE_ICON_64x64 - Static variable in class fiji.plugin.trackmate.gui.Icons
edgeAdded(GraphEdgeChangeEvent<Spot, DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex
edgeAdded(GraphEdgeChangeEvent<Spot, DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
EdgeAnalyzer - Interface in fiji.plugin.trackmate.features.edges: Interface for analyzers that can compute scalar numerical features for an edge of a TrackMate model.
EdgeAnalyzerProvider - Class in fiji.plugin.trackmate.providers: A provider for the edge analyzers provided in the GUI.
EdgeAnalyzerProvider() - Constructor for class fiji.plugin.trackmate.providers.EdgeAnalyzerProvider
edgeAnalyzers - Variable in class fiji.plugin.trackmate.Settings: The EdgeAnalyzers that will be used to compute edge features.
EdgeCollectionDataset - Class in fiji.plugin.trackmate.features
EdgeCollectionDataset(Model, SelectionModel, DisplaySettings, String, List<String>, List<DefaultWeightedEdge>, boolean) - Constructor for class fiji.plugin.trackmate.features.EdgeCollectionDataset
EdgeFeatureCalculator - Class in fiji.plugin.trackmate.features: A class dedicated to centralizing the calculation of the numerical features of spots, through EdgeAnalyzers.
EdgeFeatureCalculator(Model, Settings, boolean) - Constructor for class fiji.plugin.trackmate.features.EdgeFeatureCalculator
EdgeFeatureGrapher - Class in fiji.plugin.trackmate.features
EdgeFeatureGrapher(List<DefaultWeightedEdge>, String, List<String>, Model, SelectionModel, DisplaySettings, boolean) - Constructor for class fiji.plugin.trackmate.features.EdgeFeatureGrapher
edgeRemoved(GraphEdgeChangeEvent<Spot, DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex
edgeRemoved(GraphEdgeChangeEvent<Spot, DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
edgeSet() - Method in class fiji.plugin.trackmate.TrackModel: Returns a set of the edges contained in this model.
edgesOf(Spot) - Method in class fiji.plugin.trackmate.TrackModel: Returns the set of edges of a spot.
EdgeSpeedAnalyzer - Class in fiji.plugin.trackmate.features.edges
EdgeSpeedAnalyzer() - Constructor for class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
EdgeTargetAnalyzer - Class in fiji.plugin.trackmate.features.edges
EdgeTargetAnalyzer() - Constructor for class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
EdgeTimeLocationAnalyzer - Class in fiji.plugin.trackmate.features.edges
EdgeTimeLocationAnalyzer() - Constructor for class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
EDIT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
EDIT_SETTINGS_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
EditAction(String, Icon, TrackSchemeGraphComponent) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions.EditAction
editingSpot - Variable in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
editor(DisplaySettings, String, String) - Static method in class fiji.plugin.trackmate.gui.displaysettings.ConfigTrackMateDisplaySettings
EditorFileFilter(String) - Constructor for class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter: Constructs a new editor file filter using the specified description.
encounterVertex(V, E) - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
encounterVertexAgain(V, E) - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
END_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
endMoveSpot() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
endUpdate() - Method in class fiji.plugin.trackmate.Model
ensureCapacity(int) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
enumElement(String, E[], Supplier<E>, Consumer<E>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
EnumElement(String, E[]) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
equals(Object) - Method in class fiji.plugin.trackmate.Spot
equals(Object) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
error(String) - Method in class fiji.plugin.trackmate.Logger: Send the message to the error channel of this logger.
error(String) - Method in class fiji.plugin.trackmate.Logger.SlaveLogger
error(String) - Method in class fiji.plugin.trackmate.Logger.StringBuilderLogger
error(String) - Method in class fiji.plugin.trackmate.util.LogRecorder
ERROR_COLOR - Static variable in class fiji.plugin.trackmate.Logger
errorMessage - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector
errorMessage - Variable in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
errorMessage - Variable in class fiji.plugin.trackmate.detection.LogDetector
errorMessage - Variable in class fiji.plugin.trackmate.detection.LogDetectorFactory
errorMessage - Variable in class fiji.plugin.trackmate.detection.ManualDetectorFactory
errorMessage - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
errorMessage - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector
errorMessage - Variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
errorMessage - Variable in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
errorMessage - Variable in class fiji.plugin.trackmate.Settings
errorMessage - Variable in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
errorMessage - Variable in class fiji.plugin.trackmate.TrackMate
EverythingDisablerAndReenabler - Class in fiji.plugin.trackmate.util: Purpose: To recursively disable (and later re-enable) all components of a container, e.g.
EverythingDisablerAndReenabler(Container, Class<?>[]) - Constructor for class fiji.plugin.trackmate.util.EverythingDisablerAndReenabler
execDetection() - Method in class fiji.plugin.trackmate.TrackMate: Execute the detection part.
execInitialSpotFiltering() - Method in class fiji.plugin.trackmate.TrackMate: Execute the initial spot filtering part.
execSpotFiltering(boolean) - Method in class fiji.plugin.trackmate.TrackMate: Execute the spot feature filtering part.
execTrackFiltering(boolean) - Method in class fiji.plugin.trackmate.TrackMate
execTracking() - Method in class fiji.plugin.trackmate.TrackMate: Execute the tracking part.
executable - Variable in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator
ExecutablePath() - Constructor for class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator.ExecutablePath
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.CaptureOverlayAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction
execute(TrackMate, Logger) - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
execute(TrackMate, Logger) - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation
execute(TrackMate, Logger) - Method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod: Performs the gap closing.
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.CTCExporterAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ExportStatsTablesAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ExportTracksToXML
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ExtractTrackStackAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.IcyTrackExporter
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ISBIChallengeExporter
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.LabelImgExporter
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.MergeFileAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.MotilityLabExporter
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.RecomputeFeatureAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.TrackBranchAnalysis
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in interface fiji.plugin.trackmate.action.TrackMateAction: Executes this action within an application specified by the parameters.
execute(TrackMate, SelectionModel, DisplaySettings, Frame) - Method in class fiji.plugin.trackmate.action.TrimNotVisibleAction
execute(Object) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphLayout
EXECUTE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ExecuteDetectionDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
ExecuteDetectionDescriptor(TrackMate, LogPanel) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteDetectionDescriptor
ExecuteTrackingDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
ExecuteTrackingDescriptor(TrackMate, LogPanel) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteTrackingDescriptor
export(Model, Settings, File) - Static method in class fiji.plugin.trackmate.action.ExportTracksToXML: Static utility that silently exports tracks in a simplified xml format, describe in this class.
export(Iterable<Spot>) - Method in class fiji.plugin.trackmate.action.IJRoiExporter
export(Spot) - Method in class fiji.plugin.trackmate.action.IJRoiExporter
ExportableChartPanel - Class in fiji.plugin.trackmate.util
ExportableChartPanel(JFreeChart) - Constructor for class fiji.plugin.trackmate.util.ExportableChartPanel
ExportableChartPanel(JFreeChart, boolean, boolean, boolean, boolean, boolean) - Constructor for class fiji.plugin.trackmate.util.ExportableChartPanel
ExportableChartPanel(JFreeChart, int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class fiji.plugin.trackmate.util.ExportableChartPanel
ExportableChartPanel(JFreeChart, int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class fiji.plugin.trackmate.util.ExportableChartPanel
ExportableChartValueTable - Class in fiji.plugin.trackmate.util
ExportableChartValueTable(ModelDataset, String, String, String, String, String) - Constructor for class fiji.plugin.trackmate.util.ExportableChartValueTable
exportAll(String, TrackMate, CTCExporter.ExportType, Logger) - Static method in class fiji.plugin.trackmate.action.CTCExporter
ExportAllSpotsStatsAction - Class in fiji.plugin.trackmate.action
ExportAllSpotsStatsAction() - Constructor for class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction
ExportAllSpotsStatsAction.Factory - Class in fiji.plugin.trackmate.action
exportChartAsPDF(File, JFreeChart, int, int) - Static method in class fiji.plugin.trackmate.util.ChartExporter: Export a JFreeChart to PDF.
exportChartAsSVG(File, JFreeChart, int, int) - Static method in class fiji.plugin.trackmate.util.ChartExporter: Export a JFreeChart to SVG.
exportOriginalImageData(String, int, TrackMate, Logger) - Static method in class fiji.plugin.trackmate.action.CTCExporter
exportOriginalImageData(String, int, ImagePlus, Logger) - Static method in class fiji.plugin.trackmate.action.CTCExporter
exportSegmentationData(String, int, CTCExporter.ExportType, TrackMate, Logger) - Static method in class fiji.plugin.trackmate.action.CTCExporter: Writes the segmentation ground-truth files.
exportSettingsFile(String, int, TrackMate, Logger) - Static method in class fiji.plugin.trackmate.action.CTCExporter: Saves the settings part as XML for reference.
exportSpots(String, Model, boolean) - Static method in class fiji.plugin.trackmate.io.CSVExporter: Exports the spots in the specified model to a CSV file.
ExportStatsTablesAction - Class in fiji.plugin.trackmate.action
ExportStatsTablesAction() - Constructor for class fiji.plugin.trackmate.action.ExportStatsTablesAction
ExportStatsTablesAction.Factory - Class in fiji.plugin.trackmate.action
exportToCsv() - Method in class fiji.plugin.trackmate.util.ExportableChartValueTable
exportToCsv(String) - Method in class fiji.plugin.trackmate.util.ExportableChartValueTable
exportToCsv() - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
exportToCsv(String) - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
exportToCsv() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
exportToCsv(String) - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
exportToCsv(File) - Method in class fiji.plugin.trackmate.visualization.table.TablePanel
exportToFile(Model, Settings, File) - Static method in class fiji.plugin.trackmate.action.ISBIChallengeExporter
exportToFile(Model, Settings, File, Logger) - Static method in class fiji.plugin.trackmate.action.ISBIChallengeExporter
exportTrackingData(String, int, CTCExporter.ExportType, TrackMate, Logger) - Static method in class fiji.plugin.trackmate.action.CTCExporter
ExportTracksToXML - Class in fiji.plugin.trackmate.action
ExportTracksToXML() - Constructor for class fiji.plugin.trackmate.action.ExportTracksToXML
ExportTracksToXML.Factory - Class in fiji.plugin.trackmate.action
exposeSpot(Spot, Spot) - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: This method is a hook for subclassers.
exposeSpot(Spot, Spot) - Method in class fiji.plugin.trackmate.detection.semiauto.SemiAutoTracker
ext - Variable in class fiji.plugin.trackmate.util.DefaultFileFilter: Extension of accepted files.
ExtractTrackStackAction - Class in fiji.plugin.trackmate.action
ExtractTrackStackAction() - Constructor for class fiji.plugin.trackmate.action.ExtractTrackStackAction
ExtractTrackStackAction.ExtractTrackStackActionFactory - Class in fiji.plugin.trackmate.action
ExtractTrackStackActionFactory() - Constructor for class fiji.plugin.trackmate.action.ExtractTrackStackAction.ExtractTrackStackActionFactory

F

Factory() - Constructor for class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.CaptureOverlayAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.closegaps.CloseGapsAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.CTCExporterAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.ExportStatsTablesAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.ExportTracksToXML.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.IcyTrackExporter.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.ISBIChallengeExporter.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.LabelImgExporter.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.MergeFileAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.MotilityLabExporter.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.RecomputeFeatureAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.TrackBranchAnalysis.Factory
Factory() - Constructor for class fiji.plugin.trackmate.action.TrimNotVisibleAction.Factory
FAST_CALCULATION - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory: Value for the fast IoU calculation method.
FEATURE - Static variable in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
feature - Variable in class fiji.plugin.trackmate.features.FeatureFilter
FEATURE - Static variable in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
FEATURE - Static variable in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
FEATURE_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_DECLARATIONS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_DIMENSION_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
FEATURE_DIMENSIONS - Static variable in class fiji.plugin.trackmate.Spot: The 7 privileged spot feature dimensions.
FEATURE_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_ISINT_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_NAME_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
FEATURE_NAMES - Static variable in class fiji.plugin.trackmate.Spot: The 7 privileged spot feature names.
FEATURE_SHORT_NAME_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
FEATURE_SHORT_NAMES - Static variable in class fiji.plugin.trackmate.Spot: The 7 privileged spot feature short names.
FeatureAnalyzer - Interface in fiji.plugin.trackmate.features
FeatureColorGenerator<K> - Interface in fiji.plugin.trackmate.visualization: Interface for color generator that can color objects based on a feature identified by a String.
featureComparator(String) - Static method in class fiji.plugin.trackmate.Spot: A comparator used to sort spots by ascending feature values.
FeatureDisplaySelector - Class in fiji.plugin.trackmate.gui.components
FeatureDisplaySelector(Model, Settings, DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.components.FeatureDisplaySelector
featureEdgeComparator(String, FeatureModel) - Static method in class fiji.plugin.trackmate.util.ModelTools: A comparator used to sort edges by ascending feature values.
featureElement(String, Supplier<DisplaySettings.TrackMateObject>, Supplier<String>, BiConsumer<DisplaySettings.TrackMateObject, String>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
FeatureElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
FeatureFilter - Class in fiji.plugin.trackmate.features: A helper class to store a feature filter.
FeatureFilter(String, double, boolean) - Constructor for class fiji.plugin.trackmate.features.FeatureFilter
FeatureModel - Class in fiji.plugin.trackmate: This class represents the part of the Model that is in charge of dealing with spot features and track features.
FeatureModel(Model) - Constructor for class fiji.plugin.trackmate.FeatureModel: Instantiates a new feature model.
FeaturePenaltyCostFunction - Class in fiji.plugin.trackmate.tracking.jaqaman.costfunction: A cost function that tempers a square distance cost by difference in feature values.
FeaturePenaltyCostFunction(Map<String, Double>) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costfunction.FeaturePenaltyCostFunction
FeaturePlotSelectionPanel - Class in fiji.plugin.trackmate.gui.components: A simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum.
FeaturePlotSelectionPanel(String, String, Collection<String>, Map<String, String>, FeaturePlotSelectionPanel.PlotAction) - Constructor for class fiji.plugin.trackmate.gui.components.FeaturePlotSelectionPanel
FeaturePlotSelectionPanel.PlotAction - Interface in fiji.plugin.trackmate.gui.components: Action to execute when the plot button is clicked.
FEATURES - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
FEATURES - Static variable in class fiji.plugin.trackmate.Spot: The 7 privileged spot features that must be set by a spot detector: Spot.QUALITY, Spot.POSITION_X, Spot.POSITION_Y, Spot.POSITION_Z, Spot.POSITION_Z, Spot.RADIUS, Spot.FRAME .
FEATURES_COMPUTED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Event type indicated that the feature values for the objects in this model have been computed.
featureTrackComparator(String, FeatureModel) - Static method in class fiji.plugin.trackmate.util.ModelTools: A comparator used to sort tracks by ascending feature values.
FeatureUtils - Class in fiji.plugin.trackmate.features
FeatureUtils() - Constructor for class fiji.plugin.trackmate.features.FeatureUtils
fiji.plugin.trackmate - package fiji.plugin.trackmate
fiji.plugin.trackmate.action - package fiji.plugin.trackmate.action
fiji.plugin.trackmate.action.autonaming - package fiji.plugin.trackmate.action.autonaming
fiji.plugin.trackmate.action.closegaps - package fiji.plugin.trackmate.action.closegaps
fiji.plugin.trackmate.action.fit - package fiji.plugin.trackmate.action.fit
fiji.plugin.trackmate.detection - package fiji.plugin.trackmate.detection
fiji.plugin.trackmate.detection.semiauto - package fiji.plugin.trackmate.detection.semiauto
fiji.plugin.trackmate.detection.util - package fiji.plugin.trackmate.detection.util
fiji.plugin.trackmate.features - package fiji.plugin.trackmate.features
fiji.plugin.trackmate.features.edges - package fiji.plugin.trackmate.features.edges: Package for the classes that compute scalar features on links between spots (edges), such as instantaneous velocities, etc....
fiji.plugin.trackmate.features.manual - package fiji.plugin.trackmate.features.manual
fiji.plugin.trackmate.features.spot - package fiji.plugin.trackmate.features.spot
fiji.plugin.trackmate.features.track - package fiji.plugin.trackmate.features.track
fiji.plugin.trackmate.graph - package fiji.plugin.trackmate.graph: A package containing utility classes for the manipulation and analysis of tracks as JGraphT graphs.
fiji.plugin.trackmate.gui - package fiji.plugin.trackmate.gui
fiji.plugin.trackmate.gui.components - package fiji.plugin.trackmate.gui.components
fiji.plugin.trackmate.gui.components.detector - package fiji.plugin.trackmate.gui.components.detector
fiji.plugin.trackmate.gui.components.tracker - package fiji.plugin.trackmate.gui.components.tracker
fiji.plugin.trackmate.gui.displaysettings - package fiji.plugin.trackmate.gui.displaysettings
fiji.plugin.trackmate.gui.wizard - package fiji.plugin.trackmate.gui.wizard
fiji.plugin.trackmate.gui.wizard.descriptors - package fiji.plugin.trackmate.gui.wizard.descriptors
fiji.plugin.trackmate.io - package fiji.plugin.trackmate.io
fiji.plugin.trackmate.providers - package fiji.plugin.trackmate.providers
fiji.plugin.trackmate.tracking - package fiji.plugin.trackmate.tracking
fiji.plugin.trackmate.tracking.jaqaman - package fiji.plugin.trackmate.tracking.jaqaman: Classes that implements the tracking logic of the framework described first in:
fiji.plugin.trackmate.tracking.jaqaman.costfunction - package fiji.plugin.trackmate.tracking.jaqaman.costfunction
fiji.plugin.trackmate.tracking.jaqaman.costmatrix - package fiji.plugin.trackmate.tracking.jaqaman.costmatrix
fiji.plugin.trackmate.tracking.kalman - package fiji.plugin.trackmate.tracking.kalman
fiji.plugin.trackmate.tracking.kdtree - package fiji.plugin.trackmate.tracking.kdtree
fiji.plugin.trackmate.tracking.manual - package fiji.plugin.trackmate.tracking.manual: Classes implementing the manual tracker.
fiji.plugin.trackmate.tracking.overlap - package fiji.plugin.trackmate.tracking.overlap
fiji.plugin.trackmate.util - package fiji.plugin.trackmate.util
fiji.plugin.trackmate.util.cli - package fiji.plugin.trackmate.util.cli
fiji.plugin.trackmate.visualization - package fiji.plugin.trackmate.visualization
fiji.plugin.trackmate.visualization.hyperstack - package fiji.plugin.trackmate.visualization.hyperstack
fiji.plugin.trackmate.visualization.table - package fiji.plugin.trackmate.visualization.table
fiji.plugin.trackmate.visualization.trackscheme - package fiji.plugin.trackmate.visualization.trackscheme
fiji.plugin.trackmate.visualization.trackscheme.utils - package fiji.plugin.trackmate.visualization.trackscheme.utils
file - Variable in class fiji.plugin.trackmate.io.TmXmlReader
FileChooser - Class in fiji.plugin.trackmate.util
FileChooser() - Constructor for class fiji.plugin.trackmate.util.FileChooser
FileChooser.DialogType - Enum in fiji.plugin.trackmate.util
FileChooser.SelectionMode - Enum in fiji.plugin.trackmate.util
fillWith(double) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Replace all the non-infinite values of this matrix by the specified value.
filter(FeatureFilter) - Method in class fiji.plugin.trackmate.SpotCollection: Filters out the content of this collection using the specified FeatureFilter.
filter(Collection<FeatureFilter>) - Method in class fiji.plugin.trackmate.SpotCollection: Filters out the content of this collection using the specified FeatureFilter collection.
FILTER_ABOVE_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FILTER_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FILTER_FEATURE_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FILTER_VALUE_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FILTERED_TRACK_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
FilterGuiPanel - Class in fiji.plugin.trackmate.gui.components
FilterGuiPanel(Model, Settings, DisplaySettings.TrackMateObject, List<FeatureFilter>, String, FeatureDisplaySelector) - Constructor for class fiji.plugin.trackmate.gui.components.FilterGuiPanel
FilterPanel - Class in fiji.plugin.trackmate.gui.components: Revised December 2020.
FilterPanel(Map<String, String>, Function<String, double[]>, FeatureFilter) - Constructor for class fiji.plugin.trackmate.gui.components.FilterPanel
filterSpots(Collection<FeatureFilter>, boolean) - Method in class fiji.plugin.trackmate.Model: Filters the SpotCollection managed by this model with the FeatureFilters specified.
findDefaultCondaPath() - Static method in class fiji.plugin.trackmate.util.cli.CLIUtils
findLocalMaxima(RandomAccessibleInterval<T>, double, double[], double, boolean, int) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils
finish() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
firstElement() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
firstElement() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
firstKey() - Method in class fiji.plugin.trackmate.SpotCollection: Returns the first (lowest) frame currently in this collection.
fit(Spot) - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
fit(Spot) - Method in interface fiji.plugin.trackmate.action.fit.SpotFitter
fit(Spot) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter2D
fit(Spot) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter2DFixedRadius
fit(Spot) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter3D
fit(Spot) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter3DFixedRadius
FLAG_EDGE_ADDED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate that an edge was added to the model.
FLAG_EDGE_MODIFIED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate that an edge has been modified.
FLAG_EDGE_REMOVED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate that an edge was removed from the model.
FLAG_SPOT_ADDED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate that a spot was added to the model.
FLAG_SPOT_FRAME_CHANGED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate that a spot has changed of frame, and possible of position, features, etc..
FLAG_SPOT_MODIFIED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate a modification of the features of a spot.
FLAG_SPOT_REMOVED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Indicate that a spot was removed from the model.
FlagNode<K> - Class in fiji.plugin.trackmate.tracking.kdtree
FlagNode(K) - Constructor for class fiji.plugin.trackmate.tracking.kdtree.FlagNode
flagsToString - Static variable in class fiji.plugin.trackmate.ModelChangeEvent
fm - Variable in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
FONT - Static variable in class fiji.plugin.trackmate.gui.Fonts
FONT - Static variable in class fiji.plugin.trackmate.gui.wizard.WizardPanel
fontElement(String, Supplier<Font>, Consumer<Font>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
FontElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
Fonts - Class in fiji.plugin.trackmate.gui
Fonts() - Constructor for class fiji.plugin.trackmate.gui.Fonts
forbidMultithreading() - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
forbidMultithreading() - Method in interface fiji.plugin.trackmate.TrackMateModule: Returns a flag that tells TrackMate whether it should strictly forbid running this module concurrently.
FRAME - Static variable in class fiji.plugin.trackmate.Spot: The name of the frame feature.
FRAME_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
frameComparator - Static variable in class fiji.plugin.trackmate.Spot: A comparator used to sort spots by ascending frame.
frameSupplier(Supplier<Integer>) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the supplier function that will return the frame to run the preview on.
from(SimpleWeightedGraph<Spot, DefaultWeightedEdge>, Map<Integer, Set<Spot>>, Map<Integer, Set<DefaultWeightedEdge>>, Map<Integer, Boolean>, Map<Integer, String>) - Method in class fiji.plugin.trackmate.TrackModel: This method is meant to help building a model from a serialized source, such as a saved file.
fromCollection(Iterable<Spot>) - Static method in class fiji.plugin.trackmate.SpotCollection: Creates a new SpotCollection containing only the specified spots.
FromContinuousBranches - Class in fiji.plugin.trackmate.graph
FromContinuousBranches(Collection<List<Spot>>, Collection<List<Spot>>) - Constructor for class fiji.plugin.trackmate.graph.FromContinuousBranches
fromJson(String) - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
fromLabeling(ImgLabeling<Integer, R>, Interval, double[]) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Creates spots from a label image.
fromLabelingWithROI(ImgLabeling<Integer, R>, Interval, double[], boolean, RandomAccessibleInterval<S>) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Creates spots with ROIs from a 2D label image.
fromMap(Map<Integer, Set<Spot>>) - Static method in class fiji.plugin.trackmate.SpotCollection: Creates a new SpotCollection from a copy of the specified map of sets.
fromThreshold(RandomAccessible<T>, Interval, double[], double, int) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Creates spots from a grayscale image, thresholded to create a mask.
fromThreshold(RandomAccessible<T>, Interval, double[], double, int, RandomAccessibleInterval<R>) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Creates spots from a grayscale image, thresholded to create a mask.
fromThresholdWithROI(RandomAccessible<T>, Interval, double[], double, boolean, int, RandomAccessibleInterval<S>) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Creates spots with their ROIs from a 2D grayscale image, thresholded to create a mask.
fromTrackMateSettings(Map<String, Object>, CLIConfigurator) - Static method in class fiji.plugin.trackmate.util.cli.TrackMateSettingsBuilder: Serializes the parameters stored in a TrackMate map to a CLI config object.
ftfDiameter - Variable in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
ftfDiameter - Variable in class fiji.plugin.trackmate.gui.components.detector.ManualDetectorConfigurationPanel
ftfIntensityThreshold - Variable in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
ftfQualityThreshold - Variable in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
Function1<T1,T2> - Interface in fiji.plugin.trackmate.graph: Interface for function that compute values from a single input and store it in an output.
Function2<T1,T2> - Interface in fiji.plugin.trackmate.graph: Interface for function that compute values from a two inputs and store it in an output.
fwd(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
fwd() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
fwd() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor

G

GapClosingMethod - Interface in fiji.plugin.trackmate.action.closegaps
GapClosingMethod.GapClosingParameter - Class in fiji.plugin.trackmate.action.closegaps
GapClosingParameter(String, double, double, double) - Constructor for class fiji.plugin.trackmate.action.closegaps.GapClosingMethod.GapClosingParameter
gatherObservationData(Point, long[], int) - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
get() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
get(String) - Method in class fiji.plugin.trackmate.features.ModelDataset.DataItem
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
get() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
get(double) - Method in class fiji.plugin.trackmate.gui.wizard.TransitionAnimator
get(int, int, double) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Returns the value stored by this matrix at the specified row and column.
get() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceAdder
get() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.DoubleAdder
get() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.FlagAdder
get() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.IntAdder
get() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.PathAdder
get() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.StringAdder
get() - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder
get() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
getAllGaps(Model) - Static method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod: Utility method that can return all the edges of a model that have a gap.
getAlternativeCostForSource(K) - Method in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator: Returns the value of the no-linking alternative cost for the specified source.
getAlternativeCostForSource(K) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getAlternativeCostForSource(K) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
getAlternativeCostForSource(Spot) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getAlternativeCostForTarget(J) - Method in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator: Returns the value of the no-linking alternative cost for the specified target.
getAlternativeCostForTarget(J) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getAlternativeCostForTarget(J) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
getAlternativeCostForTarget(Spot) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getAnalyzer(ImgPlus<T>, int, int) - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getAnalyzer(ImgPlus<T>, int, int) - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getAnalyzer(ImgPlus<T>, int, int) - Method in interface fiji.plugin.trackmate.features.spot.SpotAnalyzerFactoryBase: Returns a configured SpotAnalyzer ready to operate on the given frame (0-based) and given channel (0-based).
getAnalyzer(ImgPlus<T>, int, int) - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getAnalyzer(ImgPlus<T>, int, int) - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getAnalyzer(ImgPlus<T>, int, int) - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getAnalyzer(ImgPlus<T>, int, int) - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getArcSize(int, int) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeSvgCanvas: Computes the arc size for the given dimension.
getArgument() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getArguments() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator: Returns the list of arguments (plus the command) in this CLI config.
getArguments() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments: Exposes all members of the selectable.
getArrayFromMaping(Collection<J>, Map<J, K>) - Static method in class fiji.plugin.trackmate.util.TMUtils: Returns the mapping in a map that is targeted by a list of keys, in the order given in the list.
getAssignmentCosts() - Method in class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker: Returns the costs associated to the assignment results.
getAvailableDatasetID(String) - Static method in class fiji.plugin.trackmate.action.CTCExporter: Returns a suitable dataset id to save in the specified folder.
getAvailableLUTs() - Static method in class fiji.plugin.trackmate.gui.displaysettings.Colormap
getBackwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseDetectorDescriptor
getBackwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ChooseTrackerDescriptor
getBackwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
getBranches() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Returns the collection of branches built by this algorithm.
getBranchesPerTrack() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Returns the mapping of each source track ID to the branches it was split in.
getBranchTable() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
getC() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
getCancelable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteDetectionDescriptor
getCancelable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteTrackingDescriptor
getCancelable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotFilterDescriptor
getCancelable() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
getCancelReason() - Method in class fiji.plugin.trackmate.features.EdgeFeatureCalculator
getCancelReason() - Method in class fiji.plugin.trackmate.features.SpotFeatureCalculator
getCancelReason() - Method in class fiji.plugin.trackmate.features.TrackFeatureCalculator
getCancelReason() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
getCancelReason() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
getCancelReason() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
getCancelReason() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
getCancelReason() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
getCancelReason() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
getCancelReason() - Method in class fiji.plugin.trackmate.TrackMate
getCellFor(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
getCellFor(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
getChangeListeners() - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
getChangeListeners() - Method in class fiji.plugin.trackmate.gui.components.FilterPanel
getChoices() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument
getClosestSpot(Spot, int, boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Returns the closest Spot to the given location (encoded as a Spot), contained in the frame frame.
getColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
getColormap() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getCommand() - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator: Returns the command that must be run in the configured conda environment.
getCommandArg() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator: Returns the command object of this tool.
getCommandArg() - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator
getCommandArg() - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator
getCondaPath() - Static method in class fiji.plugin.trackmate.util.cli.CLIUtils
getContext() - Static method in class fiji.plugin.trackmate.util.TMUtils: Obtains the SciJava Context in use by ImageJ.
getCost() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
getCostFunction(Map<String, Double>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker: Creates a suitable cost function.
getCostFunction(Map<String, Double>) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker: Creates a suitable cost function.
getCostFunctionFor(Map<String, Double>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getCosts() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Exposes the array of all the non-infinite costs.
getCurrent(long) - Method in class fiji.plugin.trackmate.gui.wizard.TransitionAnimator
getCurrentTimeString() - Static method in class fiji.plugin.trackmate.util.TMUtils
getCurrentValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
getCurrentValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
getDefaultKalmanSettingsMap() - Static method in class fiji.plugin.trackmate.gui.components.tracker.JPanelAdvancedKalmanTrackerSettingsMain
getDefaultLAPSettingsMap() - Static method in class fiji.plugin.trackmate.gui.components.tracker.JPanelTrackerSettingsMain
getDefaultSegmentSettingsMap() - Static method in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils: Returns a new settings map filled with default values suitable for the trajectory segments linking (gap/split/merge).
getDefaultSettings() - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getDefaultSettings() - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Returns a new default settings map suitable for the target detector.
getDefaultSettings() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getDefaultSettings(ImagePlus) - Static method in class fiji.plugin.trackmate.io.SettingsPersistence
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getDefaultSettings() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getDefaultSettings() - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Returns a new default settings map suitable for the tracker Settings are instantiated with default values.
getDefaultValue() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getDepthFirstIterator(Spot, boolean) - Method in class fiji.plugin.trackmate.TrackModel: Returns a new depth first iterator over the spots connected by links in this model.
getDescription() - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter: Returns the description.
getDescription() - Method in class fiji.plugin.trackmate.util.DefaultFileFilter: Returns the description for accepted files.
getDescription() - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter: Returns the description.
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.DogDetectorFactory
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getDetector(Interval, int) - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactory: Returns a new SpotDetector configured to operate on the given target frame.
getDetector(Interval) - Method in interface fiji.plugin.trackmate.detection.SpotGlobalDetectorFactory: Returns a new SpotDetector configured to operate on all the time-points.
getDetector(Interval, int) - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.DogDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getDetectorConfigurationPanel(Settings, Model) - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Returns a new GUI panel able to configure the settings suitable for this specific detector factory.
getDetectorConfigurationPanel(Settings, Model) - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getDetectorFactory() - Method in class fiji.plugin.trackmate.gui.components.detector.DogDetectorConfigurationPanel
getDetectorFactory() - Method in class fiji.plugin.trackmate.gui.components.detector.LabelImageDetectorConfigurationPanel: Returns a new instance of the SpotDetectorFactory that this configuration panels configures.
getDetectorFactory() - Method in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel: Returns a new instance of the SpotDetectorFactory that this configuration panels configures.
getDetectorFactory() - Method in class fiji.plugin.trackmate.gui.components.detector.MaskDetectorConfigurationPanel: Returns a new instance of the SpotDetectorFactory that this configuration panels configures.
getDetectorFactory() - Method in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel: Returns a new instance of the SpotDetectorFactory that this configuration panels configures.
getDetectorSettings(Element, Settings, DetectorProvider) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Update the given Settings object with the SpotDetectorFactory and settings map fields named Settings.detectorFactory and Settings.detectorSettings read within the XML file this reader is initialized with.
getDirectedNeighborIndex() - Method in class fiji.plugin.trackmate.TrackModel
getDisabled() - Method in class fiji.plugin.trackmate.providers.AbstractProvider
getDisplaySettings() - Method in class fiji.plugin.trackmate.io.TmXmlReader
getDistance() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
getDistanceSquared() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor: Return the square distance measured from the center of the domain to the current cursor position, in calibrated units.
getDomainOrder() - Method in class fiji.plugin.trackmate.features.ModelDataset
getDoublePosition(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
getDoublePosition(int) - Method in class fiji.plugin.trackmate.Spot
getDoublePosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
getDoublePosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
getEdge(Spot, Spot) - Method in class fiji.plugin.trackmate.TrackModel: Returns the specified edge.
getEdgeAnalyzers() - Method in class fiji.plugin.trackmate.Settings: Returns a copy of the list of EdgeAnalyzers configured in this settings object.
getEdgeCells() - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
getEdgeFeature(DefaultWeightedEdge, String) - Method in class fiji.plugin.trackmate.FeatureModel
getEdgeFeatureDimensions() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the dimension mapping of the edge features that are dealt with in this model.
getEdgeFeatureIsInt() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the map that states whether the target feature is integer values (true) or double valued (false).
getEdgeFeatureNames() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the name mapping of the edge features that are dealt with in this model.
getEdgeFeatures() - Method in class fiji.plugin.trackmate.FeatureModel: Returns edge features as declared in this model.
getEdgeFeatureSelectionPanel() - Method in class fiji.plugin.trackmate.gui.components.GrapherPanel
getEdgeFeatureShortNames() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the short name mapping of the edge features that are dealt with in this model.
getEdgeFlag(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.ModelChangeEvent: Returns the modification flag for the given edge affected by this event.
getEdgeFor(mxICell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
getEdges() - Method in class fiji.plugin.trackmate.ModelChangeEvent
getEdges() - Method in class fiji.plugin.trackmate.SelectionChangeEvent: Returns the edges that have been added or removed from the selection.
getEdgeSelection() - Method in class fiji.plugin.trackmate.SelectionModel
getEdgeSource(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.TrackModel: Returns the source spot of the specified edge.
getEdgeTable() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
getEdgeTarget(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.TrackModel: Returns the target spot of the specified edge.
getEdgeWeight(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.TrackModel: Returns the weight assigned to the specified edge.
getEditAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getEndAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getEnvironments() - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator.CondaEnvironmentCommand
getEnvList() - Static method in class fiji.plugin.trackmate.util.cli.CLIUtils
getEnvMap() - Static method in class fiji.plugin.trackmate.util.cli.CLIUtils
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.HessianDetector
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.LabelImageDetector
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.LogDetector
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
getErrorMessage() - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Returns a meaningful error message for the last action on this factory.
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
getErrorMessage() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition
getErrorMessage() - Method in class fiji.plugin.trackmate.graph.FromContinuousBranches
getErrorMessage() - Method in class fiji.plugin.trackmate.io.IcyTrackFormatWriter
getErrorMessage() - Method in class fiji.plugin.trackmate.io.TGMMImporter
getErrorMessage() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns an explanatory message about the last unsuccessful read attempt.
getErrorMessage() - Method in class fiji.plugin.trackmate.Settings
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getErrorMessage() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getErrorMessage() - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Returns a meaningful error message for the last action on this factory.
getErrorMessage() - Method in class fiji.plugin.trackmate.TrackMate
getEventID() - Method in class fiji.plugin.trackmate.ModelChangeEvent
getExportTrackingDataPath(String, int, CTCExporter.ExportType, TrackMate) - Static method in class fiji.plugin.trackmate.action.CTCExporter: Returns the folder in which the tracking data will be exported.
getExtension() - Method in class fiji.plugin.trackmate.util.DefaultFileFilter: Returns the extension for accepted files.
getFactory(String) - Method in class fiji.plugin.trackmate.providers.AbstractProvider
getFactory(String) - Method in class fiji.plugin.trackmate.providers.SpotAnalyzerProvider
getFactory(String) - Method in class fiji.plugin.trackmate.providers.SpotMorphologyAnalyzerProvider
getFadeTrackRange() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getFeature() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
getFeature(String) - Method in class fiji.plugin.trackmate.Spot: Returns the value corresponding to the specified spot feature.
getFeature(String) - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView.Branch: Returns the value corresponding to the specified branch feature.
getFeatureDimensions() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getFeatureDimensions() - Method in interface fiji.plugin.trackmate.features.FeatureAnalyzer: Returns the map of feature dimension this analyzer can compute.
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getFeatureDimensions() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getFeatureFilters() - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel: Returns the thresholds currently set by this GUI.
getFeatureModel() - Method in class fiji.plugin.trackmate.Model
getFeatureNames() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getFeatureNames() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getFeatureNames() - Method in interface fiji.plugin.trackmate.features.FeatureAnalyzer: Returns the map of names for any feature this analyzer can compute.
getFeatureNames() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getFeatureNames() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getFeatureNames() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getFeatureNames() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getFeatureNames() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getFeatureNames() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getFeatureNames() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getFeatureNames() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getFeatureNames() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getFeaturePenalties() - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeatureSelectionGui
getFeatures() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getFeatures() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getFeatures() - Method in interface fiji.plugin.trackmate.features.FeatureAnalyzer: Returns the list of features this analyzer can compute.
getFeatures() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getFeatures() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getFeatures() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getFeatures() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getFeatures() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getFeatures() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getFeatures() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getFeatures() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getFeatures() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getFeatures() - Method in class fiji.plugin.trackmate.Spot: Exposes the storage map of features for this spot.
getFeatureShortNames() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getFeatureShortNames() - Method in interface fiji.plugin.trackmate.features.FeatureAnalyzer: Returns the map of short names for any feature the analyzer can compute.
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getFeatureShortNames() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getFeatureThreshold() - Method in class fiji.plugin.trackmate.gui.components.InitFilterPanel: Return the feature threshold on quality set by this panel.
getFilter() - Method in class fiji.plugin.trackmate.gui.components.FilterPanel
getFirstFrame() - Method in class fiji.plugin.trackmate.action.CaptureOverlayPanel
getFloatPosition(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
getFloatPosition(int) - Method in class fiji.plugin.trackmate.Spot
getFloatPosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
getFloatPosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
getFont() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getForwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteDetectionDescriptor
getForwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteTrackingDescriptor
getForwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.InitFilterDescriptor
getForwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotFilterDescriptor
getForwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.descriptors.TrackFilterDescriptor
getForwardRunnable() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
getFromFrame(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent
getGraph() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Returns the JGraphXAdapter that serves as a model for the graph displayed in this frame.
getGraph() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
getGraphLayout() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Returns the graph layout in charge of arranging the cells on the graph.
getGUI() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Returns the GUI frame controlled by this class.
getGUIState() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns the GUI state saved in the file.
getHelp() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getHighlightColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getHomeAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getIcon() - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.CaptureOverlayAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getIcon() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.CTCExporterAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.ExportStatsTablesAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.ExportTracksToXML.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.ExtractTrackStackAction.ExtractTrackStackActionFactory
getIcon() - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.IcyTrackExporter.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterActionFactory
getIcon() - Method in class fiji.plugin.trackmate.action.ISBIChallengeExporter.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.LabelImgExporter.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.MergeFileAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.MotilityLabExporter.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.RecomputeFeatureAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.TrackBranchAnalysis.Factory
getIcon() - Method in class fiji.plugin.trackmate.action.TrimNotVisibleAction.Factory
getIcon() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getIcon() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getIcon() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getIcon() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getIcon() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getIcon() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getIcon() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getIcon() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getIcon() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getIcon() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getIcon() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getIcon() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getIcon() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getIcon() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getIcon() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getIcon() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
getIcon() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
getIcon() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
getIcon() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getIcon() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getIcon() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getIcon() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getIcon() - Method in interface fiji.plugin.trackmate.TrackMateModule: Returns the icon for this action.
getIcon() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayerFactory
getIcon() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFactory
getIconHeight() - Method in class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
getIconWidth() - Method in class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
getImageBounds(int, int, int, int) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeSvgCanvas
getImagePathWithoutExtension(Settings) - Static method in class fiji.plugin.trackmate.util.TMUtils: Returns a string of the name of the image without the extension, with the full path
getImageString(Spot, double) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SpotIconGrabber: Returns the image string for the specified spot.
getImageString(Spot, double) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SpotImageUpdater: Returns the image string of the given spot, based on the raw images contained in the given model.
getImp() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer: Exposes the ImagePlus on which the model is drawn by this view.
getInfo() - Method in enum fiji.plugin.trackmate.action.LabelImgExporter.LabelIdPainting
getInfoText() - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
getInfoText() - Method in interface fiji.plugin.trackmate.action.autonaming.AutoNamingRule: Returns a html string containing a descriptive information about this module.
getInfoText() - Method in class fiji.plugin.trackmate.action.autonaming.CopyTrackNameNamingRule
getInfoText() - Method in class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
getInfoText() - Method in class fiji.plugin.trackmate.action.CaptureOverlayAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
getInfoText() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation
getInfoText() - Method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod: Returns a html string containing a descriptive information about this module.
getInfoText() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getInfoText() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.CTCExporterAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.ExportStatsTablesAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.ExportTracksToXML.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.ExtractTrackStackAction.ExtractTrackStackActionFactory
getInfoText() - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.IcyTrackExporter.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterActionFactory
getInfoText() - Method in class fiji.plugin.trackmate.action.ISBIChallengeExporter.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.LabelImgExporter.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.MergeFileAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.MotilityLabExporter.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.RecomputeFeatureAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.TrackBranchAnalysis.Factory
getInfoText() - Method in class fiji.plugin.trackmate.action.TrimNotVisibleAction.Factory
getInfoText() - Method in class fiji.plugin.trackmate.detection.DogDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getInfoText() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getInfoText() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getInfoText() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getInfoText() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getInfoText() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getInfoText() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getInfoText() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getInfoText() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getInfoText() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getInfoText() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getInfoText() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
getInfoText() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
getInfoText() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
getInfoText() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getInfoText() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getInfoText() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getInfoText() - Method in enum fiji.plugin.trackmate.tracking.overlap.OverlapTracker.IoUCalculation
getInfoText() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getInfoText() - Method in interface fiji.plugin.trackmate.TrackMateModule: Returns a html string containing a descriptive information about this module.
getInfoText() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayerFactory
getInfoText() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFactory
getInitialFilter(Element) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Return the initial filter value on quality stored in this file.
getInputMap(int) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeKeyboardHandler
getInstance() - Static method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool: Return the singleton instance for this tool.
getInterval(ImgPlus<?>, Settings) - Static method in class fiji.plugin.trackmate.util.TMUtils: Returns an interval object that in the specified ImgPlus slice in a single time frame.
getIntervalWithTime(ImgPlus<?>, Settings) - Static method in class fiji.plugin.trackmate.util.TMUtils: Returns an interval object that slices in the specified ImgPlus in a single channel (the channel dimension is dropped).
getIntPosition(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
getIntPosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
getIntPosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
getIsIntFeature() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getIsIntFeature() - Method in interface fiji.plugin.trackmate.features.FeatureAnalyzer: Returns the map that states whether the key feature is a feature that returns integers.
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getIsIntFeature() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getItemCount(int) - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
getItemCount(int) - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
getItemCount(int) - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
getItemLabel(int) - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
getItemLabel(int) - Method in class fiji.plugin.trackmate.features.ModelDataset
getItemLabel(int) - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
getItemLabel(int) - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
getKey() - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.CaptureOverlayAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getKey() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.CTCExporterAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.ExportStatsTablesAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.ExportTracksToXML.Factory
getKey() - Method in class fiji.plugin.trackmate.action.ExtractTrackStackAction.ExtractTrackStackActionFactory
getKey() - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.IcyTrackExporter.Factory
getKey() - Method in class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterActionFactory
getKey() - Method in class fiji.plugin.trackmate.action.ISBIChallengeExporter.Factory
getKey() - Method in class fiji.plugin.trackmate.action.LabelImgExporter.Factory
getKey() - Method in class fiji.plugin.trackmate.action.MergeFileAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.MotilityLabExporter.Factory
getKey() - Method in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.RecomputeFeatureAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction.Factory
getKey() - Method in class fiji.plugin.trackmate.action.TrackBranchAnalysis.Factory
getKey() - Method in class fiji.plugin.trackmate.action.TrimNotVisibleAction.Factory
getKey() - Method in class fiji.plugin.trackmate.detection.DogDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getKey() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getKey() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getKey() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getKey() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getKey() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getKey() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getKey() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getKey() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getKey() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getKey() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getKey() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
getKey() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
getKey() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
getKey() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getKey() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getKey() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getKey() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getKey() - Method in interface fiji.plugin.trackmate.TrackMateModule: Returns a unique identifier of this module.
getKey() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getKey() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
getKey() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
getKey() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayerFactory
getKey() - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
getKey() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
getKey() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
getKey() - Method in interface fiji.plugin.trackmate.visualization.TrackMateModelView: Returns the unique key that identifies this view.
getKey() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
getKey() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFactory
getKeys() - Method in class fiji.plugin.trackmate.providers.AbstractProvider
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.LabelElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
getLabel() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
getLastFrame() - Method in class fiji.plugin.trackmate.action.CaptureOverlayPanel
getLineThickness() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getLinks() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Returns the links cut by this algorithm when splitting the model in linear, convex branches.
getLinksPerTrack() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: Returns the mapping of each source track ID to the links that were cut in it to split it in branches.
getLog() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns the log text saved in the file, or null if log text was not saved.
getLogger() - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
getLogger() - Method in class fiji.plugin.trackmate.gui.components.LogPanel
getLogger() - Method in class fiji.plugin.trackmate.Model: Return the logger currently set for this model.
getLogger() - Method in class fiji.plugin.trackmate.util.DetectionPreview
getLogger() - Method in class fiji.plugin.trackmate.util.JLabelLogger
getLogger() - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditToolConfigPanel: Returns the Logger that outputs on this config panel.
getLongPosition(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
getLongPosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
getLongPosition(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
getLowerBound() - Method in class fiji.plugin.trackmate.gui.displaysettings.Colormap
getMax() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.BoundedValueArgument
getMin() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.BoundedValueArgument
getMissingValueColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getModel() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns the model saved in the file, or null if a saved model cannot be found in the xml file.
getModel() - Method in class fiji.plugin.trackmate.TrackMate
getModel() - Method in class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView
getModel() - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
getModel() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
getModel() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
getModel() - Method in interface fiji.plugin.trackmate.visualization.TrackMateModelView: Returns the model displayed in this view.
getModel() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
getModelChangeListener() - Method in class fiji.plugin.trackmate.Model
getName() - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.CaptureOverlayAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
getName() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.CTCExporterAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.ExportStatsTablesAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.ExportTracksToXML.Factory
getName() - Method in class fiji.plugin.trackmate.action.ExtractTrackStackAction.ExtractTrackStackActionFactory
getName() - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.IcyTrackExporter.Factory
getName() - Method in class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterActionFactory
getName() - Method in class fiji.plugin.trackmate.action.ISBIChallengeExporter.Factory
getName() - Method in class fiji.plugin.trackmate.action.LabelImgExporter.Factory
getName() - Method in class fiji.plugin.trackmate.action.MergeFileAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.MotilityLabExporter.Factory
getName() - Method in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.RecomputeFeatureAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction.Factory
getName() - Method in class fiji.plugin.trackmate.action.TrackBranchAnalysis.Factory
getName() - Method in class fiji.plugin.trackmate.action.TrimNotVisibleAction.Factory
getName() - Method in class fiji.plugin.trackmate.detection.DogDetectorFactory
getName() - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
getName() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
getName() - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
getName() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
getName() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
getName() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
getName() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getName() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getName() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
getName() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
getName() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
getName() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
getName() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
getName() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getName() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getName() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getName() - Method in class fiji.plugin.trackmate.gui.displaysettings.Colormap
getName() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getName() - Method in class fiji.plugin.trackmate.Spot
getName() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
getName() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
getName() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
getName() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getName() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getName() - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getName() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getName() - Method in class fiji.plugin.trackmate.TrackMate
getName() - Method in interface fiji.plugin.trackmate.TrackMateModule: Returns the human-compliant name of this module.
getName() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getName() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayerFactory
getName() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFactory
getNBins(double[], int, int) - Static method in class fiji.plugin.trackmate.util.TMUtils: Returns the optimal bin number for a histogram of the data given in array, using the Freedman and Diaconis rule (bin_space = 2*IQR/n^(1/3)).
getNCols() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix
getNeighborhood(Spot, int) - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: Returns a small neighborhood around the specified spot, but taken at the specified frame.
getNeighborhood(Spot, int) - Method in class fiji.plugin.trackmate.detection.semiauto.SemiAutoTracker
getNextFreeColumn(int) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
getNOcclusion() - Method in class fiji.plugin.trackmate.tracking.kalman.CVMKalmanFilter: Returns the number of occlusion events that occurred since the instantiation of this filter.
getNRows() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix
getNSpots(boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Returns the total number of spots in this collection, over all frames.
getNSpots(int, boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Returns the number of spots at the given frame.
getNumThreads() - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
getNumThreads() - Method in class fiji.plugin.trackmate.detection.HessianDetector
getNumThreads() - Method in class fiji.plugin.trackmate.detection.LogDetector
getNumThreads() - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
getNumThreads() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
getNumThreads() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getNumThreads() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getNumThreads() - Method in class fiji.plugin.trackmate.features.ModelFeatureUpdater
getNumThreads() - Method in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
getNumThreads() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getNumThreads() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer: Ignore.
getNumThreads() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getNumThreads() - Method in class fiji.plugin.trackmate.SpotCollection
getNumThreads() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getNumThreads() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
getNumThreads() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
getNumThreads() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
getNumThreads() - Method in class fiji.plugin.trackmate.TrackMate
getObjectForViewRow(int) - Method in class fiji.plugin.trackmate.visualization.table.TablePanel: Returns the object listed at the specified view row index.
getPaint(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.Colormap: Return a color interpolated within the color list of this paint scale.
getPanDownAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanDownLeftAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanDownRightAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanel() - Method in class fiji.plugin.trackmate.util.DetectionPreview
getPanel() - Method in class fiji.plugin.trackmate.visualization.table.TablePanel: The panel in which the table is displayed.
getPanelComponent() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
getPanelDescriptorIdentifier() - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
getPanLeftAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanRightAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanUpAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanUpLeftAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getPanUpRightAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getParameters() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
getParameters() - Method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod: Returns the list of parameters required to configure this method.
getPenaltyWeight() - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeaturePenalty
getPercentile(double[], double) - Static method in class fiji.plugin.trackmate.util.TMUtils: Returns an estimate of the pth percentile of the values in the values array.
getPhi() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor: Return the azimuth of the spherical coordinates of this cursor, with respect to its center.
getPosition() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
getPositionError() - Method in class fiji.plugin.trackmate.tracking.kalman.CVMKalmanFilter: Return the root mean square error on position estimated through the state covariance matrix.
getPredictions() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker: Returns the saved predicted state as a SpotCollection.
getProcessingTime() - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
getProcessingTime() - Method in class fiji.plugin.trackmate.detection.HessianDetector
getProcessingTime() - Method in class fiji.plugin.trackmate.detection.LabelImageDetector
getProcessingTime() - Method in class fiji.plugin.trackmate.detection.LogDetector
getProcessingTime() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
getProcessingTime() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
getProcessingTime() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
getProcessingTime() - Method in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
getProcessingTime() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
getProcessingTime() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
getProcessingTime() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
getProcessingTime() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition
getProcessingTime() - Method in class fiji.plugin.trackmate.graph.FromContinuousBranches
getProcessingTime() - Method in class fiji.plugin.trackmate.io.IcyTrackFormatWriter
getProcessingTime() - Method in class fiji.plugin.trackmate.io.TGMMImporter
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
getProcessingTime() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
getProcessingTime() - Method in class fiji.plugin.trackmate.TrackMate
getProcessingTime() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphLayout
getR() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
getRangeMax() - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
getRangeMax() - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
getRangeMin() - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
getRangeMin() - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
getRelativePosition(double[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor: Store the relative calibrated position with respect to the neighborhood center.
getRenderer() - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
getRenderer() - Method in class fiji.plugin.trackmate.features.ModelDataset
getRenderer() - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
getRenderer() - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
getResetZoomAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getResource(String, Class<?>) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
getResult() - Method in class fiji.plugin.trackmate.detection.HessianDetector
getResult() - Method in class fiji.plugin.trackmate.detection.LabelImageDetector
getResult() - Method in class fiji.plugin.trackmate.detection.LogDetector
getResult() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
getResult() - Method in class fiji.plugin.trackmate.detection.util.MedianFilter2D
getResult() - Method in class fiji.plugin.trackmate.graph.FromContinuousBranches
getResult() - Method in class fiji.plugin.trackmate.io.TGMMImporter
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator: Returns the cost matrix generated.
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV: Returns JVS results as row assignments.
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker: Returns the resulting assignments from this algorithm.
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
getResult() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
getResult() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
getResult() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
getResult() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
getResult() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
getRoi() - Method in class fiji.plugin.trackmate.Settings
getRoi() - Method in class fiji.plugin.trackmate.Spot
getRowLengths() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphLayout
getSampler() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
getSegmentEnds() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.GraphSegmentSplitter
getSegmentMiddles() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.GraphSegmentSplitter
getSegmentStarts() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.GraphSegmentSplitter
getSelectables() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator: Returns the list of CLIConfigurator.SelectableArguments in this CLI config.
getSelectAllAction() - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getSelected() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
getSelectedArguments() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator: Returns the list of arguments set in this CLI config.
getSelectedCategory() - Method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
getSelectedChannel() - Method in class fiji.plugin.trackmate.action.fit.SpotFitterPanel: 1-based.
getSelectedFeature() - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeaturePenalty
getSelectedFitIndex() - Method in class fiji.plugin.trackmate.action.fit.SpotFitterPanel
getSelectedIndex() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument
getSelectedItem() - Method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
getSelectedModuleKey() - Method in class fiji.plugin.trackmate.gui.components.ModuleChooserPanel
getSelection() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
getSelectionChangeListener() - Method in class fiji.plugin.trackmate.SelectionModel
getSelectionLineThickness() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSelectionModel() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
getSelectionModel() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
getSelectNoneAction() - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getSeriesCount() - Method in class fiji.plugin.trackmate.features.ModelDataset
getSeriesKey(int) - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
getSeriesKey(int) - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
getSeriesKey(int) - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
getSettings() - Method in class fiji.plugin.trackmate.gui.components.ConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.detector.HessianDetectorConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.detector.LabelImageDetectorConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.detector.ManualDetectorConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.detector.MaskDetectorConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.AdvancedKalmanTrackerSettingsPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelAdvancedKalmanTrackerSettingsMain
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelTrackerSettingsMain
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.KalmanTrackerConfigPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.LAPTrackerSettingsPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.NearestNeighborTrackerSettingsPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.OverlapTrackerSettingsPanel
getSettings() - Method in class fiji.plugin.trackmate.gui.components.tracker.SimpleLAPTrackerSettingsPanel
getSettings() - Method in class fiji.plugin.trackmate.TrackMate
getSibblings(NeighborCache<Spot, DefaultWeightedEdge>, Spot) - Static method in class fiji.plugin.trackmate.graph.GraphUtils
getSlice(int) - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
getSortedDepthFirstIterator(Spot, Comparator<Spot>, boolean) - Method in class fiji.plugin.trackmate.TrackModel: Returns a new depth first iterator over the spots connected by links in this model.
getSourceList() - Method in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator: Returns the list of sources in the generated cost matrix.
getSourceList() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getSourceList() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
getSourceList() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getSpaceUnits() - Method in class fiji.plugin.trackmate.Model: Returns the spatial units for the quantities stored in this model.
getSpatialCalibration(ImgPlusMetadata) - Static method in class fiji.plugin.trackmate.util.TMUtils: Return the xyz calibration stored in an ImgPlusMetadata in a 3-elements double array.
getSpatialCalibration(ImagePlus) - Static method in class fiji.plugin.trackmate.util.TMUtils
getSpotAnalyzerFactories() - Method in class fiji.plugin.trackmate.Settings: Returns a copy of the list of SpotAnalyzerFactorys configured in this settings object.
getSpotAt(Spot, int, boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Returns the Spot at the given location (encoded as a Spot), contained in the frame frame.
getSpotColorByFeature() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSpotColorByType() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSpotDisplayRadius() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSpotFeatureDimensions() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the dimension mapping of the spot features that are dealt with in this model.
getSpotFeatureFilters(Element) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Return the list of FeatureFilter for spots stored in this file.
getSpotFeatureIsInt() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the map that states whether the target feature is integer values (true) or double valued (false).
getSpotFeatureNames() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the name mapping of the spot features that are dealt with in this model.
getSpotFeatures() - Method in class fiji.plugin.trackmate.FeatureModel: Returns spot features as declared in this model.
getSpotFeatureSelectionPanel() - Method in class fiji.plugin.trackmate.gui.components.GrapherPanel
getSpotFeatureShortNames() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the short name mapping of the spot features that are dealt with in this model.
getSpotFilters() - Method in class fiji.plugin.trackmate.Settings
getSpotFlag(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent: Returns the modification flag for the given spot affected by this event.
getSpotFor(mxICell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
getSpotMax() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSpotMin() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSpots() - Method in class fiji.plugin.trackmate.Model: Returns the spot collection managed by this model.
getSpots() - Method in class fiji.plugin.trackmate.ModelChangeEvent
getSpots() - Method in class fiji.plugin.trackmate.SelectionChangeEvent: Returns the spots that have been added or removed from the selection.
getSpotSelection() - Method in class fiji.plugin.trackmate.SelectionModel
getSpotTable() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
getSpotTransparencyAlpha() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSpotUniformColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getSquareDistance() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
getStructuringElementBoundingBox() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
getTable() - Method in class fiji.plugin.trackmate.visualization.table.TablePanel: Exposes the JTable in which the data is displayed.
getTargetList() - Method in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator: Returns the list of targets in the generated cost matrix.
getTargetList() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
getTargetList() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
getTargetList() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
getTextContent() - Method in class fiji.plugin.trackmate.gui.components.LogPanel
getTextPane() - Method in class fiji.plugin.trackmate.gui.components.LogPanel: Exposes the text pane in which the log is shown.
getTheta() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor: Return the current inclination with respect to this spot center.
getThreshold(Histogram1d<?>) - Static method in class fiji.plugin.trackmate.detection.MaskUtils
getTimeUnits() - Method in class fiji.plugin.trackmate.Model: Returns the time units for the quantities stored in this model.
getToFrame(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent
getToolIcon() - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
getToolName() - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
getTrackAnalyzers() - Method in class fiji.plugin.trackmate.Settings: Returns a copy of the list of TrackAnalyzers configured in this settings object.
getTrackColorByFeature() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackColorByType() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackDisplayMode() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
getTrackerConfigurationPanel(Model) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
getTrackerConfigurationPanel(Model, ImagePlus) - Method in interface fiji.plugin.trackmate.tracking.SpotImageTrackerFactory: Returns a new GUI panel able to configure the settings suitable for the target tracker identified by the key parameter.
getTrackerConfigurationPanel(Model) - Method in interface fiji.plugin.trackmate.tracking.SpotImageTrackerFactory
getTrackerConfigurationPanel(Model) - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Returns a new GUI panel able to configure the settings suitable for the target tracker identified by the key parameter.
getTrackerSettings(Element, Settings, TrackerProvider) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Update the given Settings object with SpotTracker proper settings map fields named Settings.trackerSettings and Settings.trackerFactory read within the XML file this reader is initialized with.
getTrackFeature(Integer, String) - Method in class fiji.plugin.trackmate.FeatureModel: Returns the numerical value of the specified track feature for the specified track.
getTrackFeatureDimensions() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the dimension mapping of the track features that are dealt with in this model.
getTrackFeatureFilters(Element) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns the list of FeatureFilter for tracks stored in this file.
getTrackFeatureIsInt() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the map that states whether the target feature is integer values (true) or double valued (false).
getTrackFeatureNames() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the name mapping of the track features that are dealt with in this model.
getTrackFeatures() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the track features that are dealt with in this model.
getTrackFeatureSelectionPanel() - Method in class fiji.plugin.trackmate.gui.components.GrapherPanel
getTrackFeatureShortNames() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the short name mapping of the track features that are dealt with in this model.
getTrackFeatureValues() - Method in class fiji.plugin.trackmate.FeatureModel: Returns the map of all track features declared for all tracks of the model.
getTrackFilters() - Method in class fiji.plugin.trackmate.Settings
getTrackMax() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackMin() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackModel() - Method in class fiji.plugin.trackmate.Model: Returns the TrackModel that manages the tracks for this model.
getTrackSchemeBackgroundColor1() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackSchemeBackgroundColor2() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackSchemeDecorationColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackSchemeForegroundColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackTable() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
getTrackTextFilePath(String, int) - Method in enum fiji.plugin.trackmate.action.CTCExporter.ExportType
getTrackTifFilePath(String, int, long, int) - Method in enum fiji.plugin.trackmate.action.CTCExporter.ExportType
getTrackUniformColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getTrackUpdated() - Method in class fiji.plugin.trackmate.ModelChangeEvent
getType() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
getUndefinedValueColor() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getUnits() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getUnitsFor(Dimension, String, String) - Static method in class fiji.plugin.trackmate.util.TMUtils: Return a String unit for the given dimension.
getUnlaidSpotColumn() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
getUpperBound() - Method in class fiji.plugin.trackmate.gui.displaysettings.Colormap
getUseAntialiasing() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings: Get the antialiasing setting.
getValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
getValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
getValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
getValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
getValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
getValue() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
getValue() - Method in class fiji.plugin.trackmate.tracking.kdtree.FlagNode
getValue() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getValueObject() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
getValues() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
getValues() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
getVelocityError() - Method in class fiji.plugin.trackmate.tracking.kalman.CVMKalmanFilter: Return the root mean square error on velocity estimated through the state covariance matrix.
getVersion() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns the version string stored in the file.
getVertexCells() - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
getViewRowForObject(O) - Method in class fiji.plugin.trackmate.visualization.table.TablePanel
getViews(ViewProvider, Model, Settings, SelectionModel, DisplaySettings) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns the collection of views that were saved in this file.
getVisibleKeys() - Method in class fiji.plugin.trackmate.providers.AbstractProvider
getWizardPanel() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
getX(int, int) - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
getX(int, int) - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
getX(int, int) - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
getXend() - Method in class fiji.plugin.trackmate.Settings
getXFeature() - Method in class fiji.plugin.trackmate.features.ModelDataset
getXstart() - Method in class fiji.plugin.trackmate.Settings
getXValue(int, int) - Method in class fiji.plugin.trackmate.features.ModelDataset
getY(int, int) - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
getY(int, int) - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
getY(int, int) - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
getY(int, int) - Method in class fiji.plugin.trackmate.gui.components.LogHistogramDataset
getYend() - Method in class fiji.plugin.trackmate.Settings
getYstart() - Method in class fiji.plugin.trackmate.Settings
getYValue(int, int) - Method in class fiji.plugin.trackmate.features.ModelDataset
getZDrawingDepth() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
getZoomInAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
getZoomOutAction(TrackSchemeGraphComponent) - Static method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions
GlasbeyLut - Class in fiji.plugin.trackmate.visualization
GlasbeyLut() - Constructor for class fiji.plugin.trackmate.visualization.GlasbeyLut
grabImage(long, long, long, long, long) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SpotIconGrabber: Returns a 2D slice extract around the specified coordinates.
grabImage(long, long, long, long, long, long) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SpotIconGrabber: Returns a 3D cropped copy around the specified coordinates.
graph - Variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
graph - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
GrapherDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
GrapherDescriptor(TrackMate, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.GrapherDescriptor
GrapherPanel - Class in fiji.plugin.trackmate.gui.components
GrapherPanel(TrackMate, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.components.GrapherPanel
GraphSegmentSplitter - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix
GraphSegmentSplitter(Graph<Spot, DefaultWeightedEdge>, boolean) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.GraphSegmentSplitter
GraphUtils - Class in fiji.plugin.trackmate.graph
GraphUtils() - Constructor for class fiji.plugin.trackmate.graph.GraphUtils
GREEN_COLOR - Static variable in class fiji.plugin.trackmate.Logger
GUI_STATE_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_STATE_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_VIEW_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_VIEW_ATTRIBUTE_POSITION_HEIGHT - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_VIEW_ATTRIBUTE_POSITION_WIDTH - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_VIEW_ATTRIBUTE_POSITION_X - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_VIEW_ATTRIBUTE_POSITION_Y - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GUI_VIEW_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
GuiUtils - Class in fiji.plugin.trackmate.gui
GuiUtils() - Constructor for class fiji.plugin.trackmate.gui.GuiUtils

H

handle(String) - Method in class fiji.plugin.trackmate.util.cli.CLIUtils.LoggerTailerListener
has2Dsegmentation() - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
has2Dsegmentation() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
has2Dsegmentation() - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
has2Dsegmentation() - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Return true for the detectors that can provide a spot with a 2D SpotRoi when they operate on 2D images.
has2Dsegmentation() - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
hasDefaultValue() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
hashCode() - Method in class fiji.plugin.trackmate.Spot
hashCode() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
hasMax() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.BoundedValueArgument
hasMin() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.BoundedValueArgument
hasNext() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
hasNext() - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
hasNext() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
hasNext() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns true if the sequence has an element after the current one.
hasNext() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
hasPrevious() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
hasPrevious() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns true if the sequence has an element before the current one.
hcat(SparseCostMatrix) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Returns the horizontal concatenation of this matrix with the specified one.
height - Variable in class fiji.plugin.trackmate.Settings
help - Variable in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
help(String) - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator.ExecutablePath
HessianDetector<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
HessianDetector(RandomAccessible<T>, Interval, double[], double, double, double, boolean, boolean) - Constructor for class fiji.plugin.trackmate.detection.HessianDetector
HessianDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector: Configuration panel the Hessian detector.
HessianDetectorConfigurationPanel(Settings, Model, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.detector.HessianDetectorConfigurationPanel: Creates a new HessianDetectorConfigurationPanel, a GUI able to configure settings suitable to HessianDetector and derived implementations.
HessianDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
HessianDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.HessianDetectorFactory
highlight - Variable in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
HOME_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
hyperSlice(ImgPlus<T>, long, long) - Static method in class fiji.plugin.trackmate.util.TMUtils
HyperStackDisplayer - Class in fiji.plugin.trackmate.visualization.hyperstack
HyperStackDisplayer(Model, SelectionModel, ImagePlus, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
HyperStackDisplayer(Model, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
HyperStackDisplayerFactory - Class in fiji.plugin.trackmate.visualization.hyperstack
HyperStackDisplayerFactory() - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayerFactory

I

ICON - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction
Icons - Class in fiji.plugin.trackmate.gui
Icons() - Constructor for class fiji.plugin.trackmate.gui.Icons
ICY_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
IcyTrackExporter - Class in fiji.plugin.trackmate.action
IcyTrackExporter() - Constructor for class fiji.plugin.trackmate.action.IcyTrackExporter
IcyTrackExporter.Factory - Class in fiji.plugin.trackmate.action
IcyTrackFormatWriter - Class in fiji.plugin.trackmate.io
IcyTrackFormatWriter(File, Model, double[]) - Constructor for class fiji.plugin.trackmate.io.IcyTrackFormatWriter
IcyTrackFormatWriter(File, Model, double[], String) - Constructor for class fiji.plugin.trackmate.io.IcyTrackFormatWriter
ID() - Method in class fiji.plugin.trackmate.Spot
IDcounter - Static variable in class fiji.plugin.trackmate.Spot
idGenerator(TrackModel, boolean) - Method in enum fiji.plugin.trackmate.action.LabelImgExporter.LabelIdPainting
IJ_LOGGER - Static variable in class fiji.plugin.trackmate.Logger: This Logger outputs to the ImageJ log window, and to the ImageJ toolbar to report progress.
IJRoiExporter - Class in fiji.plugin.trackmate.action
IJRoiExporter(ImagePlus, Logger) - Constructor for class fiji.plugin.trackmate.action.IJRoiExporter
IJRoiExporter.IJRoiExporterAction - Class in fiji.plugin.trackmate.action
IJRoiExporter.IJRoiExporterActionFactory - Class in fiji.plugin.trackmate.action
IJRoiExporterAction() - Constructor for class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterAction
IJRoiExporterActionFactory() - Constructor for class fiji.plugin.trackmate.action.IJRoiExporter.IJRoiExporterActionFactory
IJTOOLBAR_LOGGER - Static variable in class fiji.plugin.trackmate.Logger: This Logger outputs everything to the ImageJ toolbar.
IMAGE_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_FILENAME_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_FOLDER_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_HEIGHT_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_NFRAMES_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_NSLICES_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_PIXEL_HEIGHT_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_PIXEL_WIDTH_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_TIME_INTERVAL_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_VOXEL_DEPTH_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
IMAGE_WIDTH_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
ImageFileFilter(String) - Constructor for class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter: Constructs a new file filter for all supported image formats using the specified description.
imageFileName - Variable in class fiji.plugin.trackmate.Settings
imageFolder - Variable in class fiji.plugin.trackmate.Settings
imageFormats - Static variable in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter: Holds the accepted file format extensions for images.
ImageHelper - Class in fiji.plugin.trackmate.util: Taken from https://www.java-forums.org/blogs/ozzyman/1141-simple-frame-transitions-without-complex-code.html
ImageHelper() - Constructor for class fiji.plugin.trackmate.util.ImageHelper
img - Variable in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
img - Variable in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory: The image to operate on.
img - Variable in class fiji.plugin.trackmate.detection.LogDetector: The image to segment.
img - Variable in class fiji.plugin.trackmate.detection.LogDetectorFactory: The image to operate on.
img - Variable in class fiji.plugin.trackmate.detection.semiauto.SemiAutoTracker
img - Variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory: The image to operate on.
imp - Variable in class fiji.plugin.trackmate.Settings: The ImagePlus to operate on.
imp - Variable in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
implementations - Variable in class fiji.plugin.trackmate.providers.AbstractProvider
INDENT - Static variable in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
indexOf(Comparable) - Method in class fiji.plugin.trackmate.features.ModelDataset
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.CaptureOverlayAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.CTCExporterAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.ExportStatsTablesAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.ExportTracksToXML
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.ExtractTrackStackAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.ISBIChallengeExporter
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.LabelImgExporter
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.MergeFileAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.MotilityLabExporter
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.RecomputeFeatureAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.action.TrimNotVisibleAction
INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.HessianDetectorFactory
INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory: An html information text.
INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.LogDetectorFactory: An html information text.
INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.ManualDetectorFactory
INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.MaskDetectorFactory: An html information text.
INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory: An html information text.
INFO_TEXT - Static variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
INFO_TEXT - Static variable in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
INFO_TEXT - Static variable in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
infoDisplay() - Static method in class fiji.plugin.trackmate.gui.GuiUtils: Returns an editor pane suitable to display information about a TrackMate module.
infoDisplay(String) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
infoDisplay(String, boolean) - Static method in class fiji.plugin.trackmate.gui.GuiUtils: Returns an editor pane suitable to display information about a TrackMate module.
InfoPane - Class in fiji.plugin.trackmate.visualization.trackscheme
InfoPane(Model, SelectionModel) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.InfoPane: Creates a new Info pane that displays information on the current spot selection in a table.
init() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
init(JGraphXAdapter) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFrame
InitFilterDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
InitFilterDescriptor(TrackMate, FeatureFilter) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.InitFilterDescriptor
InitFilterPanel - Class in fiji.plugin.trackmate.gui.components
InitFilterPanel(FeatureFilter, Function<String, double[]>) - Constructor for class fiji.plugin.trackmate.gui.components.InitFilterPanel: Default constructor, initialize component.
INITIAL_SPOT_FILTER_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
initialize() - Method in class fiji.plugin.trackmate.TrackMateService
initialSpotFilterValue - Variable in class fiji.plugin.trackmate.Settings: The initial quality filter value that is used to clip spots of low quality from spots.
input - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector: The mask.
input - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector: The mask.
installKeyboardActions(JComponent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeKeyboardHandler
instance - Static variable in class fiji.plugin.trackmate.util.AlphanumComparator
IntAdder() - Constructor for class fiji.plugin.trackmate.util.cli.CLIConfigurator.IntAdder
intElement(String, int, int, IntSupplier, Consumer<Integer>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
IntElement(String, int, int) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
interpolate(Model, DefaultWeightedEdge) - Static method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod: Returns a list of newly created spots obtained by interpolating the position, radius, quality and time features of the source and target spot of the specified edge.
interpolateFeature(Spot, Spot, Spot, double, String) - Static method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod
interval - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector
interval - Variable in class fiji.plugin.trackmate.detection.LogDetector
interval - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker.SearchRegion: The neighborhood in the source image to inspect, in pixel coordinates.
interval - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector
invert(Color) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
invoke(Object, mxEventObject) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent: This listener method will be invoked when a new edge has been created interactively in the graph component.
IOUtils - Class in fiji.plugin.trackmate.io: A collection of static utilities for the input/output of xml files.
IOUtils() - Constructor for class fiji.plugin.trackmate.io.IOUtils
is2D(ImgPlus<?>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Returns true if the specified image is 2D.
is2D(ImagePlus) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils
IS_INT - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
IS_INT - Static variable in class fiji.plugin.trackmate.Spot: The 7 privileged spot feature isInt flags.
isAbove - Variable in class fiji.plugin.trackmate.features.FeatureFilter
ISBI_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ISBIChallengeExporter - Class in fiji.plugin.trackmate.action
ISBIChallengeExporter() - Constructor for class fiji.plugin.trackmate.action.ISBIChallengeExporter
ISBIChallengeExporter.Factory - Class in fiji.plugin.trackmate.action
isCanceled() - Method in class fiji.plugin.trackmate.features.EdgeFeatureCalculator
isCanceled() - Method in class fiji.plugin.trackmate.features.SpotFeatureCalculator
isCanceled() - Method in class fiji.plugin.trackmate.features.TrackFeatureCalculator
isCanceled() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
isCanceled() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
isCanceled() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
isCanceled() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
isCanceled() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
isCanceled() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
isCanceled() - Method in class fiji.plugin.trackmate.TrackMate
isComplete() - Method in class fiji.plugin.trackmate.gui.wizard.AbstractAnimator: Returns true if the animation is completed at the current time.
isEmpty() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray: Returns true if this list contains no elements.
isExportSpotsAsDots() - Method in class fiji.plugin.trackmate.action.LabelImgExporterPanel
isExportTracksOnly() - Method in class fiji.plugin.trackmate.action.LabelImgExporterPanel
isFadeTracks() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isHideImage() - Method in class fiji.plugin.trackmate.action.CaptureOverlayPanel
isInCLI() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
isLaunched() - Static method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool: Return true if the tool is currently present in ImageJ toolbar.
isLocal() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
isLocal() - Method in interface fiji.plugin.trackmate.features.edges.EdgeAnalyzer: Returns true if this analyzer is a local analyzer.
isLocal() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
isLocal() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
isLocal() - Method in interface fiji.plugin.trackmate.features.track.TrackAnalyzer: Returns true if this analyzer is a local analyzer.
isLocal() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer: TrackIndexAnalyzer is not local, since the indices are re-arranged according to names.
isLocal() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
isManualFeature() - Method in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
isManualFeature() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
isManualFeature() - Method in interface fiji.plugin.trackmate.features.FeatureAnalyzer: Returns whether all the features declared in this FeatureAnalyzer are manual features.
isManualFeature() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
isManualFeature() - Method in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
isManualFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
isManualFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
isManualFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
isManualFeature() - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
isManualFeature() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
isManualFeature() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
isManualFeature() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
isOutOfBounds() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
isPanningEvent(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
isReadingOk() - Method in class fiji.plugin.trackmate.io.TmXmlReader: Returns true if the last reading method call happened without any warning or error, false otherwise.
isRequired() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
isSet() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
isSpotDisplayedAsRoi() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isSpotFilled() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isSpotShowName() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isSpotVisible() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isToggleEvent(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
isTrackSchemeFillBox() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isTrackVisible() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
isTree(TrackModel, TimeDirectedNeighborIndex) - Static method in class fiji.plugin.trackmate.graph.GraphUtils
isTree(Iterable<Spot>, TimeDirectedNeighborIndex) - Static method in class fiji.plugin.trackmate.graph.GraphUtils
isVisible(Integer) - Method in class fiji.plugin.trackmate.TrackModel: Returns true if the track with the specified ID is marked as visible, false otherwise.
isVisible() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
isVisited() - Method in class fiji.plugin.trackmate.tracking.kdtree.FlagNode
isWhiteBackground() - Method in class fiji.plugin.trackmate.action.CaptureOverlayPanel
isZDrawingDepthLimited() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
item - Variable in class fiji.plugin.trackmate.features.ModelDataset.DataItem
iterable(boolean) - Method in class fiji.plugin.trackmate.SpotCollection: A convenience methods that returns an Iterable wrapper for this collection as a whole.
iterable(int, boolean) - Method in class fiji.plugin.trackmate.SpotCollection: A convenience methods that returns an Iterable wrapper for a specific frame of this spot collection.
iterable(SpotRoi, RealLocalizable, ImgPlus<T>) - Static method in class fiji.plugin.trackmate.util.SpotUtil
iterable(Spot, ImgPlus<T>) - Static method in class fiji.plugin.trackmate.util.SpotUtil
iterationOrder() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
iterationOrder() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
iterator() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
iterator() - Method in class fiji.plugin.trackmate.features.ModelDataset
iterator(boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Return an iterator that iterates over all the spots contained in this collection.
iterator(Integer, boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Return an iterator that iterates over the spots in the specified frame.
iterator() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood

J

JaqamanLinker<K extends Comparable<K>,J extends Comparable<J>> - Class in fiji.plugin.trackmate.tracking.jaqaman: Links two lists of objects based on the LAP framework described in Jaqaman et al., Nature Methods, 2008.
JaqamanLinker(CostMatrixCreator<K, J>, Logger) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker: Creates a new linker for the specified cost matrix creator.
JaqamanLinker(CostMatrixCreator<K, J>) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker
JaqamanLinkingCostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>> - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix: A CostMatrixCreator that can generate a cost matrix from a list of sources, a list of targets and a CostFunction that can generate a cost for any combination.
JaqamanLinkingCostMatrixCreator(Iterable<K>, Iterable<J>, CostFunction<K, J>, double, double, double) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
JaqamanSegmentCostMatrixCreator - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix: This class generates the top-left quadrant of the LAP segment linking cost matrix, following Jaqaman et al., 2008 Nature Methods.
JaqamanSegmentCostMatrixCreator(Graph<Spot, DefaultWeightedEdge>, Map<String, Object>) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator: Instantiates a cost matrix creator for the top-left quadrant of the segment linking cost matrix.
jCheckBoxMedianFilter - Variable in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
jCheckSubPixel - Variable in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
Jet - Static variable in class fiji.plugin.trackmate.gui.displaysettings.Colormap: An Colormap that maps a typical "Jet" colormap going from blue to red to the range [0, 1].
JGraphXAdapter - Class in fiji.plugin.trackmate.visualization.trackscheme
JGraphXAdapter(Model) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
JLabelLogger - Class in fiji.plugin.trackmate.util
JLabelLogger() - Constructor for class fiji.plugin.trackmate.util.JLabelLogger
JPanelAdvancedKalmanTrackerSettingsMain - Class in fiji.plugin.trackmate.gui.components.tracker
JPanelAdvancedKalmanTrackerSettingsMain(String, String, Collection<String>, Map<String, String>) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.JPanelAdvancedKalmanTrackerSettingsMain
JPanelFeaturePenalty - Class in fiji.plugin.trackmate.gui.components.tracker
JPanelFeaturePenalty(List<String>, Map<String, String>, int) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.JPanelFeaturePenalty
JPanelFeatureSelectionGui - Class in fiji.plugin.trackmate.gui.components.tracker
JPanelFeatureSelectionGui() - Constructor for class fiji.plugin.trackmate.gui.components.tracker.JPanelFeatureSelectionGui
JPanelTrackerSettingsMain - Class in fiji.plugin.trackmate.gui.components.tracker
JPanelTrackerSettingsMain(String, String, Collection<String>, Map<String, String>) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.JPanelTrackerSettingsMain
jumpFwd(long) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
jumpFwd(long) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor

K

KalmanTracker - Class in fiji.plugin.trackmate.tracking.kalman
KalmanTracker(SpotCollection, double, int, double, Map<String, Double>) - Constructor for class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
KalmanTrackerConfigPanel - Class in fiji.plugin.trackmate.gui.components.tracker
KalmanTrackerConfigPanel(String, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.KalmanTrackerConfigPanel
KalmanTrackerFactory - Class in fiji.plugin.trackmate.tracking.kalman
KalmanTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
KEY - Static variable in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
KEY - Static variable in class fiji.plugin.trackmate.action.CaptureOverlayAction
KEY - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction
KEY - Static variable in class fiji.plugin.trackmate.action.CTCExporterAction
KEY - Static variable in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction
KEY - Static variable in class fiji.plugin.trackmate.action.ExportStatsTablesAction
KEY - Static variable in class fiji.plugin.trackmate.action.ExportTracksToXML
KEY - Static variable in class fiji.plugin.trackmate.action.ExtractTrackStackAction
KEY - Static variable in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
KEY - Static variable in class fiji.plugin.trackmate.action.ISBIChallengeExporter
KEY - Static variable in class fiji.plugin.trackmate.action.LabelImgExporter
KEY - Static variable in class fiji.plugin.trackmate.action.MergeFileAction
KEY - Static variable in class fiji.plugin.trackmate.action.MotilityLabExporter
KEY - Static variable in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction
KEY - Static variable in class fiji.plugin.trackmate.action.RecomputeFeatureAction
KEY - Static variable in class fiji.plugin.trackmate.action.TrimNotVisibleAction
KEY - Static variable in class fiji.plugin.trackmate.features.edges.DirectionalChangeAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
KEY - Static variable in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
KEY - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
KEY - Static variable in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer: The key for this analyzer.
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.ConfigureViewsDescriptor
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteDetectionDescriptor
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.ExecuteTrackingDescriptor
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.InitFilterDescriptor
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.LogPanelDescriptor2
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotDetectorDescriptor
KEY - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.SpotTrackerDescriptor
KEY - Static variable in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
key(String) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
key(String) - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator.ExecutablePath
KEY - Static variable in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
KEY - Static variable in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
KEY_ALLOW_GAP_CLOSING - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying whether we allow the detection of gap-closing events.
KEY_ALLOW_TRACK_MERGING - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying whether we allow the detection of merging events.
KEY_ALLOW_TRACK_SPLITTING - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying whether we allow the detection of splitting events.
KEY_ALTERNATIVE_LINKING_COST_FACTOR - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the factor used to compute alternative linking costs.
KEY_BLOCKING_VALUE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter that stores the blocking value: cost for non-physical, forbidden links.
KEY_CONDA_ENV - Static variable in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator
KEY_CUTOFF_PERCENTILE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the cutoff percentile parameter.
KEY_DO_MEDIAN_FILTERING - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key identifying the parameter setting whether we pre-filter the target image with a median filter or not.
KEY_DO_SUBPIXEL_LOCALIZATION - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key identifying the parameter setting whether we use sub-pixel localization for spot position.
KEY_DOWNSAMPLE_FACTOR - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key identifying the parameter that sets the downsampling factor applied to the source image prior to segmentation.
KEY_GAP_CLOSING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the feature penalties when detecting gap-closing events.
KEY_GAP_CLOSING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the max gap-closing distance.
KEY_GAP_CLOSING_MAX_FRAME_GAP - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter that specify the maximal number of frames to bridge when detecting gap closing.
KEY_INTENSITY_THRESHOLD - Static variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
KEY_IOU_CALCULATION - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory: The key to the parameter that stores how the IoU should be calculated.
KEY_KALMAN_SEARCH_RADIUS - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Search radius for the Kalman tracker.
KEY_LINKING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the feature penalties when linking particles.
KEY_LINKING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the maximal linking distance.
KEY_MERGING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the feature penalties when dealing with merging events.
KEY_MERGING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the max merging distance.
KEY_MIN_IOU - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory: The key to the parameter that stores the minimal IoU below which links are not created.
KEY_NORMALIZE - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key for the parameter that states whether the quality values are normalized from 0 to 1.
KEY_RADIUS - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key identifying the parameter that sets the target radius for the detector.
KEY_RADIUS_Z - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key for the parameter that sets the target radius in the Z direction for the detector.
KEY_SCALE_FACTOR - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory: The key to the parameter that stores scale factor parameter.
KEY_SIMPLIFY_CONTOURS - Static variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
KEY_SPLITTING_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the feature penalties when dealing with splitting events.
KEY_SPLITTING_MAX_DISTANCE - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: Key for the parameter specifying the max splitting distance.
KEY_TARGET_CHANNEL - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key identifying the parameter setting the target channel for detection in a possible multi-channel image.
KEY_THRESHOLD - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The key identifying the parameter that sets the threshold for the LoG detector.
keyPressed(KeyEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
keyReleased(KeyEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
keys - Variable in class fiji.plugin.trackmate.providers.AbstractProvider
keySet() - Method in class fiji.plugin.trackmate.SpotCollection: Returns a NavigableSet view of the frames contained in this collection.
keyTyped(KeyEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool

L

label(String) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
LABEL_IMG_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
LabelElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.LabelElement
labelGenerator() - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Start at 1.
labelIdPainting() - Method in class fiji.plugin.trackmate.action.LabelImgExporterPanel
LabelImageDetector<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
LabelImageDetector(RandomAccessible<T>, Interval, double[], boolean) - Constructor for class fiji.plugin.trackmate.detection.LabelImageDetector
LabelImageDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector: Configuration panel for spot detectors based on label images.
LabelImageDetectorConfigurationPanel(Settings, Model) - Constructor for class fiji.plugin.trackmate.gui.components.detector.LabelImageDetectorConfigurationPanel
LabelImageDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
LabelImageDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
LabelImgExporter - Class in fiji.plugin.trackmate.action
LabelImgExporter() - Constructor for class fiji.plugin.trackmate.action.LabelImgExporter
LabelImgExporter.Factory - Class in fiji.plugin.trackmate.action
LabelImgExporter.LabelIdPainting - Enum in fiji.plugin.trackmate.action: Specifies how spots will be labeled in the exported label image.
LabelImgExporter.SpotAsDotWriter<T extends RealType<T>> - Class in fiji.plugin.trackmate.action
LabelImgExporter.SpotRoiWriter<T extends RealType<T>> - Class in fiji.plugin.trackmate.action
LabelImgExporter.SpotWriter - Interface in fiji.plugin.trackmate.action: Interface for classes that can 'write' a spot into a label image.
LabelImgExporterPanel - Class in fiji.plugin.trackmate.action
LabelImgExporterPanel() - Constructor for class fiji.plugin.trackmate.action.LabelImgExporterPanel
LAPJV - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix: Implements the Jonker-Volgenant algorithm for linear assignment problems, tailored for sparse cost matrices.
LAPJV(SparseCostMatrix) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV: Instantiates a new Jonker-Volgenant algorithm for the specified sparse cost matrix.
LAPTrackerSettingsPanel - Class in fiji.plugin.trackmate.gui.components.tracker
LAPTrackerSettingsPanel(String, String, Collection<String>, Map<String, String>) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.LAPTrackerSettingsPanel
LAPUtils - Class in fiji.plugin.trackmate.tracking.jaqaman
LAPUtils() - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
lastDir - Variable in class fiji.plugin.trackmate.visualization.trackscheme.SaveAction
lastKey() - Method in class fiji.plugin.trackmate.SpotCollection: Returns the last (highest) frame currently in this collection.
lblIntensityThreshold - Variable in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
linkedCheckBox(StyleElements.BooleanElement, String) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedColorButton(StyleElements.ColorElement, JColorChooser) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedColormapChooser(StyleElements.ColormapElement) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedComboBoxEnumSelector(StyleElements.EnumElement<E>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedComboBoxSelector(StyleElements.ListElement<E>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedFeatureSelector(StyleElements.FeatureElement) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedFontButton(StyleElements.FontElement, Window) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedFormattedTextField(StyleElements.DoubleElement) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedLabel(StyleElements.LabelElement) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedSliderPanel(StyleElements.IntElement, int) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedSliderPanel(StyleElements.BoundedDoubleElement, int) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedSliderPanel(StyleElements.BoundedDoubleElement, int, double) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedSpinner(StyleElements.IntElement) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedSpinnerEnumSelector(StyleElements.EnumElement<E>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
linkedTextField(StyleElements.StringElement) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
LINKING_OFF_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
LINKING_ON_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
linkingCost(K, J) - Method in interface fiji.plugin.trackmate.tracking.jaqaman.costfunction.CostFunction: Returns the cost to link two objects.
linkingCost(Spot, Spot) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costfunction.FeaturePenaltyCostFunction
linkingCost(Spot, Spot) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costfunction.SquareDistCostFunction
links - Variable in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition.TrackBranchDecomposition: Links, as a collection of 2-elements list.
linkSpots(Model, SelectionModel) - Static method in class fiji.plugin.trackmate.util.ModelTools: Links all the spots in the selection, in time-forward order.
linkSpots() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Create links between all the spots currently in the Model selection.
listElement(String, List<E>, Supplier<E>, Consumer<E>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
ListElement(String, List<E>) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
listeners() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
LoadTrackMatePlugIn - Class in fiji.plugin.trackmate
LoadTrackMatePlugIn() - Constructor for class fiji.plugin.trackmate.LoadTrackMatePlugIn
localize(float[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
localize(double[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
localize(int[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
localize(long[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
localize(float[]) - Method in class fiji.plugin.trackmate.Spot
localize(double[]) - Method in class fiji.plugin.trackmate.Spot
localize(int[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
localize(long[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
localize(float[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
localize(double[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
localize(float[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
localize(double[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
localize(int[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
localize(long[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
localizingCursor() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
localizingCursor() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
log(boolean) - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
log(String, Color) - Method in class fiji.plugin.trackmate.Logger: Append the message to the logger, with the specified color.
log(String) - Method in class fiji.plugin.trackmate.Logger: Append the message to the logger with default black color.
log(String, Color) - Method in class fiji.plugin.trackmate.Logger.SlaveLogger
log(String, Color) - Method in class fiji.plugin.trackmate.Logger.StringBuilderLogger
log(String, Color) - Method in class fiji.plugin.trackmate.util.LogRecorder
LOG_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
LOG_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
logDescriptor() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
logDescriptor() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns the descriptor in charge of logging events.
LogDetector<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
LogDetector(RandomAccessible<T>, Interval, double[], double, double, boolean, boolean) - Constructor for class fiji.plugin.trackmate.detection.LogDetector
LogDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector: Configuration panel for spot detectors based on LoG detector.
LogDetectorConfigurationPanel(Settings, Model, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel: Creates a new LogDetectorConfigurationPanel, a GUI able to configure settings suitable to LogDetectorFactory and derived implementations.
LogDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
LogDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.LogDetectorFactory
logger - Variable in class fiji.plugin.trackmate.action.AbstractTMAction
logger - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
logger - Variable in class fiji.plugin.trackmate.io.TmXmlReader
logger - Variable in class fiji.plugin.trackmate.io.TmXmlWriter
Logger - Class in fiji.plugin.trackmate: This class is used to log messages occurring during TrackMate execution.
Logger() - Constructor for class fiji.plugin.trackmate.Logger
logger - Variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
logger - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
logger - Variable in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFrame
Logger.SlaveLogger - Class in fiji.plugin.trackmate: A logger that wraps a master logger and uses it to echo any received message.
Logger.StringBuilderLogger - Class in fiji.plugin.trackmate: This Logger outputs to a StringBuilder given at construction.
LoggerTailerListener(Logger) - Constructor for class fiji.plugin.trackmate.util.cli.CLIUtils.LoggerTailerListener
LogHistogramDataset - Class in fiji.plugin.trackmate.gui.components: A HistogramDataset that returns the log of the count in each bin (plus one), so as to have a logarithmic plot.
LogHistogramDataset() - Constructor for class fiji.plugin.trackmate.gui.components.LogHistogramDataset
LogPanel - Class in fiji.plugin.trackmate.gui.components: A panel using s JTextPane to log events.
LogPanel() - Constructor for class fiji.plugin.trackmate.gui.components.LogPanel
LogPanelDescriptor2 - Class in fiji.plugin.trackmate.gui.wizard.descriptors
LogPanelDescriptor2(LogPanel) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.LogPanelDescriptor2
LogRecorder - Class in fiji.plugin.trackmate.util
LogRecorder(Logger) - Constructor for class fiji.plugin.trackmate.util.LogRecorder
LONGEST_GAP - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
loopPaintDecorationLevel() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent

M

MAGNIFIER_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
main(String[]) - Static method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
main(String[]) - Static method in class fiji.plugin.trackmate.action.MotilityLabExporter
main(String[]) - Static method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox: Demo
main(String[]) - Static method in class fiji.plugin.trackmate.gui.components.FeatureDisplaySelector
main(String[]) - Static method in class fiji.plugin.trackmate.gui.displaysettings.Colormap
main(String[]) - Static method in class fiji.plugin.trackmate.gui.displaysettings.ConfigTrackMateDisplaySettings
main(String[]) - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
main(String[]) - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
main(String[]) - Static method in class fiji.plugin.trackmate.io.CSVExporter
main(String[]) - Static method in class fiji.plugin.trackmate.io.IcyTrackFormatWriter
main(String[]) - Static method in class fiji.plugin.trackmate.LoadTrackMatePlugIn
main(String[]) - Static method in class fiji.plugin.trackmate.ManualTrackingPlugIn
main(String[]) - Static method in class fiji.plugin.trackmate.providers.ActionProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.DetectorProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.EdgeAnalyzerProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.SpotAnalyzerProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.SpotMorphologyAnalyzerProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.TrackAnalyzerProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.TrackerProvider
main(String[]) - Static method in class fiji.plugin.trackmate.providers.ViewProvider
main(String[]) - Static method in class fiji.plugin.trackmate.TrackMatePlugIn
main(String[]) - Static method in class fiji.plugin.trackmate.TrackMateRunner
main(String[]) - Static method in class fiji.plugin.trackmate.util.AlphanumComparator
main(String[]) - Static method in class fiji.plugin.trackmate.util.cli.CLIUtils
main(String[]) - Static method in class fiji.plugin.trackmate.util.cli.CondaPathConfigCommand
MAJOR - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
makeEmptyImagePlus(int, int, int, int, double[]) - Static method in class fiji.plugin.trackmate.visualization.ViewUtils
makeEmpytImagePlus(Model) - Static method in class fiji.plugin.trackmate.visualization.ViewUtils
makeSettingsForRoiAround(Spot, double, Settings) - Static method in interface fiji.plugin.trackmate.action.closegaps.GapClosingMethod: Returns a new Settings object copied from the specified settings, but configured with a small ROI centered on the specified spot, with a radius proportional to the radius of the specified spot, and set to operate only on the frame in which the specified spot it.
ManualDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector: Configuration panel for spot detectors based on LoG detector.
ManualDetectorConfigurationPanel(String, String) - Constructor for class fiji.plugin.trackmate.gui.components.detector.ManualDetectorConfigurationPanel: Creates a new ManualDetectorConfigurationPanel.
ManualDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
ManualDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.ManualDetectorFactory
ManualEdgeColorAnalyzer - Class in fiji.plugin.trackmate.features.manual
ManualEdgeColorAnalyzer() - Constructor for class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
ManualEdgeColorGenerator - Class in fiji.plugin.trackmate.visualization
ManualEdgeColorGenerator(Model, Color) - Constructor for class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator
ManualEdgePerSpotColorGenerator - Class in fiji.plugin.trackmate.visualization: Color an edge by the manual color of its target spot.
ManualEdgePerSpotColorGenerator(Model, Color) - Constructor for class fiji.plugin.trackmate.visualization.ManualEdgePerSpotColorGenerator
ManualSpotColorAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.features.manual
ManualSpotColorAnalyzerFactory() - Constructor for class fiji.plugin.trackmate.features.manual.ManualSpotColorAnalyzerFactory
ManualSpotColorGenerator - Class in fiji.plugin.trackmate.visualization
ManualSpotColorGenerator(Color) - Constructor for class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator
ManualSpotPerEdgeColorGenerator - Class in fiji.plugin.trackmate.visualization: Color a spot by the manual color of its first incoming edges.
ManualSpotPerEdgeColorGenerator(Model, Color) - Constructor for class fiji.plugin.trackmate.visualization.ManualSpotPerEdgeColorGenerator
ManualTrackerFactory - Class in fiji.plugin.trackmate.tracking.manual
ManualTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
ManualTrackingPlugIn - Class in fiji.plugin.trackmate
ManualTrackingPlugIn() - Constructor for class fiji.plugin.trackmate.ManualTrackingPlugIn
mapEdgeToCell(DefaultWeightedEdge, mxCell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
marshall(Map<String, Object>, Element) - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Marshalls a settings map to a JDom element, ready for saving to XML.
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory: Marshall into the Element the settings in the Map that relate to segment linking: gap-closing, merging segments, splitting segments.
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory: Marshall into the Element the settings in the Map that relate to segment linking: gap-closing, merging segments, splitting segments.
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
marshall(Map<String, Object>, Element) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
marshall(Map<String, Object>, Element) - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Marshalls a settings map to a JDom element, ready for saving to XML.
marshallMap(Map<String, Double>, Element) - Static method in class fiji.plugin.trackmate.io.IOUtils: Stores the given mapping in a given JDom element, using attributes in a KEY="VALUE" fashion.
MaskDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector: Configuration panel for spot detectors based on thresholding operations.
MaskDetectorConfigurationPanel(Settings, Model) - Constructor for class fiji.plugin.trackmate.gui.components.detector.MaskDetectorConfigurationPanel
MaskDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
MaskDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.MaskDetectorFactory
MaskUtils - Class in fiji.plugin.trackmate.detection
MaskUtils() - Constructor for class fiji.plugin.trackmate.detection.MaskUtils
max(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
max(long[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
max(Positionable) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
max(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
max(long[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
max(Positionable) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
maxValue - Variable in class fiji.plugin.trackmate.action.closegaps.GapClosingMethod.GapClosingParameter
MedianFilter2D<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection.util: A simple median filter that operates on 1D, 2D or 3D images.
MedianFilter2D(RandomAccessibleInterval<T>, int) - Constructor for class fiji.plugin.trackmate.detection.util.MedianFilter2D: Instantiate a new median filter that will operate on the specified source.
MERGE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
MergeFileAction - Class in fiji.plugin.trackmate.action
MergeFileAction() - Constructor for class fiji.plugin.trackmate.action.MergeFileAction
MergeFileAction.Factory - Class in fiji.plugin.trackmate.action
min(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
min(long[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
min(Positionable) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
min(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
min(long[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
min(Positionable) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
MINOR - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
minValue - Variable in class fiji.plugin.trackmate.action.closegaps.GapClosingMethod.GapClosingParameter
MISSING_STR - Static variable in class fiji.plugin.trackmate.io.CSVExporter: The symbol that will be appended when a value is missing.
model - Variable in class fiji.plugin.trackmate.features.ModelDataset
Model - Class in fiji.plugin.trackmate: The model for the data managed by TrackMate.
Model() - Constructor for class fiji.plugin.trackmate.Model
model - Variable in class fiji.plugin.trackmate.TrackMate: The model this trackmate will shape.
model(Model) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the model to update with the preview action.
model - Variable in class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView: The model displayed by this class.
model - Variable in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
model - Variable in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
MODEL_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
MODEL_MODIFIED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Event type indicating that model was modified, by adding, removing or changing the feature of some spots, and/or adding or removing edges in the tracks.
modelChanged(ModelChangeEvent) - Method in class fiji.plugin.trackmate.features.ModelFeatureUpdater: Updates the model features against the change notified here.
modelChanged(ModelChangeEvent) - Method in interface fiji.plugin.trackmate.ModelChangeListener: This notification is fired when a Model has been changed.
modelChanged(ModelChangeEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
modelChanged(ModelChangeEvent) - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
modelChanged(ModelChangeEvent) - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
modelChanged(ModelChangeEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Used to catch spot creation events that occurred elsewhere, for instance by manual editing in the AbstractTrackMateModelView.
ModelChangeEvent - Class in fiji.plugin.trackmate
ModelChangeEvent(Object, int) - Constructor for class fiji.plugin.trackmate.ModelChangeEvent: Create a new event, reflecting a change in a Model.
ModelChangeListener - Interface in fiji.plugin.trackmate: An interface for listeners that will be notified when a Model is been changed.
ModelDataset - Class in fiji.plugin.trackmate.features
ModelDataset(Model, SelectionModel, DisplaySettings, String, List<String>) - Constructor for class fiji.plugin.trackmate.features.ModelDataset
ModelDataset.DataItem - Class in fiji.plugin.trackmate.features
ModelEditActions - Class in fiji.plugin.trackmate.visualization.hyperstack
ModelEditActions(ImagePlus, Model, SelectionModel, Logger) - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
ModelFeatureUpdater - Class in fiji.plugin.trackmate.features: A utility class that listens to the change occurring in a model, and updates its spot, edge and track features accordingly.
ModelFeatureUpdater(Model, Settings) - Constructor for class fiji.plugin.trackmate.features.ModelFeatureUpdater: Constructs and activate a ModelFeatureUpdater.
ModelTools - Class in fiji.plugin.trackmate.util: A collection of static utilities made to ease the manipulation of a TrackMate Model and SelectionModel.
ModuleChooserPanel<K extends TrackMateModule> - Class in fiji.plugin.trackmate.gui.components
ModuleChooserPanel(AbstractProvider<K>, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.ModuleChooserPanel
MotilityLabExporter - Class in fiji.plugin.trackmate.action
MotilityLabExporter() - Constructor for class fiji.plugin.trackmate.action.MotilityLabExporter
MotilityLabExporter.Factory - Class in fiji.plugin.trackmate.action
mouseClicked(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
mouseDragged(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
mouseEntered(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
mouseExited(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
mouseMoved(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
mousePressed(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
mouseReleased(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
move(int, int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
move(long, int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
move(Localizable) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
move(int[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
move(long[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
moveSpot(Point) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
moveSpotFrom(Spot, Integer, Integer) - Method in class fiji.plugin.trackmate.Model: Moves a single spot from a frame to another, make it visible if it was not, then mark it for feature update.
mxScaledLabelShape - Class in fiji.plugin.trackmate.visualization.trackscheme: This is a shape that is made to display a cell in a way that suits for our spots objects.
mxScaledLabelShape() - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.mxScaledLabelShape

N

n - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
NAME - Static variable in class fiji.plugin.trackmate.action.autonaming.AutoNamingAction.Factory
NAME - Static variable in class fiji.plugin.trackmate.action.CaptureOverlayAction
NAME - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsAction
NAME - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
NAME - Static variable in class fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation
name - Variable in class fiji.plugin.trackmate.action.closegaps.GapClosingMethod.GapClosingParameter
NAME - Static variable in class fiji.plugin.trackmate.action.ComputeDistanceToRoiAction.DistanceToRoiFeature
NAME - Static variable in class fiji.plugin.trackmate.action.CTCExporterAction
NAME - Static variable in class fiji.plugin.trackmate.action.ExportAllSpotsStatsAction
NAME - Static variable in class fiji.plugin.trackmate.action.ExportStatsTablesAction
NAME - Static variable in class fiji.plugin.trackmate.action.ExportTracksToXML
NAME - Static variable in class fiji.plugin.trackmate.action.ExtractTrackStackAction
NAME - Static variable in class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction.Factory
NAME - Static variable in class fiji.plugin.trackmate.action.ISBIChallengeExporter
NAME - Static variable in class fiji.plugin.trackmate.action.LabelImgExporter
NAME - Static variable in class fiji.plugin.trackmate.action.MergeFileAction
NAME - Static variable in class fiji.plugin.trackmate.action.MotilityLabExporter
NAME - Static variable in class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction
NAME - Static variable in class fiji.plugin.trackmate.action.RecomputeFeatureAction
NAME - Static variable in class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction
NAME - Static variable in class fiji.plugin.trackmate.action.TrimNotVisibleAction
NAME - Static variable in class fiji.plugin.trackmate.detection.HessianDetectorFactory
NAME - Static variable in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory: The pretty name of the target detector.
NAME - Static variable in class fiji.plugin.trackmate.detection.LogDetectorFactory: The pretty name of the target detector.
NAME - Static variable in class fiji.plugin.trackmate.detection.ManualDetectorFactory
NAME - Static variable in class fiji.plugin.trackmate.detection.MaskDetectorFactory: The pretty name of the target detector.
NAME - Static variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory: The pretty name of the target detector.
NAME - Static variable in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
NAME - Static variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
NAME - Static variable in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
name(Integer) - Method in class fiji.plugin.trackmate.TrackModel: Returns the name of the track with the specified ID.
name - Variable in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
name(String) - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator.ExecutablePath
nameBranches(Spot, Collection<Spot>) - Method in interface fiji.plugin.trackmate.action.autonaming.AutoNamingRule: Sets the name of individual branches possibly based on the mother spot name.
nameBranches(Spot, Collection<Spot>) - Method in class fiji.plugin.trackmate.action.autonaming.CopyTrackNameNamingRule
nameBranches(Spot, Collection<Spot>) - Method in class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
nameComparator - Static variable in class fiji.plugin.trackmate.Spot: A comparator used to sort spots by name.
nameRoot(Spot, TrackModel) - Method in interface fiji.plugin.trackmate.action.autonaming.AutoNamingRule: Sets the name of the root.
nameRoot(Spot, TrackModel) - Method in class fiji.plugin.trackmate.action.autonaming.CopyTrackNameNamingRule
nameRoot(Spot, TrackModel) - Method in class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
nameSpot(Spot, Spot) - Method in interface fiji.plugin.trackmate.action.autonaming.AutoNamingRule: Name a spot within a branch, based on the name of its predecessor in the same branch.
nameSpot(Spot, Spot) - Method in class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
navigateToChild() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
navigateToNextSibling() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
navigateToNextTrack() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
navigateToParent() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
navigateToPreviousSibling() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
navigateToPreviousTrack() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
NearestNeighborFlagSearchOnKDTree<T> - Class in fiji.plugin.trackmate.tracking.kdtree
NearestNeighborFlagSearchOnKDTree(KDTree<FlagNode<T>>) - Constructor for class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
NearestNeighborTracker - Class in fiji.plugin.trackmate.tracking.kdtree
NearestNeighborTracker(SpotCollection, Map<String, Object>) - Constructor for class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
NearestNeighborTrackerFactory - Class in fiji.plugin.trackmate.tracking.kdtree
NearestNeighborTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
NearestNeighborTrackerSettingsPanel - Class in fiji.plugin.trackmate.gui.components.tracker
NearestNeighborTrackerSettingsPanel(String, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.NearestNeighborTrackerSettingsPanel
neighborhood - Variable in class fiji.plugin.trackmate.util.SpotNeighborhood
NEIGHBORHOOD_FACTOR - Static variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: Minimal size of neighborhoods, in spot diameter units.
newCachedThreadPool() - Static method in class fiji.plugin.trackmate.util.Threads
newFixedThreadPool(int) - Static method in class fiji.plugin.trackmate.util.Threads
newSingleThreadExecutor() - Static method in class fiji.plugin.trackmate.util.Threads
newSingleThreadScheduledExecutor() - Static method in class fiji.plugin.trackmate.util.Threads
next() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
next() - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
next() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
next() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
next() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns the next descriptor to display.
next() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
next() - Static method in class fiji.plugin.trackmate.visualization.GlasbeyLut
NEXT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
nextInTime() - Method in class fiji.plugin.trackmate.util.TrackNavigator
nextSibling() - Method in class fiji.plugin.trackmate.util.TrackNavigator
nextTrack() - Method in class fiji.plugin.trackmate.util.TrackNavigator
nframes - Variable in class fiji.plugin.trackmate.Settings
nObjects(Model, DisplaySettings.TrackMateObject, boolean) - Static method in class fiji.plugin.trackmate.features.FeatureUtils
NORMAL_COLOR - Static variable in class fiji.plugin.trackmate.Logger
normalize(Iterable<T>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Normalize the pixel value of an image between 0 and 1.
normalizeDiffTo(Spot, String) - Method in class fiji.plugin.trackmate.Spot: Returns the absolute normalized difference of the feature value of this spot with the one of the given spot.
notifyFeaturesComputed() - Method in class fiji.plugin.trackmate.Model: Notify the ModelChangeListeners of this model that feature values have been computed.
nslices - Variable in class fiji.plugin.trackmate.Settings
nTracks(boolean) - Method in class fiji.plugin.trackmate.TrackModel
NUMBER_COMPLEX - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
NUMBER_GAPS - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
NUMBER_MERGES - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
NUMBER_SPLITS - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
NUMBER_SPOTS - Static variable in class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
numDimensions() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
numDimensions() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
numDimensions() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
numDimensions() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
numDimensions() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
numThreads - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector
numThreads - Variable in class fiji.plugin.trackmate.detection.LogDetector
numThreads - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector
numThreads - Variable in class fiji.plugin.trackmate.TrackMate

O

ok - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
ok - Variable in class fiji.plugin.trackmate.io.TmXmlReader: If false, an error occurred during reading.
onClose() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
onClose() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Method called when the wizard is closed.
ONE - Static variable in class fiji.plugin.trackmate.SpotCollection
OnRequestUpdater - Class in fiji.plugin.trackmate.util: This class extends Thread and is suited to call methods that are typically called often, but takes time to complete, such as display refreshing.
OnRequestUpdater(OnRequestUpdater.Refreshable) - Constructor for class fiji.plugin.trackmate.util.OnRequestUpdater: Constructor autostarts thread
OnRequestUpdater.Refreshable - Interface in fiji.plugin.trackmate.util
onSet(Consumer<Boolean>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
onSet(Consumer<Color>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
onSet(Consumer<Colormap>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
onSet(Consumer<Double>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
onSet(Consumer<E>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
onSet(BiConsumer<DisplaySettings.TrackMateObject, String>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
onSet(Consumer<Font>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
onSet(Consumer<E>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
onSet(Consumer<String>) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
optimizer - Variable in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
ORANGE_ASTERISK_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
otsuThreshold(RandomAccessibleInterval<T>) - Static method in class fiji.plugin.trackmate.detection.MaskUtils
otsuThreshold(double[]) - Static method in class fiji.plugin.trackmate.util.TMUtils: Return a threshold for the given data, using an Otsu histogram thresholding method.
OutputFunction<E> - Interface in fiji.plugin.trackmate.graph: Interface for functions that return a new object, computed from two input arguments.
OverlapTracker - Class in fiji.plugin.trackmate.tracking.overlap
OverlapTracker(SpotCollection, OverlapTracker.IoUCalculation, double, double) - Constructor for class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
OverlapTracker.IoUCalculation - Enum in fiji.plugin.trackmate.tracking.overlap
OverlapTrackerFactory - Class in fiji.plugin.trackmate.tracking.overlap
OverlapTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
OverlapTrackerSettingsPanel - Class in fiji.plugin.trackmate.gui.components.tracker
OverlapTrackerSettingsPanel() - Constructor for class fiji.plugin.trackmate.gui.components.tracker.OverlapTrackerSettingsPanel

P

paint() - Method in interface fiji.plugin.trackmate.util.PainterThread.Paintable: This is called by the painter thread to repaint the display.
paintBackground(Graphics) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent: Override this so as to paint the background with colored rows and columns.
PainterThread - Class in fiji.plugin.trackmate.util: Thread to repaint display.
PainterThread(PainterThread.Paintable) - Constructor for class fiji.plugin.trackmate.util.PainterThread
PainterThread(ThreadGroup, PainterThread.Paintable) - Constructor for class fiji.plugin.trackmate.util.PainterThread
PainterThread(ThreadGroup, String, PainterThread.Paintable) - Constructor for class fiji.plugin.trackmate.util.PainterThread
PainterThread.Paintable - Interface in fiji.plugin.trackmate.util
paintIcon(Component, Graphics, int, int) - Method in class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
paintShape(mxGraphics2DCanvas, mxCellState) - Method in class fiji.plugin.trackmate.visualization.trackscheme.mxScaledLabelShape
PANEL_SIZE - Static variable in class fiji.plugin.trackmate.gui.displaysettings.SliderPanel
panelIdentifier - Variable in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
PENCIL_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
PerEdgeFeatureColorGenerator - Class in fiji.plugin.trackmate.visualization
PerEdgeFeatureColorGenerator(Model, String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.PerEdgeFeatureColorGenerator
PERIMETER - Static variable in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
PerSpotFeatureColorGenerator - Class in fiji.plugin.trackmate.visualization
PerSpotFeatureColorGenerator(Model, String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.PerSpotFeatureColorGenerator
PerTrackFeatureColorGenerator - Class in fiji.plugin.trackmate.visualization: A TrackColorGenerator that generate colors based on the whole track feature.
PerTrackFeatureColorGenerator(Model, String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator
pinv(Matrix) - Static method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzer: Computes the Moore–Penrose pseudoinverse using the SVD method.
plot(String, List<String>) - Method in interface fiji.plugin.trackmate.gui.components.FeaturePlotSelectionPanel.PlotAction
PLOT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
PlotNSpotsVsTimeAction - Class in fiji.plugin.trackmate.action
PlotNSpotsVsTimeAction() - Constructor for class fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction
PlotNSpotsVsTimeAction.Factory - Class in fiji.plugin.trackmate.action
PLUGIN_NAME_STR - Static variable in class fiji.plugin.trackmate.TrackMate
PLUGIN_NAME_VERSION - Static variable in class fiji.plugin.trackmate.TrackMate
PLUGIN_VERSION_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
pos - Variable in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter.Observation
pos - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
POSITION_FEATURES - Static variable in class fiji.plugin.trackmate.Spot: The position features.
POSITION_T - Static variable in class fiji.plugin.trackmate.Spot: The name of the spot T position feature.
POSITION_X - Static variable in class fiji.plugin.trackmate.Spot: The name of the spot X position feature.
POSITION_Y - Static variable in class fiji.plugin.trackmate.Spot: The name of the spot Y position feature.
POSITION_Z - Static variable in class fiji.plugin.trackmate.Spot: The name of the spot Z position feature.
positionWindow(Window, Component) - Static method in class fiji.plugin.trackmate.gui.GuiUtils: Positions a JFrame more or less cleverly next a Component.
postRead(TrackMate) - Method in class fiji.plugin.trackmate.LoadTrackMatePlugIn: Hook for subclassers:
The TrackMate object is loaded and properly configured.
PRECISE_CALCULATION - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory: Value for the precise IoU calculation method.
predecessorListOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex: Returns the set of vertices which are the predecessors of a specified vertex.
predecessorsOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex: Returns the set of vertices which are the predecessors of a specified vertex.
predict() - Method in class fiji.plugin.trackmate.tracking.kalman.CVMKalmanFilter: Runs the prediction step of the Kalman filter and returns the state predicted by the evolution process.
prepareFrameImg(ImgPlus<T>, int, int) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Return a view of the specified input image, at the specified channel (0-based) and the specified frame (0-based too).
prepareFrameImg(int) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
prettyPrintFeatureAnalyzer(List<? extends FeatureAnalyzer>, StringBuilder) - Static method in class fiji.plugin.trackmate.Settings
preview(Model, Settings, SpotDetectorFactoryBase<?>, Map<String, Object>, int, Logger, Consumer<Boolean>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Preview a detection results.
preview(Model, Settings, SpotDetectorFactoryBase<?>, Map<String, Object>, int, String) - Method in class fiji.plugin.trackmate.util.DetectionPreview
PREVIEW_BUTTON_PUSHED - Variable in class fiji.plugin.trackmate.gui.components.ConfigurationPanel: This event is fired when a preview button is fired within this configuration panel.
PREVIEW_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
previous() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
previous() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
previous() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns the previous descriptor to display.
PREVIOUS_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
previousInTime() - Method in class fiji.plugin.trackmate.util.TrackNavigator
previousSibling() - Method in class fiji.plugin.trackmate.util.TrackNavigator
previousTrack() - Method in class fiji.plugin.trackmate.util.TrackNavigator
process(Iterable<Spot>, Logger) - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
process(Iterable<Spot>, Logger) - Method in interface fiji.plugin.trackmate.action.fit.SpotFitter
process(Iterable<Spot>, Logger) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter2D
process(Iterable<Spot>, Logger) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter2DFixedRadius
process(Iterable<Spot>, Logger) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter3D
process(Iterable<Spot>, Logger) - Method in class fiji.plugin.trackmate.action.fit.SpotGaussianFitter3DFixedRadius
process() - Method in class fiji.plugin.trackmate.detection.DogDetector
process() - Method in class fiji.plugin.trackmate.detection.HessianDetector
process() - Method in class fiji.plugin.trackmate.detection.LabelImageDetector
process() - Method in class fiji.plugin.trackmate.detection.LogDetector
process() - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
process() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
process() - Method in class fiji.plugin.trackmate.detection.util.MedianFilter2D
process() - Method in class fiji.plugin.trackmate.features.EdgeFeatureCalculator: Calculates the edge features configured in the Settings for all the edges of this model.
process(Collection<DefaultWeightedEdge>, Model) - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
process(Collection<DefaultWeightedEdge>, Model) - Method in interface fiji.plugin.trackmate.features.edges.EdgeAnalyzer: Scores a collection of link between two spots.
process(Collection<DefaultWeightedEdge>, Model) - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
process(Spot) - Method in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
process(Iterable<Spot>) - Method in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
process(Iterable<Spot>) - Method in class fiji.plugin.trackmate.features.spot.SpotAnalyzer.DummySpotAnalyzer
process(Iterable<Spot>) - Method in interface fiji.plugin.trackmate.features.spot.SpotAnalyzer: Scores a collection spots for the specified channel.
process(Spot) - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzer
process(Spot) - Method in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzer
process(Spot) - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzer
process(Spot) - Method in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzer
process() - Method in class fiji.plugin.trackmate.features.SpotFeatureCalculator: Calculates the spot features configured in the Settings for all the spots of this model,
process(Collection<Integer>, Model) - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
process(Collection<Integer>, Model) - Method in interface fiji.plugin.trackmate.features.track.TrackAnalyzer: Compute the features of the track whose ID is given.
process(Collection<Integer>, Model) - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
process(Collection<Integer>, Model) - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
process() - Method in class fiji.plugin.trackmate.features.TrackFeatureCalculator: Calculates the track features configured in the Settings for all the tracks of this model.
process() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition
process() - Method in class fiji.plugin.trackmate.graph.FromContinuousBranches
process() - Method in class fiji.plugin.trackmate.io.IcyTrackFormatWriter
process() - Method in class fiji.plugin.trackmate.io.TGMMImporter
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
process() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
process() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
process() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
process() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
process() - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
process() - Method in class fiji.plugin.trackmate.TrackMate
processingTime - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector: The processing time in ms.
processingTime - Variable in class fiji.plugin.trackmate.detection.LogDetector: The processing time in ms.
processingTime - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector: The processing time in ms.
processingTime - Variable in class fiji.plugin.trackmate.TrackMate
processSpot(Spot) - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: Recursively investigates a neighborhood to find the most likely successor of a spot, starting with the specified spot and operating recursively.
processTrack(Integer, TrackModel, TimeDirectedNeighborIndex, boolean, boolean) - Static method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition: A static utility that generates the convex branch decomposition of a specific track in a model.
proposeTrackMateSaveFile(Settings, Logger) - Static method in class fiji.plugin.trackmate.util.TMUtils: Creates a default file path to save the TrackMate session to, based on the image TrackMate works on.
PUB1_TXT - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor
PUB1_URL - Static variable in class fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor
put(int, Collection<Spot>) - Method in class fiji.plugin.trackmate.SpotCollection: Stores the specified spots as the content of the specified frame.
putEdgeFeature(DefaultWeightedEdge, String, Double) - Method in class fiji.plugin.trackmate.FeatureModel: Stores a numerical feature for an edge of this model.
putEdgeFlag(DefaultWeightedEdge, Integer) - Method in class fiji.plugin.trackmate.ModelChangeEvent
putFeature(String, Double) - Method in class fiji.plugin.trackmate.Spot: Stores the specified feature value for this spot.
putFeature(String, Double) - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView.Branch: Stores the specified feature value for this branch.
putFromFrame(Spot, Integer) - Method in class fiji.plugin.trackmate.ModelChangeEvent
putSpotFlag(Spot, Integer) - Method in class fiji.plugin.trackmate.ModelChangeEvent
putToFrame(Spot, Integer) - Method in class fiji.plugin.trackmate.ModelChangeEvent
putTrackFeature(Integer, String, Double) - Method in class fiji.plugin.trackmate.FeatureModel: Stores a track numerical feature.

Q

QUALITY - Static variable in class fiji.plugin.trackmate.Spot: The name of the spot quality feature.
QualityHistogramChart - Class in fiji.plugin.trackmate.util
QualityHistogramChart(DoubleConsumer, String) - Constructor for class fiji.plugin.trackmate.util.QualityHistogramChart
qualityThreshold - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: The fraction of the initial quality above which we keep new spots.
quit() - Method in class fiji.plugin.trackmate.features.ModelFeatureUpdater: Re-registers this instance from the listeners of the model, and stop updating its features.
quit() - Method in class fiji.plugin.trackmate.util.OnRequestUpdater

R

RAD_PERCENTAGE - Static variable in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzer
radius - Variable in class fiji.plugin.trackmate.detection.LogDetector
RADIUS - Static variable in class fiji.plugin.trackmate.Spot: The name of the radius spot feature.
radius() - Method in class fiji.plugin.trackmate.SpotRoi
RandomSpotColorGenerator - Class in fiji.plugin.trackmate.visualization
RandomSpotColorGenerator() - Constructor for class fiji.plugin.trackmate.visualization.RandomSpotColorGenerator
rangeChanged() - Method in interface fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble.RangeListener
ratioComplete() - Method in class fiji.plugin.trackmate.gui.wizard.AbstractAnimator: Returns the completion ratio.
rawWraps(ImagePlus) - Static method in class fiji.plugin.trackmate.util.TMUtils: Wraps an IJ ImagePlus in an imglib2 ImgPlus, without parameterized types.
readBooleanAttribute(Element, String, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
readBooleanAttribute(Element, String, Logger, boolean) - Static method in class fiji.plugin.trackmate.io.IOUtils
readBooleanAttribute(Element, Map<String, Object>, String, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
readDoubleAttribute(Element, String, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
readDoubleAttribute(Element, String, Logger, double) - Static method in class fiji.plugin.trackmate.io.IOUtils
readDoubleAttribute(Element, Map<String, Object>, String, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
readFloatAttribute(Element, String, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
readImage() - Method in class fiji.plugin.trackmate.io.TmXmlReader
readIntAttribute(Element, String, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils: Read and return an integer attribute from a JDom Element, and substitute a default value of 0 if the attribute is not found or of the wrong type.
readIntAttribute(Element, String, Logger, int) - Static method in class fiji.plugin.trackmate.io.IOUtils
readIntegerAttribute(Element, Map<String, Object>, String, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
readLastUsedSettings(ImagePlus, Logger) - Static method in class fiji.plugin.trackmate.io.SettingsPersistence
readSettings(ImagePlus) - Method in class fiji.plugin.trackmate.io.TmXmlReader
readSettings(ImagePlus, DetectorProvider, TrackerProvider, SpotAnalyzerProvider, EdgeAnalyzerProvider, TrackAnalyzerProvider, SpotMorphologyAnalyzerProvider) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Reads the settings element of the file, and sets the fields of the specified Settings object according to the xml file content.
readStringAttribute(Element, Map<String, Object>, String, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
readTracks(Element, Model) - Method in class fiji.plugin.trackmate.io.TmXmlReader: Load the tracks, the track features and the ID of the filtered tracks into the model specified.
readUserDefault() - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
realMax(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
realMax(double[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
realMax(RealPositionable) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
realMax(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
realMax(double[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
realMax(RealPositionable) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
realMin(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
realMin(double[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
realMin(RealPositionable) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
realMin(int) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
realMin(double[]) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
realMin(RealPositionable) - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
recompute(TrackMate, Logger) - Static method in class fiji.plugin.trackmate.action.RecomputeFeatureAction
RecomputeFeatureAction - Class in fiji.plugin.trackmate.action
RecomputeFeatureAction() - Constructor for class fiji.plugin.trackmate.action.RecomputeFeatureAction
RecomputeFeatureAction.Factory - Class in fiji.plugin.trackmate.action
RecursiveCumSum<V,E> - Class in fiji.plugin.trackmate.graph
RecursiveCumSum(SimpleDirectedGraph<V, E>, Function2<V, V>) - Constructor for class fiji.plugin.trackmate.graph.RecursiveCumSum
recursiveDeleteOnShutdownHook(Path) - Static method in class fiji.plugin.trackmate.util.cli.CLIUtils: Add a hook to delete the content of given path when Fiji quits.
reenable() - Method in class fiji.plugin.trackmate.util.EverythingDisablerAndReenabler
refresh() - Method in class fiji.plugin.trackmate.gui.components.FilterPanel: Refreshes the histogram content.
refresh() - Method in class fiji.plugin.trackmate.gui.components.InitFilterPanel
refresh() - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder.CliConfigPanel
refresh() - Method in interface fiji.plugin.trackmate.util.OnRequestUpdater.Refreshable
refresh() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
refresh() - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
refresh() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
refresh() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
refresh() - Method in interface fiji.plugin.trackmate.visualization.TrackMateModelView: Refreshes the displayer display with current model.
refresh() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
REFRESH_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
refreshValues() - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel: Refresh the histograms displayed in the filter panels.
register(HyperStackDisplayer) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool: Register the given HyperStackDisplayer.
registerTool(ImageCanvas) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
remove() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
remove(Spot, Integer) - Method in class fiji.plugin.trackmate.SpotCollection: Removes the given spot from this collection, at the specified frame.
remove() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
REMOVE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
removeAttributeFromName(List<Attribute>, String) - Static method in class fiji.plugin.trackmate.io.TmXmlReader
removeChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel: Remove a ChangeListener from this panel.
removeChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.components.FilterPanel: Remove an ChangeListener.
removeEdge(Spot, Spot) - Method in class fiji.plugin.trackmate.Model: Removes an edge between two spots and returns it.
removeEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.Model: Removes an existing edge from the model.
removeEdgeAnalyzer(EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings: Removes the specified EdgeAnalyzer from the analyzers configured.
removeEdgeFeature(DefaultWeightedEdge, String) - Method in class fiji.plugin.trackmate.FeatureModel: Remove the value of the designated feature for the specified edge.
removeEdgeFromSelection(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.SelectionModel
removeEdgeFromSelection(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.SelectionModel
removeMapping(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
removeMapping(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
removeModelChangeListener(ModelChangeListener) - Method in class fiji.plugin.trackmate.Model
removeSelectedCells() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Removes the cell selected by the user in the GUI.
removeSelectedLinkCells() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
removeSelectionChangeListener(SelectionChangeListener) - Method in class fiji.plugin.trackmate.SelectionModel
removeSpot(Spot) - Method in class fiji.plugin.trackmate.Model: Removes a single spot from the collections managed by this model.
removeSpotAnalyzerFactory(SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings: Removes the specified SpotAnalyzerFactory from the analyzers configured.
removeSpotFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings
removeSpotFromSelection(Spot) - Method in class fiji.plugin.trackmate.SelectionModel
removeSpotFromSelection(Collection<Spot>) - Method in class fiji.plugin.trackmate.SelectionModel
removeTrackAnalyzer(TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings: Removes the specified TrackAnalyzer from the analyzers configured.
removeTrackFeature(Integer, String) - Method in class fiji.plugin.trackmate.FeatureModel: Remove the value of the designated feature for the track with the specified ID.
removeTrackFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings
render() - Method in class fiji.plugin.trackmate.features.AbstractFeatureGrapher: Draws and renders the graph in a new JFrame.
render() - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
render() - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
render() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView
render() - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
render() - Method in interface fiji.plugin.trackmate.visualization.TrackMateModelView: Initializes this displayer and render it according to its concrete implementation.
render() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
requestRepaint() - Method in class fiji.plugin.trackmate.util.PainterThread: Request repaint.
reset() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
reset() - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
reset() - Method in class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
reset() - Static method in class fiji.plugin.trackmate.visualization.GlasbeyLut
RESET_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
RESET_ZOOM_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ResetSpotTimeFeatureAction - Class in fiji.plugin.trackmate.action
ResetSpotTimeFeatureAction() - Constructor for class fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction
ResetSpotTimeFeatureAction.Factory - Class in fiji.plugin.trackmate.action
resetZoom() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
ResizableDoubleArray - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix
ResizableDoubleArray(double[]) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
ResizableDoubleArray(int) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
ResizableDoubleArray() - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray: Creates an empty ResizableIntArray with the a initial capacity of 10.
resultToString() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV
resultToString(List<?>, List<?>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.LAPJV
resultToString() - Method in class fiji.plugin.trackmate.tracking.jaqaman.JaqamanLinker
resume() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
REVERT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ROI_N_POINTS_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
roiEdit(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
root - Variable in class fiji.plugin.trackmate.io.TmXmlReader
root - Variable in class fiji.plugin.trackmate.io.TmXmlWriter
ROOT_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
run() - Method in class fiji.plugin.trackmate.gui.displaysettings.ConfigTrackMateDisplaySettings
run(String) - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Launches the wizard to play this sequence.
run(String) - Method in class fiji.plugin.trackmate.LoadTrackMatePlugIn: Loads a TrackMate file in the GUI.
run(String) - Method in class fiji.plugin.trackmate.TrackMatePlugIn
run(String) - Method in class fiji.plugin.trackmate.TrackMateRunner
run() - Method in class fiji.plugin.trackmate.util.cli.CondaPathConfigCommand
run() - Method in class fiji.plugin.trackmate.util.OnRequestUpdater
run() - Method in class fiji.plugin.trackmate.util.PainterThread
run(Runnable) - Static method in class fiji.plugin.trackmate.util.Threads
run(String, Runnable) - Static method in class fiji.plugin.trackmate.util.Threads
runPreviewDetection(Settings, int, SpotDetectorFactoryBase<?>, Map<String, Object>, String) - Method in class fiji.plugin.trackmate.util.DetectionPreview: Runs the preview with the specified parameters.

S

sample(Spot, ImgPlus<T>) - Method in class fiji.plugin.trackmate.SpotRoi
sample(double, double, RandomAccessibleInterval<T>, double, double) - Method in class fiji.plugin.trackmate.SpotRoi
save() - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
save() - Method in class fiji.plugin.trackmate.gui.wizard.WizardController
save() - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Returns the panel in charge of saving the data.
SAVE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
SaveAction - Class in fiji.plugin.trackmate.visualization.trackscheme
SaveAction(TrackScheme) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.SaveAction
SaveDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
SaveDescriptor(TrackMate, DisplaySettings, WizardSequence) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.SaveDescriptor
saveLastUsedSettings(Settings, Logger) - Static method in class fiji.plugin.trackmate.io.SettingsPersistence
saveToUserDefault(DisplaySettings) - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
saveXmlPng(TrackSchemeFrame, String, Color) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SaveAction: Saves XML+PNG format.
scale(double) - Method in class fiji.plugin.trackmate.SpotRoi
scaleImage(ImageIcon, int, int) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
scrollToObject(O) - Method in class fiji.plugin.trackmate.visualization.table.TablePanel
search(int) - Method in class fiji.plugin.trackmate.SpotCollection: Retrieves and returns the Spot object in this collection with the specified ID.
search(RealLocalizable) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
SearchBar - Class in fiji.plugin.trackmate.visualization.trackscheme.utils
SearchBar(Model, TrackMateModelView) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.utils.SearchBar: Creates new form SearchBox
searchNode(KDTreeNode<FlagNode<T>>) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
SearchRegion() - Constructor for class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker.SearchRegion
seen - Variable in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator: Stores the vertices that have been seen during iteration and (optionally) some additional traversal info regarding each vertex.
SegmentTracker - Class in fiji.plugin.trackmate.tracking.jaqaman: This class tracks deals with the second step of tracking according to the LAP tracking framework formulated by Jaqaman, K.
SegmentTracker(SimpleWeightedGraph<Spot, DefaultWeightedEdge>, Map<String, Object>) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
SegmentTracker(SimpleWeightedGraph<Spot, DefaultWeightedEdge>, Map<String, Object>, Logger) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
SegmentTrackerFactory - Class in fiji.plugin.trackmate.tracking.jaqaman: Base class for trackers with split/merge actions.
SegmentTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
select(int) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
select(CLIConfigurator.Argument<?, ?>) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
select(String) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
select(Point, boolean, boolean) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
SELECT_STYLE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
SELECT_TRACK_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
SELECT_TRACK_ICON_DOWNWARDS - Static variable in class fiji.plugin.trackmate.gui.Icons
SELECT_TRACK_ICON_UPWARDS - Static variable in class fiji.plugin.trackmate.gui.Icons
SelectableArguments() - Constructor for class fiji.plugin.trackmate.util.cli.CLIConfigurator.SelectableArguments
selectables - Variable in class fiji.plugin.trackmate.util.cli.CLIConfigurator
selectAllOnFocus(JTextField) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
selectedFile - Static variable in class fiji.plugin.trackmate.util.ExportableChartValueTable
selectInRoi(MouseEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
selectionChanged(SelectionChangeEvent) - Method in interface fiji.plugin.trackmate.SelectionChangeListener: Called whenever the value of the selection changes.
selectionChanged(SelectionChangeEvent) - Method in class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView: This needs to be overridden for concrete implementation to display selection.
selectionChanged(SelectionChangeEvent) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
selectionChanged(SelectionChangeEvent) - Method in class fiji.plugin.trackmate.visualization.table.AllSpotsTableView
selectionChanged(SelectionChangeEvent) - Method in class fiji.plugin.trackmate.visualization.table.TrackTableView
selectionChanged(SelectionChangeEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.InfoPane
selectionChanged(SelectionChangeEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
SelectionChangeEvent - Class in fiji.plugin.trackmate: An event that characterizes a change in the current selection.
SelectionChangeEvent(Object, Map<Spot, Boolean>, Map<DefaultWeightedEdge, Boolean>) - Constructor for class fiji.plugin.trackmate.SelectionChangeEvent: Represents a change in the selection of a displayed TM model.
SelectionChangeListener - Interface in fiji.plugin.trackmate
selectionModel - Variable in class fiji.plugin.trackmate.features.ModelDataset
SelectionModel - Class in fiji.plugin.trackmate: A component of Model that handles spot and edges selection.
SelectionModel(Model) - Constructor for class fiji.plugin.trackmate.SelectionModel
selectionModel - Variable in class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView
selectionStroke - Variable in class fiji.plugin.trackmate.features.ModelDataset
selectTrack(Collection<Spot>, Collection<DefaultWeightedEdge>, int) - Method in class fiji.plugin.trackmate.SelectionModel: Search and add all spots and links belonging to the same track(s) that of given spots and edges to current selection.
selectTrack(SelectionModel) - Static method in class fiji.plugin.trackmate.util.ModelTools: Sets the content of the specified selection model to be the whole tracks the selected spots belong to.
selectTrack() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
selectTrack(Collection<mxCell>, Collection<mxCell>, int) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
selectTrackDownward(SelectionModel) - Static method in class fiji.plugin.trackmate.util.ModelTools: Sets the content of the specified selection model to be the whole tracks the selected spots belong to, but searched for only forward in time (downward).
selectTrackDownward() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
selectTrackUpward(SelectionModel) - Static method in class fiji.plugin.trackmate.util.ModelTools: Sets the content of the specified selection model to be the whole tracks the selected spots belong to, but searched for only backward in time (backward).
selectTrackUpward() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
SemiAutoTracker<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection.semiauto
SemiAutoTracker(Model, SelectionModel, ImagePlus, Logger) - Constructor for class fiji.plugin.trackmate.detection.semiauto.SemiAutoTracker
semiAutoTracking(double, double, int) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
separator() - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
Separator() - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.Separator
set(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
set(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
set(Colormap) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
set(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
set(Font) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
set(int) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
set(String) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
set(O) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
set(String) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument
set(int) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument
set() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Flag
set(String) - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator.CondaEnvironmentCommand
set(int) - Method in class fiji.plugin.trackmate.util.cli.CondaCLIConfigurator.CondaEnvironmentCommand
setColor(Color) - Method in class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation
setColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.ColorIcon
setColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
setColormap(Colormap) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setCurrent(String) - Method in class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
setCurrent(String) - Method in interface fiji.plugin.trackmate.gui.wizard.WizardSequence: Position the sequence so that its current descriptor is the one with the specified identifier.
setCurrentValue(int) - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
setCurrentValue(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
setDecimalFormat(String) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble
setDisableIndex(HashSet<Integer>) - Method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
setDisplayFeatures(Collection<String>, Map<String, String>) - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeatureSelectionGui: Set the features and their names that should be presented by this GUI.
setEdgeWeight(DefaultWeightedEdge, double) - Method in class fiji.plugin.trackmate.Model: Sets the weight of the specified edge.
setEnabled(boolean) - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeaturePenalty
setEnabled(boolean) - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeatureSelectionGui
setEnabled(boolean) - Method in class fiji.plugin.trackmate.util.EverythingDisablerAndReenabler: Convenience method that calls EverythingDisablerAndReenabler.reenable() or EverythingDisablerAndReenabler.disable() depending on the specified boolean flag.
setExtension(String) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter: Sets the extension for accepted files.
setFadeTrackRange(int) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setFadeTracks(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setFeatures(Collection<String>, Map<String, String>) - Method in class fiji.plugin.trackmate.gui.components.FeaturePlotSelectionPanel
setFont(Font) - Method in class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation
setFont(Font) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setFont(Font) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanel
setFont(Font) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble
setHighlight(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
setHighlightColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setItemLabel(int, String) - Method in class fiji.plugin.trackmate.features.EdgeCollectionDataset
setItemLabel(int, String) - Method in class fiji.plugin.trackmate.features.ModelDataset
setItemLabel(int, String) - Method in class fiji.plugin.trackmate.features.SpotCollectionDataset
setItemLabel(int, String) - Method in class fiji.plugin.trackmate.features.TrackCollectionDataset
setItems(Map<K, Collection<V>>, Map<V, String>, Map<K, String>) - Method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
setLineThickness(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setLocation(float, float) - Method in class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation
setLogger(Logger) - Method in class fiji.plugin.trackmate.action.AbstractTMAction
setLogger(Logger) - Method in interface fiji.plugin.trackmate.action.TrackMateAction: Sets the logger that will receive logs when this action is executed.
setLogger(Logger) - Method in class fiji.plugin.trackmate.Model: Set the logger that will receive the messages from the processes occurring within this trackmate.
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
setLogger(Logger) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTracker
setLogger(Logger) - Method in interface fiji.plugin.trackmate.tracking.SpotTracker: Sets the Logger instance that will receive messages from this SpotTracker.
setMissingValueColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setName(String) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setName(String) - Method in class fiji.plugin.trackmate.Spot: Set the name of this Spot.
setName(String) - Method in class fiji.plugin.trackmate.TrackMate
setName(Integer, String) - Method in class fiji.plugin.trackmate.TrackModel: Sets the name of the track with the specified ID.
setNChannels(int) - Method in interface fiji.plugin.trackmate.features.spot.SpotAnalyzerFactoryBase: Sets the number if channels in the source image that will be analyzed by the analyzers created by this factory.
setNChannels(int) - Method in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
setNChannels(int) - Method in class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
setNumColummns(int) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanel
setNumColummns(int) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble
setNumThreads() - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
setNumThreads(int) - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter
setNumThreads() - Method in class fiji.plugin.trackmate.detection.HessianDetector
setNumThreads(int) - Method in class fiji.plugin.trackmate.detection.HessianDetector
setNumThreads() - Method in class fiji.plugin.trackmate.detection.LogDetector
setNumThreads(int) - Method in class fiji.plugin.trackmate.detection.LogDetector
setNumThreads() - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
setNumThreads(int) - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
setNumThreads() - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
setNumThreads(int) - Method in class fiji.plugin.trackmate.detection.ThresholdDetector
setNumThreads() - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.edges.AbstractEdgeAnalyzer
setNumThreads() - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.manual.ManualEdgeColorAnalyzer
setNumThreads() - Method in class fiji.plugin.trackmate.features.ModelFeatureUpdater
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.ModelFeatureUpdater
setNumThreads() - Method in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.spot.AbstractSpotFeatureAnalyzer
setNumThreads() - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.track.AbstractTrackAnalyzer
setNumThreads() - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer: Ignored.
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer: Ignored.
setNumThreads() - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
setNumThreads(int) - Method in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
setNumThreads() - Method in class fiji.plugin.trackmate.SpotCollection
setNumThreads(int) - Method in class fiji.plugin.trackmate.SpotCollection
setNumThreads() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
setNumThreads(int) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanSegmentCostMatrixCreator
setNumThreads() - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
setNumThreads(int) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTracker
setNumThreads() - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
setNumThreads(int) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
setNumThreads() - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
setNumThreads(int) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker
setNumThreads() - Method in class fiji.plugin.trackmate.TrackMate
setNumThreads(int) - Method in class fiji.plugin.trackmate.TrackMate
setObjects(Iterable<O>) - Method in class fiji.plugin.trackmate.visualization.table.TablePanel
setParameters(double, double, int) - Method in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker: Configures this semi-automatic tracker.
setPhysicalUnits(String, String) - Method in class fiji.plugin.trackmate.Model: Sets the physical units for the quantities stored in this model.
setPopupVisible(boolean) - Method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
setPosition(Localizable) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
setPosition(int[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
setPosition(long[]) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
setPosition(int, int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
setPosition(long, int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
setProgress(double) - Method in class fiji.plugin.trackmate.Logger: Set the progress value of the process logged by this logger.
setProgress(double) - Method in class fiji.plugin.trackmate.Logger.SlaveLogger
setProgress(double) - Method in class fiji.plugin.trackmate.Logger.StringBuilderLogger
setProgress(double) - Method in class fiji.plugin.trackmate.util.LogRecorder
setRange(int, int) - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
setRange(double, double) - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
setRangeListener(SliderPanelDouble.RangeListener) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble
setRoi(Roi) - Method in class fiji.plugin.trackmate.Settings
setRoi(SpotRoi) - Method in class fiji.plugin.trackmate.Spot
setSavePredictions(boolean) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTracker: Sets whether the tracker saves the predicted states.
setSelectedFeature(String, double) - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeaturePenalty
setSelectedFeaturePenalties(Map<String, Double>) - Method in class fiji.plugin.trackmate.gui.components.tracker.JPanelFeatureSelectionGui
setSelectedIndex(int) - Method in class fiji.plugin.trackmate.gui.components.CategoryJComboBox
setSelectedModuleKey(String) - Method in class fiji.plugin.trackmate.gui.components.ModuleChooserPanel
setSelectionLineThickness(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.ConfigurationPanel: Echo the parameters of the given settings on this panel.
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.detector.HessianDetectorConfigurationPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.detector.LabelImageDetectorConfigurationPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.detector.ManualDetectorConfigurationPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.detector.MaskDetectorConfigurationPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.tracker.AdvancedKalmanTrackerSettingsPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.tracker.KalmanTrackerConfigPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.tracker.LAPTrackerSettingsPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.tracker.NearestNeighborTrackerSettingsPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.tracker.OverlapTrackerSettingsPanel
setSettings(Map<String, Object>) - Method in class fiji.plugin.trackmate.gui.components.tracker.SimpleLAPTrackerSettingsPanel
setSource(Object) - Method in class fiji.plugin.trackmate.ModelChangeEvent
setSpotColorBy(DisplaySettings.TrackMateObject, String) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotDisplayedAsRoi(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotDisplayRadius(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotFilled(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotFilters(List<FeatureFilter>) - Method in class fiji.plugin.trackmate.Settings
setSpotImageUpdater(SpotImageUpdater) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
setSpotMinMax(double, double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpots(SpotCollection, boolean) - Method in class fiji.plugin.trackmate.Model: Set the SpotCollection managed by this model.
setSpotSelection(Collection<Spot>) - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
setSpotShowName(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotTransparencyAlpha(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotUniformColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setSpotVisible(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setStatus(String) - Method in class fiji.plugin.trackmate.Logger: Set the status to be displayed by this logger.
setStatus(String) - Method in class fiji.plugin.trackmate.Logger.SlaveLogger
setStatus(String) - Method in class fiji.plugin.trackmate.Logger.StringBuilderLogger
setStatus(String) - Method in class fiji.plugin.trackmate.util.LogRecorder
setStyle(String) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeStylist
setSystemLookAndFeel() - Static method in class fiji.plugin.trackmate.gui.GuiUtils
setTarget(ImgPlus<T>, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
setTarget(ImgPlus<T>, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
setTarget(ImgPlus<T>, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
setTarget(ImgPlus<T>, Map<String, Object>) - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Configure this factory to operate on the given source image (possibly 5D), with the given settings map.
setTarget(ImgPlus<T>, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
setText(String) - Method in class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation
setTextContent(String) - Method in class fiji.plugin.trackmate.gui.components.LogPanel: Set the text content currently displayed in the log panel.
setTime(long) - Method in class fiji.plugin.trackmate.gui.wizard.AbstractAnimator: Sets the current time for the animation.
settings - Variable in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
settings - Variable in class fiji.plugin.trackmate.detection.LogDetectorFactory
settings - Variable in class fiji.plugin.trackmate.detection.ManualDetectorFactory
settings - Variable in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
settings - Variable in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
Settings - Class in fiji.plugin.trackmate: This class is used to store user settings for the TrackMate trackmate.
Settings() - Constructor for class fiji.plugin.trackmate.Settings
Settings(ImagePlus) - Constructor for class fiji.plugin.trackmate.Settings
settings - Variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
settings - Variable in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTracker
settings - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
settings - Variable in class fiji.plugin.trackmate.TrackMate
settings(Settings) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the Settings object to use for preview.
SETTINGS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SettingsPersistence - Class in fiji.plugin.trackmate.io: Static utilities to have some persistence of settings across runs.
SettingsPersistence() - Constructor for class fiji.plugin.trackmate.io.SettingsPersistence
setToolTipText(String) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanel
setToolTipText(String) - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble
setTrackColorBy(DisplaySettings.TrackMateObject, String) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackDisplayMode(DisplaySettings.TrackDisplayMode) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackFilters(List<FeatureFilter>) - Method in class fiji.plugin.trackmate.Settings
setTrackMinMax(double, double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTracks(SimpleWeightedGraph<Spot, DefaultWeightedEdge>, boolean) - Method in class fiji.plugin.trackmate.Model: Sets the tracks stored in this model in bulk.
setTrackSchemeBackgroundColor1(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackSchemeBackgroundColor2(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackSchemeDecorationColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackschemeFillBox(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackSchemeForegroundColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTracksUpdated(Set<Integer>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
setTrackUniformColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTrackVisibility(Integer, boolean) - Method in class fiji.plugin.trackmate.Model: Sets the visibility of the specified track.
setTrackVisible(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setTranslator(CLIConfigurator.Argument<?, ?>, Function<Object, List<String>>) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
setUndefinedValueColor(Color) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setUpdateListener(BoundedValue.UpdateListener) - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValue
setUpdateListener(BoundedValueDouble.UpdateListener) - Method in class fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble
setUseAntialiasing(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings: Sets whether to use anti-aliasing for drawing.
setUseColoring(boolean) - Method in class fiji.plugin.trackmate.visualization.table.TablePanel
setValue(E) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
setValue(DisplaySettings.TrackMateObject, String) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
setValue(E) - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
setValue(K) - Method in class fiji.plugin.trackmate.tracking.kdtree.FlagNode
setValueObject(Object) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.AbstractStringArgument
setValueObject(Object) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument: Sets the value of this argument via the specified object.
setValueObject(Object) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.DoubleArgument
setValueObject(Object) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Flag
setValueObject(Object) - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.IntArgument
setVisible(boolean) - Method in class fiji.plugin.trackmate.SpotCollection: Marks all the content of this collection as visible or invisible.
setVisited(boolean) - Method in class fiji.plugin.trackmate.tracking.kdtree.FlagNode
setZDrawingDepth(double) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
setZDrawingDepthLimited(boolean) - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
SHAPE_INDEX - Static variable in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
SHAPE_NAME - Static variable in class fiji.plugin.trackmate.visualization.trackscheme.mxScaledLabelShape
show() - Method in class fiji.plugin.trackmate.action.autonaming.AutoNamingController
show() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsController
show() - Method in class fiji.plugin.trackmate.action.fit.SpotFitterController
showOptionDialog() - Method in class fiji.plugin.trackmate.visualization.hyperstack.SpotEditTool
showProgressBar(boolean) - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel
SIDE_BY_SIDE - Static variable in class fiji.plugin.trackmate.util.ImageHelper: Some constant to define how I'd like to merge my images
SimpleLAPTrackerSettingsPanel - Class in fiji.plugin.trackmate.gui.components.tracker: A simplified configuration panel for the simple LAP tracker.
SimpleLAPTrackerSettingsPanel(String, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.tracker.SimpleLAPTrackerSettingsPanel
SimpleSparseLAPTrackerFactory - Class in fiji.plugin.trackmate.tracking.jaqaman
SimpleSparseLAPTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
simplify - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector: If true, the contours will be smoothed and simplified.
simplify(PolygonRoi, double, double) - Static method in class fiji.plugin.trackmate.detection.MaskUtils
simplify - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector: If true, the contours will be smoothed and simplified.
simplyContour() - Static method in class fiji.plugin.trackmate.util.cli.CommonTrackMateArguments
size() - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
size - Variable in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
size() - Method in class fiji.plugin.trackmate.util.SpotNeighborhood
SlaveLogger(Logger, double, double) - Constructor for class fiji.plugin.trackmate.Logger.SlaveLogger: Create a new slave logger that will report progress to its master in the following way: If a sub-process reports a progress of val, then the master logger will receive the progress value progressStart + progressRange * val.
sliderChannel - Variable in class fiji.plugin.trackmate.gui.components.detector.LogDetectorConfigurationPanel
sliderChannel - Variable in class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
SliderPanel - Class in fiji.plugin.trackmate.gui.displaysettings: A JSlider with a JSpinner next to it, both modifying the same value.
SliderPanel(String, BoundedValue, int) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.SliderPanel: Create a SliderPanel to modify a given value.
SliderPanelDouble - Class in fiji.plugin.trackmate.gui.displaysettings: A JSlider with a JSpinner next to it, both modifying the same value.
SliderPanelDouble(String, BoundedValueDouble, double) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble: Create a SliderPanelDouble to modify a given value.
SliderPanelDouble.RangeListener - Interface in fiji.plugin.trackmate.gui.displaysettings
SMALL_FONT - Static variable in class fiji.plugin.trackmate.gui.Fonts
SMALL_FONT - Static variable in class fiji.plugin.trackmate.gui.wizard.WizardPanel
SMALL_FONT_MONOSPACED - Static variable in class fiji.plugin.trackmate.gui.Fonts
SmallFeaturePlotSelectionPanel - Class in fiji.plugin.trackmate.visualization.trackscheme: A simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum.
SmallFeaturePlotSelectionPanel(String, List<String>, Map<String, String>, FeaturePlotSelectionPanel.PlotAction) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.SmallFeaturePlotSelectionPanel
SNR - Static variable in class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
SOLIDITY - Static variable in class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
sortByValue(Map<K, V>, Comparator<V>) - Static method in class fiji.plugin.trackmate.util.TMUtils: Return a new map sorted by its values.
SortedDepthFirstIterator<V,E> - Class in fiji.plugin.trackmate.graph: A depth-first iterator, that - when branching - chooses the next vertex according to a specified comparator.
SortedDepthFirstIterator(Graph<V, E>, V, Comparator<V>) - Constructor for class fiji.plugin.trackmate.graph.SortedDepthFirstIterator: Creates a new iterator for the specified graph.
source - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker.SearchRegion: The source image.
SparseCostMatrix - Class in fiji.plugin.trackmate.tracking.jaqaman.costmatrix: A class to represent a sparse cost matrix.
SparseCostMatrix(double[], int[], int[], int) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Instantiate a new sparse cost matrix.
SparseLAPFrameToFrameTracker - Class in fiji.plugin.trackmate.tracking.jaqaman
SparseLAPFrameToFrameTracker(SpotCollection, Map<String, Object>) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
SparseLAPTracker - Class in fiji.plugin.trackmate.tracking.jaqaman
SparseLAPTracker(SpotCollection, Map<String, Object>) - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTracker
SparseLAPTrackerFactory - Class in fiji.plugin.trackmate.tracking.jaqaman
SparseLAPTrackerFactory() - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
SPATIAL_UNITS_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
specifics - Variable in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
SPEED - Static variable in class fiji.plugin.trackmate.features.edges.EdgeSpeedAnalyzer
Spot - Class in fiji.plugin.trackmate: A RealLocalizable implementation, used in TrackMate to represent a detection.
Spot(double, double, double, double, double, String) - Constructor for class fiji.plugin.trackmate.Spot: Creates a new spot.
Spot(double, double, double, double, double) - Constructor for class fiji.plugin.trackmate.Spot: Creates a new spot, and gives it a default name.
Spot(RealLocalizable, double, double, String) - Constructor for class fiji.plugin.trackmate.Spot: Creates a new spot, taking its 3D coordinates from a RealLocalizable.
Spot(RealLocalizable, double, double) - Constructor for class fiji.plugin.trackmate.Spot: Creates a new spot, taking its 3D coordinates from a RealLocalizable.
Spot(Spot) - Constructor for class fiji.plugin.trackmate.Spot: Creates a new spot, taking its location, its radius, its quality value and its name from the specified spot.
Spot(int) - Constructor for class fiji.plugin.trackmate.Spot: Blank constructor meant to be used when loading a spot collection from a file.
SPOT_ANALYSERS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_COLLECTION_NSPOTS_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_FEATURES_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_FILTER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_FRAME_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
SPOT_ICON_16x16 - Static variable in class fiji.plugin.trackmate.gui.Icons
SPOT_ICON_64x64 - Static variable in class fiji.plugin.trackmate.gui.Icons
SPOT_ID_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_NAME_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
SPOT_SOURCE_ID - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
SPOT_TABLE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
SPOT_TARGET_ID - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer
SpotAnalyzer<T> - Interface in fiji.plugin.trackmate.features.spot: Interface for a class that can compute feature of spots.
SpotAnalyzer.DummySpotAnalyzer<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.features.spot
spotAnalyzerFactories - Variable in class fiji.plugin.trackmate.Settings: The SpotAnalyzerFactorys that will be used to compute spot features.
SpotAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.features.spot: Interface for factories that can generate a SpotAnalyzer configured to operate on a specific frame of a model.
SpotAnalyzerFactoryBase<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.features.spot: Top-level interface for spot analyzer factories, both classical and morphological.
SpotAnalyzerProvider - Class in fiji.plugin.trackmate.providers: A provider for the spot analyzer factories provided in the GUI.
SpotAnalyzerProvider(int) - Constructor for class fiji.plugin.trackmate.providers.SpotAnalyzerProvider
SpotAsDotWriter(ImgPlus<T>) - Constructor for class fiji.plugin.trackmate.action.LabelImgExporter.SpotAsDotWriter
SpotCollection - Class in fiji.plugin.trackmate: A utility class that wrap the SortedMap we use to store the spots contained in each frame with a few utility methods.
SpotCollection() - Constructor for class fiji.plugin.trackmate.SpotCollection: Construct a new empty spot collection.
SpotCollectionDataset - Class in fiji.plugin.trackmate.features
SpotCollectionDataset(Model, SelectionModel, DisplaySettings, String, List<String>, List<Spot>, boolean) - Constructor for class fiji.plugin.trackmate.features.SpotCollectionDataset
SpotColorGenerator - Class in fiji.plugin.trackmate.visualization
SpotColorGenerator(String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.SpotColorGenerator
SpotColorGeneratorPerEdgeFeature - Class in fiji.plugin.trackmate.visualization
SpotColorGeneratorPerEdgeFeature(Model, String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerEdgeFeature
SpotColorGeneratorPerTrackFeature - Class in fiji.plugin.trackmate.visualization
SpotColorGeneratorPerTrackFeature(Model, String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerTrackFeature
SpotContrastAndSNRAnalyzer<T extends RealType<T>> - Class in fiji.plugin.trackmate.features.spot: This FeatureAnalyzer computes both the Michelson contrast and the SNR for each spot:
SpotContrastAndSNRAnalyzer(ImgPlus<T>, int) - Constructor for class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzer: Instantiates an analyzer for contrast and SNR.
SpotContrastAndSNRAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.features.spot: A factory for SpotContrastAndSNRAnalyzers.
SpotContrastAndSNRAnalyzerFactory() - Constructor for class fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory
SpotDetector<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.detection: Interface for Spot detector classes, that are able to segment spots of a given estimated radius within a 2D or 3D image.
SpotDetectorDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
SpotDetectorDescriptor(Settings, ConfigurationPanel, Logger) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.SpotDetectorDescriptor
SpotDetectorFactory<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.detection: For detectors that process one time-point at a time, independently, and for which we can therefore propose multithreading.
SpotDetectorFactoryBase<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.detection: Mother interface for detector factories.
SpotEditTool - Class in fiji.plugin.trackmate.visualization.hyperstack
SpotEditToolConfigPanel - Class in fiji.plugin.trackmate.visualization.hyperstack
SpotEditToolConfigPanel(SpotEditTool.SpotEditToolParams) - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.SpotEditToolConfigPanel
SpotFeatureCalculator - Class in fiji.plugin.trackmate.features: A class dedicated to centralizing the calculation of the numerical features of spots, through SpotAnalyzers.
SpotFeatureCalculator(Model, Settings, boolean) - Constructor for class fiji.plugin.trackmate.features.SpotFeatureCalculator
SpotFeatureGrapher - Class in fiji.plugin.trackmate.features
SpotFeatureGrapher(List<Spot>, String, List<String>, Model, SelectionModel, DisplaySettings, boolean) - Constructor for class fiji.plugin.trackmate.features.SpotFeatureGrapher
SpotFilterDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
SpotFilterDescriptor(TrackMate, List<FeatureFilter>, FeatureDisplaySelector) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.SpotFilterDescriptor
spotFilters - Variable in class fiji.plugin.trackmate.Settings: The feature filter list.
SpotFitEllipseAnalyzer<T extends RealType<T>> - Class in fiji.plugin.trackmate.features.spot
SpotFitEllipseAnalyzer(boolean) - Constructor for class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzer
SpotFitEllipseAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.features.spot
SpotFitEllipseAnalyzerFactory() - Constructor for class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
SpotFitter - Interface in fiji.plugin.trackmate.action.fit
SpotFitterController - Class in fiji.plugin.trackmate.action.fit
SpotFitterController(TrackMate, SelectionModel, Logger) - Constructor for class fiji.plugin.trackmate.action.fit.SpotFitterController
SpotFitterPanel - Class in fiji.plugin.trackmate.action.fit
SpotFitterPanel(List<String>, List<String>, int) - Constructor for class fiji.plugin.trackmate.action.fit.SpotFitterPanel
SpotGaussianFitter2D - Class in fiji.plugin.trackmate.action.fit: 2D case!
SpotGaussianFitter2D(ImagePlus, int) - Constructor for class fiji.plugin.trackmate.action.fit.SpotGaussianFitter2D
SpotGaussianFitter2DFixedRadius - Class in fiji.plugin.trackmate.action.fit: 2D case with fixed radius.
SpotGaussianFitter2DFixedRadius(ImagePlus, int) - Constructor for class fiji.plugin.trackmate.action.fit.SpotGaussianFitter2DFixedRadius
SpotGaussianFitter3D - Class in fiji.plugin.trackmate.action.fit: 3D case!
SpotGaussianFitter3D(ImagePlus, int) - Constructor for class fiji.plugin.trackmate.action.fit.SpotGaussianFitter3D
SpotGaussianFitter3DFixedRadius - Class in fiji.plugin.trackmate.action.fit: 3D case! Fixed radius
SpotGaussianFitter3DFixedRadius(ImagePlus, int) - Constructor for class fiji.plugin.trackmate.action.fit.SpotGaussianFitter3DFixedRadius
SpotGaussianFittingAction - Class in fiji.plugin.trackmate.action.fit
SpotGaussianFittingAction() - Constructor for class fiji.plugin.trackmate.action.fit.SpotGaussianFittingAction
SpotGaussianFittingAction.Factory - Class in fiji.plugin.trackmate.action.fit
SpotGlobalDetector<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.detection
SpotGlobalDetectorFactory<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.detection: Interface for detector factories that need to process all the time-points at once.
SpotIconGrabber<T extends RealType<T>> - Class in fiji.plugin.trackmate.visualization.trackscheme: This class is used to take a snapshot of a Spot object (or collection) from its coordinates and an ImagePlus that contain the pixel data.
SpotIconGrabber(ImgPlus<T>) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.SpotIconGrabber
SpotImageTrackerFactory - Interface in fiji.plugin.trackmate.tracking: A specialization of SpotTrackerFactory for trackers that require the source image as input.
SpotImageUpdater - Class in fiji.plugin.trackmate.visualization.trackscheme
SpotImageUpdater(Settings) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.SpotImageUpdater: Instantiates a new spot image updater.
SpotIntensityMultiCAnalyzer<T extends RealType<T>> - Class in fiji.plugin.trackmate.features.spot
SpotIntensityMultiCAnalyzer(ImgPlus<T>, int) - Constructor for class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzer
SpotIntensityMultiCAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.features.spot
SpotIntensityMultiCAnalyzerFactory() - Constructor for class fiji.plugin.trackmate.features.spot.SpotIntensityMultiCAnalyzerFactory
SpotMorphologyAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Interface in fiji.plugin.trackmate.features.spot: Special interface for spot analyzers that can compute feature values based on the contour of spots.
SpotMorphologyAnalyzerProvider - Class in fiji.plugin.trackmate.providers
SpotMorphologyAnalyzerProvider(int) - Constructor for class fiji.plugin.trackmate.providers.SpotMorphologyAnalyzerProvider
SpotNeighborhood<T extends RealType<T>> - Class in fiji.plugin.trackmate.util
SpotNeighborhood(Spot, ImgPlus<T>) - Constructor for class fiji.plugin.trackmate.util.SpotNeighborhood
SpotNeighborhoodCursor<T extends RealType<T>> - Class in fiji.plugin.trackmate.util
SpotNeighborhoodCursor(SpotNeighborhood<T>) - Constructor for class fiji.plugin.trackmate.util.SpotNeighborhoodCursor
spotOverlay - Variable in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
SpotOverlay - Class in fiji.plugin.trackmate.visualization.hyperstack: The overlay class in charge of drawing the spot images on the hyperstack window.
SpotOverlay(Model, ImagePlus, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
SpotRoi - Class in fiji.plugin.trackmate
SpotRoi(double[], double[]) - Constructor for class fiji.plugin.trackmate.SpotRoi
SpotRoiWriter(ImgPlus<T>) - Constructor for class fiji.plugin.trackmate.action.LabelImgExporter.SpotRoiWriter
spots - Variable in class fiji.plugin.trackmate.detection.LabelImageDetector: The list of Spot that will be populated by this detector.
spots - Variable in class fiji.plugin.trackmate.detection.LogDetector: The list of Spot that will be populated by this detector.
spots - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector: The list of Spot that will be populated by this detector.
spots - Variable in class fiji.plugin.trackmate.Model: The spots managed by this model.
spots - Variable in class fiji.plugin.trackmate.SelectionChangeEvent: Changes in Spot selection this event represents.
spots - Variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPFrameToFrameTracker
spots - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTracker
SPOTS_COMPUTED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Event type indicating that the spots of the model were computed, and are now accessible through Model.getSpots().
SPOTS_FILTERED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Event type indicating that the spots of the model were filtered.
spotSelection - Variable in class fiji.plugin.trackmate.visualization.hyperstack.SpotOverlay
SpotShapeAnalyzer<T extends RealType<T>> - Class in fiji.plugin.trackmate.features.spot
SpotShapeAnalyzer(boolean) - Constructor for class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzer
SpotShapeAnalyzerFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.features.spot
SpotShapeAnalyzerFactory() - Constructor for class fiji.plugin.trackmate.features.spot.SpotShapeAnalyzerFactory
SpotTracker - Interface in fiji.plugin.trackmate.tracking: This interface should be used when creating algorithms for linking objects across multiple frames in time-lapse images.
SpotTrackerDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
SpotTrackerDescriptor(Settings, ConfigurationPanel, Logger) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.SpotTrackerDescriptor
SpotTrackerFactory - Interface in fiji.plugin.trackmate.tracking
SpotUtil - Class in fiji.plugin.trackmate.util
SpotUtil() - Constructor for class fiji.plugin.trackmate.util.SpotUtil
squareDistanceTo(RealLocalizable) - Method in class fiji.plugin.trackmate.Spot: Returns the square distance from this spot to the specified spot.
SquareDistCostFunction - Class in fiji.plugin.trackmate.tracking.jaqaman.costfunction: A cost function that returns cost equal to the square distance.
SquareDistCostFunction() - Constructor for class fiji.plugin.trackmate.tracking.jaqaman.costfunction.SquareDistCostFunction
SquareNeighborhood3x3<T> - Class in fiji.plugin.trackmate.detection.util
SquareNeighborhood3x3(RandomAccessibleInterval<T>, OutOfBoundsFactory<T, RandomAccessibleInterval<T>>) - Constructor for class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
SquareNeighborhoodCursor3x3<T> - Class in fiji.plugin.trackmate.detection.util
SquareNeighborhoodCursor3x3(ExtendedRandomAccessibleInterval<T, RandomAccessibleInterval<T>>, long[]) - Constructor for class fiji.plugin.trackmate.detection.util.SquareNeighborhoodCursor3x3
squeeze(Interval) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils: Returns a new Interval, built by squeezing out singleton dimensions from the specified interval.
standardDeviation(double[]) - Static method in class fiji.plugin.trackmate.util.TMUtils
standardDeviation(DoubleArray) - Static method in class fiji.plugin.trackmate.util.TMUtils
StartDialogDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
StartDialogDescriptor(Settings, Logger) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.StartDialogDescriptor
startMoveSpot() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
stateChanged(ChangeEvent) - Method in class fiji.plugin.trackmate.gui.components.FilterGuiPanel: Called when one of the FilterPanel is changed by the user.
stepInTime(boolean, int) - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
StringBuilderLogger(StringBuilder) - Constructor for class fiji.plugin.trackmate.Logger.StringBuilderLogger
StringBuilderLogger() - Constructor for class fiji.plugin.trackmate.Logger.StringBuilderLogger
stringElement(String, Supplier<String>, Consumer<String>) - Static method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements
StringElement(String) - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
StringFormater<V> - Interface in fiji.plugin.trackmate.graph: Interface for function that can build a human-readable string representation of an object
stroke - Variable in class fiji.plugin.trackmate.features.ModelDataset
StyleElements - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements() - Constructor for class fiji.plugin.trackmate.gui.displaysettings.StyleElements
StyleElements.BooleanElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.BoundedDoubleElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.ColorElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.ColormapElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.DoubleElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.EnumElement<E> - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.FeatureElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.FontElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.IntElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.LabelElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.ListElement<E> - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.Separator - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.StringElement - Class in fiji.plugin.trackmate.gui.displaysettings
StyleElements.StyleElement - Interface in fiji.plugin.trackmate.gui.displaysettings
StyleElements.StyleElementVisitor - Interface in fiji.plugin.trackmate.gui.displaysettings
successorListOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex: Returns the set of vertices which are the successors of a specified vertex.
successorsOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex: Returns the set of vertices which are the successors of a specified vertex.
suffix() - Method in enum fiji.plugin.trackmate.action.CTCExporter.ExportType
sum(double[]) - Static method in class fiji.plugin.trackmate.util.TMUtils
sum(DoubleArray) - Static method in class fiji.plugin.trackmate.util.TMUtils

T

TablePanel<O> - Class in fiji.plugin.trackmate.visualization.table
TablePanel(Iterable<O>, List<String>, BiFunction<O, String, Double>, Map<String, String>, Map<String, String>, Map<String, String>, Map<String, Boolean>, Map<String, String>, Supplier<FeatureColorGenerator<O>>, Function<O, String>, BiConsumer<O, String>) - Constructor for class fiji.plugin.trackmate.visualization.table.TablePanel
TablePanel(Iterable<O>, List<String>, BiFunction<O, String, Double>, Map<String, String>, Map<String, String>, Map<String, String>, Map<String, Boolean>, Map<String, String>, Supplier<FeatureColorGenerator<O>>, Function<O, String>, BiConsumer<O, String>, String, BiConsumer<O, Color>) - Constructor for class fiji.plugin.trackmate.visualization.table.TablePanel
targetChannel(int) - Static method in class fiji.plugin.trackmate.util.cli.CommonTrackMateArguments: Creates an argument used to specify on what channel in the input image to operate on.
targetPanel - Variable in class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
tend - Variable in class fiji.plugin.trackmate.Settings: The time-frame index, 0-based, of the last time-point to process.
test() - Method in class fiji.plugin.trackmate.util.cli.CondaPathConfigCommand
textColorForBackground(Color) - Static method in class fiji.plugin.trackmate.gui.GuiUtils: Returns the black color or white color depending on the specified background color, to ensure proper readability of the text on said background.
TEXTFIELD_DIMENSION - Static variable in class fiji.plugin.trackmate.gui.Fonts
textInScrollPanel(JComponent) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
TGMMImporter - Class in fiji.plugin.trackmate.io
TGMMImporter(File, List<AffineTransform3D>, Pattern, Logger) - Constructor for class fiji.plugin.trackmate.io.TGMMImporter
TGMMImporter(File, List<AffineTransform3D>, Pattern) - Constructor for class fiji.plugin.trackmate.io.TGMMImporter
TGMMImporter(File, List<AffineTransform3D>) - Constructor for class fiji.plugin.trackmate.io.TGMMImporter
TGMMImporter(File, List<AffineTransform3D>, Logger) - Constructor for class fiji.plugin.trackmate.io.TGMMImporter
THETA - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
THIS2_INFO_TEXT - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
THIS2_NAME - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
THIS2_TRACKER_KEY - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.SimpleSparseLAPTrackerFactory
THIS_DETECTOR_KEY - Static variable in class fiji.plugin.trackmate.detection.DogDetectorFactory: A string key identifying this factory.
THIS_INFO_TEXT - Static variable in class fiji.plugin.trackmate.detection.DogDetectorFactory: An html information text.
THIS_INFO_TEXT - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
THIS_INFO_TEXT - Static variable in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
THIS_NAME - Static variable in class fiji.plugin.trackmate.detection.DogDetectorFactory: The pretty name of the target detector.
THIS_NAME - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
THIS_NAME - Static variable in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
THIS_TRACKER_KEY - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
THIS_TRACKER_KEY - Static variable in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
Threads - Class in fiji.plugin.trackmate.util
Threads() - Constructor for class fiji.plugin.trackmate.util.Threads
threshold - Variable in class fiji.plugin.trackmate.detection.LogDetector
threshold - Variable in class fiji.plugin.trackmate.detection.ThresholdDetector
ThresholdDetector<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
ThresholdDetector(RandomAccessible<T>, Interval, double[], double, boolean) - Constructor for class fiji.plugin.trackmate.detection.ThresholdDetector
ThresholdDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.components.detector: Configuration panel for spot detectors based on thresholding operations.
ThresholdDetectorConfigurationPanel(Settings, Model) - Constructor for class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel
ThresholdDetectorConfigurationPanel(Settings, Model, String, String) - Constructor for class fiji.plugin.trackmate.gui.components.detector.ThresholdDetectorConfigurationPanel: Creates a new ThresholdDetectorConfigurationPanel, a GUI able to configure settings suitable to a LogDetectorFactory and derived implementations.
ThresholdDetectorFactory<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection
ThresholdDetectorFactory() - Constructor for class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
thresholdKey(String) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the key to the parameters that thresholds the quality values displayed on the histogram.
thresholdTextField(JFormattedTextField) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the JFormattedTextField to update when the user changes the threshold value on the quality histogram.
thresholdUpdater(DoubleConsumer) - Method in class fiji.plugin.trackmate.util.DetectionPreview.Builder: Sets the consumer function that will be called with the threshold value sets by the user on the quality histogram.
THUMBNAIL_OFF_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
THUMBNAIL_ON_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
TIME - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
TIME_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
TIME_UNITS_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
timeComparator - Static variable in class fiji.plugin.trackmate.Spot: A comparator used to sort spots by ascending time feature.
TimeDirectedDepthFirstIterator - Class in fiji.plugin.trackmate.graph
TimeDirectedDepthFirstIterator(Graph<Spot, DefaultWeightedEdge>, Spot) - Constructor for class fiji.plugin.trackmate.graph.TimeDirectedDepthFirstIterator
TimeDirectedNeighborIndex - Class in fiji.plugin.trackmate.graph
TimeDirectedNeighborIndex(Graph<Spot, DefaultWeightedEdge>) - Constructor for class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex
TimeDirectedSortedDepthFirstIterator - Class in fiji.plugin.trackmate.graph
TimeDirectedSortedDepthFirstIterator(Graph<Spot, DefaultWeightedEdge>, Spot, Comparator<Spot>) - Constructor for class fiji.plugin.trackmate.graph.TimeDirectedSortedDepthFirstIterator
TMUtils - Class in fiji.plugin.trackmate.util: List of static utilities for TrackMate.
TmXmlKeys - Class in fiji.plugin.trackmate.io: Contains the key string used for xml marshaling.
TmXmlKeys() - Constructor for class fiji.plugin.trackmate.io.TmXmlKeys
TmXmlReader - Class in fiji.plugin.trackmate.io
TmXmlReader(File) - Constructor for class fiji.plugin.trackmate.io.TmXmlReader: Initialize this reader to read the file given in argument.
TmXmlWriter - Class in fiji.plugin.trackmate.io
TmXmlWriter(File) - Constructor for class fiji.plugin.trackmate.io.TmXmlWriter: Creates a new XML file writer for TrackMate.
TmXmlWriter(File, Logger) - Constructor for class fiji.plugin.trackmate.io.TmXmlWriter: Creates a new XML file writer for TrackMate.
toCIELab(Color) - Static method in class fiji.plugin.trackmate.gui.GuiUtils
toFullMatrix() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Creates and returns a new double[][] matrix representing a non-sparse version of this cost matrix.
toggleDisplayDecoration() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
toggleLink() - Method in class fiji.plugin.trackmate.visualization.hyperstack.ModelEditActions
toggleLinking() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Toggles whether drag-&-drop linking is allowed.
toggleThumbnail() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme: Toggles whether thumbnail capture is enabled.
toImg() - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter.Observation
toJson(DisplaySettings) - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
toLabeling(RandomAccessible<T>, Interval, double, int) - Static method in class fiji.plugin.trackmate.detection.MaskUtils: Creates a zero-min label image from a thresholded input image.
toLUT() - Static method in class fiji.plugin.trackmate.visualization.GlasbeyLut
toPolygonX(double, double, double, double) - Method in class fiji.plugin.trackmate.SpotRoi: Returns a new int array containing the X pixel coordinates to which to paint this polygon.
toPolygonY(double, double, double, double) - Method in class fiji.plugin.trackmate.SpotRoi: Returns a new int array containing the Y pixel coordinates to which to paint this polygon.
toString() - Method in class fiji.plugin.trackmate.action.autonaming.CopyTrackNameNamingRule
toString() - Method in class fiji.plugin.trackmate.action.autonaming.DefaultAutoNamingRule
toString() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByDetection
toString() - Method in class fiji.plugin.trackmate.action.closegaps.CloseGapsByLinearInterpolation
toString() - Method in enum fiji.plugin.trackmate.action.CTCExporter.ExportType
toString() - Method in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter.Observation
toString() - Method in enum fiji.plugin.trackmate.action.LabelImgExporter.LabelIdPainting
toString() - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
toString() - Method in class fiji.plugin.trackmate.FeatureModel
toString() - Method in class fiji.plugin.trackmate.features.FeatureFilter
toString() - Method in class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition.TrackBranchDecomposition
toString(TrackModel) - Static method in class fiji.plugin.trackmate.graph.GraphUtils
toString(V) - Method in interface fiji.plugin.trackmate.graph.StringFormater: Convert the given instance to a string representation.
toString() - Method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettings
toString() - Method in enum fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackDisplayMode
toString() - Method in enum fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackMateObject
toString() - Method in class fiji.plugin.trackmate.io.TmXmlWriter
toString() - Method in class fiji.plugin.trackmate.Logger.StringBuilderLogger
toString() - Method in class fiji.plugin.trackmate.Model
toString() - Method in class fiji.plugin.trackmate.ModelChangeEvent
toString() - Method in class fiji.plugin.trackmate.Settings
toString() - Method in class fiji.plugin.trackmate.Spot
toString() - Method in class fiji.plugin.trackmate.SpotCollection
toString() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.DefaultCostMatrixCreator.Assignment
toString() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
toString() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix
toString(List<?>, List<?>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
toString() - Method in enum fiji.plugin.trackmate.tracking.overlap.OverlapTracker.IoUCalculation
toString(Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
toString(Map<String, Object>) - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: A utility method that builds a string representation of a settings map owing to the currently selected tracker in this provider.
toString() - Method in class fiji.plugin.trackmate.TrackMate
toString() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
toString() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.BoundedValueArgument
toString() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument
toString() - Method in class fiji.plugin.trackmate.util.cli.CLIConfigurator
toString() - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
toString() - Method in class fiji.plugin.trackmate.util.cli.CommandCLIConfigurator
toString() - Method in class fiji.plugin.trackmate.util.LogRecorder
toString() - Method in class fiji.plugin.trackmate.visualization.table.BranchTableView.Branch
toStringFeatureAnalyzersInfo() - Method in class fiji.plugin.trackmate.Settings
toStringImageInfo() - Method in class fiji.plugin.trackmate.Settings: Returns a string description of the target image.
totalAssignmentCost(int[]) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Computes the total cost for an assignment specified by row.
toTrackMateSettings(Map<String, Object>, CLIConfigurator) - Static method in class fiji.plugin.trackmate.util.cli.TrackMateSettingsBuilder: Serializes the specified CLI config and extra parameters to a TrackMate settings map.
toXML(DisplaySettings, Element) - Static method in class fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO
TRACK_ANALYSERS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_CONFINEMENT_RATIO - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TRACK_DISPLACEMENT - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
TRACK_DURATION - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
TRACK_EDGE_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_FEATURES_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_FILTER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
TRACK_ICON_64x64 - Static variable in class fiji.plugin.trackmate.gui.Icons
TRACK_ID - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
TRACK_ID_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_INDEX - Static variable in class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer: The key for the feature TRACK_INDEX
TRACK_LINEARITY_OF_FORWARD_PROGRESSION - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TRACK_MAX_DISTANCE_TRAVELED - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TRACK_MAX_SPEED - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
TRACK_MEAN_DIRECTIONAL_CHANGE_RATE - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TRACK_MEAN_QUALITY - Static variable in class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
TRACK_MEAN_SPEED - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
TRACK_MEAN_STRAIGHT_LINE_SPEED - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TRACK_MEDIAN_SPEED - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
TRACK_MIN_SPEED - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
TRACK_NAME_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACK_SCHEME_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
TRACK_SCHEME_ICON_16x16 - Static variable in class fiji.plugin.trackmate.gui.Icons
TRACK_START - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
TRACK_STD_SPEED - Static variable in class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
TRACK_STOP - Static variable in class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
TRACK_TABLES_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
TRACK_TOTAL_DISTANCE_TRAVELED - Static variable in class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TrackAnalyzer - Interface in fiji.plugin.trackmate.features.track: Mother interface for the classes that can compute the feature of tracks.
TrackAnalyzerProvider - Class in fiji.plugin.trackmate.providers: A provider for the track analyzers provided in the GUI.
TrackAnalyzerProvider() - Constructor for class fiji.plugin.trackmate.providers.TrackAnalyzerProvider
trackAnalyzers - Variable in class fiji.plugin.trackmate.Settings: The TrackAnalyzers that will be used to compute track features.
TrackBranchAnalysis - Class in fiji.plugin.trackmate.action
TrackBranchAnalysis() - Constructor for class fiji.plugin.trackmate.action.TrackBranchAnalysis
TrackBranchAnalysis.Factory - Class in fiji.plugin.trackmate.action
TrackBranchDecomposition() - Constructor for class fiji.plugin.trackmate.graph.ConvexBranchesDecomposition.TrackBranchDecomposition
TrackBranchingAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackBranchingAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackBranchingAnalyzer
TrackCollectionDataset - Class in fiji.plugin.trackmate.features
TrackCollectionDataset(Model, SelectionModel, DisplaySettings, String, List<String>, List<Integer>) - Constructor for class fiji.plugin.trackmate.features.TrackCollectionDataset
TrackColorGenerator - Interface in fiji.plugin.trackmate.visualization: Interface for functions that can generate track colors, with a different color for each vertex and edge.
TrackDurationAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackDurationAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackDurationAnalyzer
trackEdges(Integer) - Method in class fiji.plugin.trackmate.TrackModel: Returns the edges of the track with the specified ID.
TRACKER_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACKER_INFO_TEXT - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
TRACKER_KEY - Static variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
TRACKER_KEY - Static variable in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
TRACKER_KEY - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
TRACKER_NAME - Static variable in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
TRACKER_SETTINGS_ALLOW_EVENT_ATTNAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_ALTERNATE_COST_FACTOR_ATTNAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_BLOCKING_VALUE_ATTNAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_CLASS_ATTRIBUTE_NAME - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACKER_SETTINGS_CUTOFF_PERCENTILE_ATTNAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_DISTANCE_CUTOFF_ATTNAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_DISTANCE_CUTOFF_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
TRACKER_SETTINGS_FEATURE_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_GAP_CLOSING_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_LINKING_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_MERGING_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_SPLITTING_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_TIME_CUTOFF_ATTNAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
TRACKER_SETTINGS_TIME_CUTOFF_ELEMENT - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys
trackerFactory - Variable in class fiji.plugin.trackmate.Settings: The the tracker to use.
TrackerKeys - Class in fiji.plugin.trackmate.tracking
TrackerKeys() - Constructor for class fiji.plugin.trackmate.tracking.TrackerKeys
TrackerProvider - Class in fiji.plugin.trackmate.providers
TrackerProvider() - Constructor for class fiji.plugin.trackmate.providers.TrackerProvider
trackerSettings - Variable in class fiji.plugin.trackmate.Settings: Settings map for SpotTracker.
TrackFeatureCalculator - Class in fiji.plugin.trackmate.features: A class dedicated to centralizing the calculation of the numerical features of tracks, through TrackAnalyzers.
TrackFeatureCalculator(Model, Settings, boolean) - Constructor for class fiji.plugin.trackmate.features.TrackFeatureCalculator
TrackFeatureGrapher - Class in fiji.plugin.trackmate.features
TrackFeatureGrapher(List<Integer>, String, List<String>, Model, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.features.TrackFeatureGrapher
TrackFilterDescriptor - Class in fiji.plugin.trackmate.gui.wizard.descriptors
TrackFilterDescriptor(TrackMate, List<FeatureFilter>, FeatureDisplaySelector) - Constructor for class fiji.plugin.trackmate.gui.wizard.descriptors.TrackFilterDescriptor
trackFilters - Variable in class fiji.plugin.trackmate.Settings: The track filter list that is used to prune track and spots.
trackIDOf(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.TrackModel: Returns the track ID the specified edge belong to, or null if the specified edge cannot be found in this model.
trackIDOf(Spot) - Method in class fiji.plugin.trackmate.TrackModel: Returns the track ID the specified spot belong to, or null if the specified spot cannot be found in this model.
trackIDs(boolean) - Method in class fiji.plugin.trackmate.TrackModel: Returns the set of track IDs managed by this model, ordered by track names (alpha-numerically sorted).
TrackIndexAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackIndexAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackIndexAnalyzer
TrackLocationAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackLocationAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
TrackMate - Class in fiji.plugin.trackmate: The TrackMate_ class runs on the currently active time-lapse image (2D or 3D) and both identifies and tracks bright spots over time.
TrackMate(Settings) - Constructor for class fiji.plugin.trackmate.TrackMate
TrackMate(Model, Settings) - Constructor for class fiji.plugin.trackmate.TrackMate
TrackMate() - Constructor for class fiji.plugin.trackmate.TrackMate
TRACKMATE_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
TRACKMATE_ICON_16x16 - Static variable in class fiji.plugin.trackmate.gui.Icons
TrackMateAction - Interface in fiji.plugin.trackmate.action: This interface describe a track mate action, that can be run on a TrackMate object to change its content or properties.
TrackMateActionFactory - Interface in fiji.plugin.trackmate.action
TrackMateModelView - Interface in fiji.plugin.trackmate.visualization
TrackMateModule - Interface in fiji.plugin.trackmate: Interface for TrackMate modules.
TrackMatePlugIn - Class in fiji.plugin.trackmate
TrackMatePlugIn() - Constructor for class fiji.plugin.trackmate.TrackMatePlugIn
TrackMateRunner - Class in fiji.plugin.trackmate: An extension of TrackMate plugin that makes it executable from a macro.
TrackMateRunner() - Constructor for class fiji.plugin.trackmate.TrackMateRunner
TrackMateService - Class in fiji.plugin.trackmate
TrackMateService() - Constructor for class fiji.plugin.trackmate.TrackMateService
TrackMateSettingsBuilder - Class in fiji.plugin.trackmate.util.cli
TrackMateWizardSequence - Class in fiji.plugin.trackmate.gui.wizard
TrackMateWizardSequence(TrackMate, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.gui.wizard.TrackMateWizardSequence
TrackModel - Class in fiji.plugin.trackmate: A component of Model specialized for tracks.
TrackMotilityAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackMotilityAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackMotilityAnalyzer
TrackNavigator - Class in fiji.plugin.trackmate.util
TrackNavigator(Model, SelectionModel) - Constructor for class fiji.plugin.trackmate.util.TrackNavigator
trackOverlay - Variable in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
TrackOverlay - Class in fiji.plugin.trackmate.visualization.hyperstack: The overlay class in charge of drawing the tracks on the hyperstack window.
TrackOverlay(Model, ImagePlus, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay
TRACKS_COMPUTED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Event type indicating that the tracks of the model were computed.
TRACKS_VISIBILITY_CHANGED - Static variable in class fiji.plugin.trackmate.ModelChangeEvent: Event type indicating that the tracks of the model had their visibility changed.
TrackScheme - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackScheme(Model, SelectionModel, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
TrackSchemeActions - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeActions.EditAction - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeFactory - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeFactory() - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFactory
TrackSchemeFrame - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeFrame(TrackScheme, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeFrame
TrackSchemeGraphComponent - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeGraphComponent(JGraphXAdapter, TrackScheme, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
TrackSchemeGraphLayout - Class in fiji.plugin.trackmate.visualization.trackscheme: This mxGraphLayout arranges cells on a graph in lanes corresponding to tracks.
TrackSchemeGraphLayout(JGraphXAdapter, Model, TrackSchemeGraphComponent) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphLayout
TrackSchemeKeyboardHandler - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeKeyboardHandler(TrackSchemeGraphComponent, TrackNavigator) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeKeyboardHandler
TrackSchemePopupMenu - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemePopupMenu(TrackScheme, Object, Point) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemePopupMenu
TrackSchemeStylist - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeStylist(Model, JGraphXAdapter, DisplaySettings) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeStylist
TrackSchemeSvgCanvas - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeSvgCanvas(Document) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeSvgCanvas
TrackSchemeToolbar - Class in fiji.plugin.trackmate.visualization.trackscheme
TrackSchemeToolbar(TrackScheme) - Constructor for class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeToolbar
TrackSpeedStatisticsAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackSpeedStatisticsAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer
TrackSpotQualityFeatureAnalyzer - Class in fiji.plugin.trackmate.features.track
TrackSpotQualityFeatureAnalyzer() - Constructor for class fiji.plugin.trackmate.features.track.TrackSpotQualityFeatureAnalyzer
trackSpots(Integer) - Method in class fiji.plugin.trackmate.TrackModel: Returns the spots of the track with the specified ID.
trackStack(TrackMate, Spot, boolean, Logger) - Static method in class fiji.plugin.trackmate.action.ExtractTrackStackAction
trackStack(TrackMate, Spot, Spot, boolean, Logger) - Static method in class fiji.plugin.trackmate.action.ExtractTrackStackAction
trackStack(Settings, List<Spot>, double, boolean, Logger) - Static method in class fiji.plugin.trackmate.action.ExtractTrackStackAction
TrackTableView - Class in fiji.plugin.trackmate.visualization.table
TrackTableView(Model, SelectionModel, DisplaySettings, String) - Constructor for class fiji.plugin.trackmate.visualization.table.TrackTableView
transform - Variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker.SearchRegion: An affine transform that will convert the spot coordinates in the calibrated image coordinates to the global coordinate system whatever it is.
transition(WizardPanelDescriptor, WizardPanelDescriptor, TransitionAnimator.Direction) - Method in class fiji.plugin.trackmate.gui.wizard.WizardPanel
TransitionAnimator - Class in fiji.plugin.trackmate.gui.wizard
TransitionAnimator(Component, Component, TransitionAnimator.Direction, long) - Constructor for class fiji.plugin.trackmate.gui.wizard.TransitionAnimator
TransitionAnimator.Direction - Enum in fiji.plugin.trackmate.gui.wizard
translators - Variable in class fiji.plugin.trackmate.util.cli.CLIConfigurator
transpose() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Returns the transpose of this matrix.
tree - Variable in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborFlagSearchOnKDTree
TrimNotVisibleAction - Class in fiji.plugin.trackmate.action
TrimNotVisibleAction() - Constructor for class fiji.plugin.trackmate.action.TrimNotVisibleAction
TrimNotVisibleAction.Factory - Class in fiji.plugin.trackmate.action
trimToSize() - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.ResizableDoubleArray
tstart - Variable in class fiji.plugin.trackmate.Settings: The time-frame index, 0-based, of the first time-point to process.
Turbo - Static variable in class fiji.plugin.trackmate.gui.displaysettings.Colormap: The TURBO color-map, from Google LLC, Anton Mikhailov.

U

UniformSpotColorGenerator - Class in fiji.plugin.trackmate.visualization: A dummy spot color generator that always return the default color.
UniformSpotColorGenerator(Color) - Constructor for class fiji.plugin.trackmate.visualization.UniformSpotColorGenerator
UniformTrackColorGenerator - Class in fiji.plugin.trackmate.visualization: A dummy track color generator that always return the default color.
UniformTrackColorGenerator(Color) - Constructor for class fiji.plugin.trackmate.visualization.UniformTrackColorGenerator
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.HessianDetectorFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.LabelImageDetectorFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.LogDetectorFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.ManualDetectorFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.MaskDetectorFactory
unmarshall(Element, Map<String, Object>) - Method in interface fiji.plugin.trackmate.detection.SpotDetectorFactoryBase: Un-marshalls a JDom element to update a settings map.
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.detection.ThresholdDetectorFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SparseLAPTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.AdvancedKalmanTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kalman.KalmanTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.kdtree.NearestNeighborTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.manual.ManualTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in class fiji.plugin.trackmate.tracking.overlap.OverlapTrackerFactory
unmarshall(Element, Map<String, Object>) - Method in interface fiji.plugin.trackmate.tracking.SpotTrackerFactory: Un-marshall a JDom element to update a settings map, and sets the target tracker of this provider from the element.
unmarshallMap(Element, Map<String, Double>, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils: Unmarshall the attributes of a JDom element in a map of doubles.
unmarshallSegment(Element, Map<String, Object>, StringBuilder) - Method in class fiji.plugin.trackmate.tracking.jaqaman.SegmentTrackerFactory
unsortedTrackIDs(boolean) - Method in class fiji.plugin.trackmate.TrackModel: Returns the set of track IDs managed by this model, unsorted.
update() - Method in interface fiji.plugin.trackmate.gui.displaysettings.BoundedValue.UpdateListener
update() - Method in interface fiji.plugin.trackmate.gui.displaysettings.BoundedValueDouble.UpdateListener
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanel
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.SliderPanelDouble
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BooleanElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.BoundedDoubleElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColorElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ColormapElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.DoubleElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.EnumElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FeatureElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.FontElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.IntElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.ListElement
update() - Method in class fiji.plugin.trackmate.gui.displaysettings.StyleElements.StringElement
update() - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElement
update(double[]) - Method in class fiji.plugin.trackmate.tracking.kalman.CVMKalmanFilter: Runs the update step of the Kalman filter based on the specified measurement.
updateEdgeStyle(Collection<mxCell>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeStylist: Change the style of the edge cells to reflect the currently set color generator.
updateFeatures(Spot) - Method in class fiji.plugin.trackmate.Model: Mark the specified spot for update.
updateModelAndHistogram(Model, Model, int, double) - Method in class fiji.plugin.trackmate.util.DetectionPreview
updateVertexStyle(Collection<mxCell>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeStylist
USE_RANDOM_COLOR_KEY - Static variable in class fiji.plugin.trackmate.features.FeatureUtils
USE_UNIFORM_COLOR_KEY - Static variable in class fiji.plugin.trackmate.features.FeatureUtils
useJFileChooser - Static variable in class fiji.plugin.trackmate.util.FileChooser
userCheckImpDimensions(ImagePlus) - Static method in class fiji.plugin.trackmate.gui.GuiUtils

V

value - Variable in class fiji.plugin.trackmate.action.closegaps.GapClosingMethod.GapClosingParameter
value - Variable in class fiji.plugin.trackmate.features.FeatureFilter
valueOf(String) - Static method in enum fiji.plugin.trackmate.action.CTCExporter.ExportType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.action.LabelImgExporter.LabelIdPainting: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.Dimension: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackDisplayMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackMateObject: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.gui.wizard.TransitionAnimator.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.tracking.overlap.OverlapTracker.IoUCalculation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.util.FileChooser.DialogType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fiji.plugin.trackmate.util.FileChooser.SelectionMode: Returns the enum constant of this type with the specified name.
values() - Static method in enum fiji.plugin.trackmate.action.CTCExporter.ExportType: Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class fiji.plugin.trackmate.action.fit.AbstractSpotFitter.Observation
values() - Static method in enum fiji.plugin.trackmate.action.LabelImgExporter.LabelIdPainting: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.Dimension: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackDisplayMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.gui.displaysettings.DisplaySettings.TrackMateObject: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.gui.wizard.TransitionAnimator.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.tracking.overlap.OverlapTracker.IoUCalculation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.util.FileChooser.DialogType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fiji.plugin.trackmate.util.FileChooser.SelectionMode: Returns an array containing the constants of this enum type, in the order they are declared.
variance(double[]) - Static method in class fiji.plugin.trackmate.util.TMUtils
variance(DoubleArray) - Static method in class fiji.plugin.trackmate.util.TMUtils
vcat(SparseCostMatrix) - Method in class fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix: Returns the vertical concatenation of this matrix with the specified one.
VECTOR_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
vertexAdded(GraphVertexChangeEvent<Spot>) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex
vertexAdded(GraphVertexChangeEvent<Spot>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
vertexRemoved(GraphVertexChangeEvent<Spot>) - Method in class fiji.plugin.trackmate.graph.TimeDirectedNeighborIndex
vertexRemoved(GraphVertexChangeEvent<Spot>) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
vertexSet() - Method in class fiji.plugin.trackmate.TrackModel: Returns a set of the vertices contained in this graph.
ViewFactory - Interface in fiji.plugin.trackmate.visualization
ViewProvider - Class in fiji.plugin.trackmate.providers
ViewProvider() - Constructor for class fiji.plugin.trackmate.providers.ViewProvider
ViewUtils - Class in fiji.plugin.trackmate.visualization: A collection of static utilities related to TrackMateModelViews.
Viridis - Static variable in class fiji.plugin.trackmate.gui.displaysettings.Colormap: An Colormap that replicates the matplotlib "Viridis" colormap.
VISIBILITY - Static variable in class fiji.plugin.trackmate.SpotCollection
visible - Variable in class fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument
visibleKeys - Variable in class fiji.plugin.trackmate.providers.AbstractProvider
visit(StyleElements.Separator) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.LabelElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.ColorElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.BooleanElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.BoundedDoubleElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.DoubleElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.IntElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.EnumElement<E>) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.FeatureElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.ColormapElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.FontElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.StringElement) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(StyleElements.ListElement<E>) - Method in interface fiji.plugin.trackmate.gui.displaysettings.StyleElements.StyleElementVisitor
visit(CLIConfigurator.Flag) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CLIConfigurator.StringArgument) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CLIConfigurator.DoubleArgument) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CLIConfigurator.IntArgument) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CLIConfigurator.ChoiceArgument) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CLIConfigurator.PathArgument) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CommandCLIConfigurator.ExecutablePath) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CondaCLIConfigurator.CondaEnvironmentCommand) - Method in interface fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor
visit(CommandCLIConfigurator.ExecutablePath) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CLIConfigurator.Flag) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CLIConfigurator.IntArgument) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CLIConfigurator.DoubleArgument) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CLIConfigurator.StringArgument) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CLIConfigurator.PathArgument) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CLIConfigurator.ChoiceArgument) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CondaCLIConfigurator.CondaEnvironmentCommand) - Method in class fiji.plugin.trackmate.util.cli.CliGuiBuilder
visit(CommandCLIConfigurator.ExecutablePath) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CondaCLIConfigurator.CondaEnvironmentCommand) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CLIConfigurator.Flag) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CLIConfigurator.IntArgument) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CLIConfigurator.DoubleArgument) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CLIConfigurator.StringArgument) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CLIConfigurator.PathArgument) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
visit(CLIConfigurator.ChoiceArgument) - Method in class fiji.plugin.trackmate.util.cli.CommandBuilder
VOID_LOGGER - Static variable in class fiji.plugin.trackmate.Logger: This logger discard any message.

W

WholeTrackFeatureColorGenerator - Class in fiji.plugin.trackmate.visualization
WholeTrackFeatureColorGenerator(Model, String, Color, Color, Colormap, double, double) - Constructor for class fiji.plugin.trackmate.visualization.WholeTrackFeatureColorGenerator
width - Variable in class fiji.plugin.trackmate.Settings
WizardController - Class in fiji.plugin.trackmate.gui.wizard
WizardController(WizardSequence) - Constructor for class fiji.plugin.trackmate.gui.wizard.WizardController
WizardPanel - Class in fiji.plugin.trackmate.gui.wizard
WizardPanel() - Constructor for class fiji.plugin.trackmate.gui.wizard.WizardPanel
WizardPanelDescriptor - Class in fiji.plugin.trackmate.gui.wizard
WizardPanelDescriptor(String) - Constructor for class fiji.plugin.trackmate.gui.wizard.WizardPanelDescriptor
WizardSequence - Interface in fiji.plugin.trackmate.gui.wizard: Interface for classes that allows specifying what descriptors are traversed in the Wizard.
write(Spot, int) - Method in class fiji.plugin.trackmate.action.LabelImgExporter.SpotAsDotWriter
write(Spot, int) - Method in class fiji.plugin.trackmate.action.LabelImgExporter.SpotRoiWriter
write(Spot, int) - Method in interface fiji.plugin.trackmate.action.LabelImgExporter.SpotWriter
writeAttribute(Map<String, Object>, Element, String, Class<?>, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils: Add a parameter attribute to the given element, taken from the given settings map.
writeDoMedian(Map<String, Object>, Element, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
writeDoSubPixel(Map<String, Object>, Element, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
writeDownsamplingFactor(Map<String, Object>, Element, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
writeRadius(Map<String, Object>, Element, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
writeTargetChannel(Map<String, Object>, Element, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
writeThreshold(Map<String, Object>, Element, StringBuilder) - Static method in class fiji.plugin.trackmate.io.IOUtils
writeToFile() - Method in class fiji.plugin.trackmate.io.TmXmlWriter: Writes the document to the file.

X

x - Variable in class fiji.plugin.trackmate.SpotRoi: Polygon points X coordinates, in physical units.
X0 - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
X_LOCATION - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
X_LOCATION - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
xFeature - Variable in class fiji.plugin.trackmate.features.AbstractFeatureGrapher
xFeature - Variable in class fiji.plugin.trackmate.features.ModelDataset
XML_ATTRIBUTE_DETECTOR_NAME - Static variable in class fiji.plugin.trackmate.detection.DetectorKeys: The attribute name for the SpotDetectorFactory key when marshalling to or unmarhsalling from XML.
XML_ATTRIBUTE_TRACKER_NAME - Static variable in class fiji.plugin.trackmate.tracking.TrackerKeys: The attribute name for the SpotTracker key when marshalling to or unmarhsalling from XML.
XML_ELEMENT_NAME_FEATURE_PENALTIES - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
XML_ELEMENT_NAME_GAP_CLOSING - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
XML_ELEMENT_NAME_LINKING - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
XML_ELEMENT_NAME_MERGING - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
XML_ELEMENT_NAME_SPLITTING - Static variable in class fiji.plugin.trackmate.tracking.jaqaman.LAPUtils
XYTextSimpleAnnotation - Class in fiji.plugin.trackmate.gui.components
XYTextSimpleAnnotation(ChartPanel) - Constructor for class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation
XYTextSimpleAnnotation(ChartPanel, boolean) - Constructor for class fiji.plugin.trackmate.gui.components.XYTextSimpleAnnotation

Y

y - Variable in class fiji.plugin.trackmate.SpotRoi: Polygon points Y coordinates, in physical units.
Y0 - Static variable in class fiji.plugin.trackmate.features.spot.SpotFitEllipseAnalyzerFactory
Y_LOCATION - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
Y_LOCATION - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
yFeatures - Variable in class fiji.plugin.trackmate.features.AbstractFeatureGrapher
yFeatures - Variable in class fiji.plugin.trackmate.features.ModelDataset

Z

Z_LOCATION - Static variable in class fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer
Z_LOCATION - Static variable in class fiji.plugin.trackmate.features.track.TrackLocationAnalyzer
zend - Variable in class fiji.plugin.trackmate.Settings: The lowest pixel Z position, 0-based, of the volume to process.
ZERO - Static variable in class fiji.plugin.trackmate.SpotCollection
ZOOM_IN_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
ZOOM_OUT_ICON - Static variable in class fiji.plugin.trackmate.gui.Icons
zoomIn() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
zoomOut() - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
zoomTo(double, boolean) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
zstart - Variable in class fiji.plugin.trackmate.Settings: The lowest pixel Z position, 0-based, of the volume to process.

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