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#Fiji.plugin Classes and Interfaces - 380 results found.
NameDescriptionTypePackageFramework
AbstractFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
AbstractProviderClassfiji.plugin.trackmate.providersFiji
AbstractSemiAutoTrackerA class made to perform semi-automated tracking of spots in TrackMate & The user has to select one spot, one a meaningful location.Classfiji.plugin.trackmate.detection.semiautoFiji
AbstractSemiAutoTracker .SearchRegionA utility class made to return the information on a neighborhood generated from a source around a Spot.Classfiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTrackerFiji
AbstractTMActionClassfiji.plugin.trackmate.actionFiji
AbstractTrackMateModelViewAn abstract class for spot displayers, that can overlay detected spots and tracks on top of the image data.Classfiji.plugin.trackmate.visualizationFiji
ActionChooserDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
ActionChooserPanelClassfiji.plugin.trackmate.gui.panelsFiji
ActionListenablePanelClassfiji.plugin.trackmate.gui.panelsFiji
ActionProviderClassfiji.plugin.trackmate.providersFiji
AlphanumComparatorThe Alphanum Algorithm is an improved sorting algorithm for strings containing numbers.Classfiji.plugin.trackmate.utilFiji
Apply_External_TransformationClassfiji.pluginFiji
Apply_TransformationClassspim.fiji.pluginFiji
ApplyParametersClassspim.fiji.plugin.applyFiji
AssignmentAlgorithmJust in case I want to try more than one implementation of the assignment algorithm.Interfacefiji.plugin.trackmate.tracking.oldlap.hungarianFiji
AssignmentProblemAn implementation of this: http://en.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
BasicDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
Bead_RegistrationClassfiji.pluginFiji
BigDataViewerTransformationWindowClassspim.fiji.plugin.applyFiji
BlockLogDetectorClassfiji.plugin.trackmate.detectionFiji
BlockLogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
BlockLogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
CaptureOverlayActionClassfiji.plugin.trackmate.actionFiji
CaptureOverlayAction .FactoryClassfiji.plugin.trackmate.action.CaptureOverlayActionFiji
CategoryJComboBoxA JcomboBox that displays categories, and return the category the selectedAuthor:Jean-Yves Tinevez, adapted fromClassfiji.plugin.trackmate.gui.panels.componentsFiji
ControlClassfiji.plugin.volumeviewerFiji
ConvexBranchesDecompositionA class that can decompose the tracks of a Model in convex branches.Classfiji.plugin.trackmate.graphFiji
ConvexBranchesDecomposition .TrackBranchDecompositionClassfiji.plugin.trackmate.graph.ConvexBranchesDecompositionFiji
CopyOverlayActionClassfiji.plugin.trackmate.actionFiji
CopyOverlayAction .FactoryClassfiji.plugin.trackmate.action.CopyOverlayActionFiji
CostFunctionInterface representing a function that can calculate the cost to link a source object to a target object.Interfacefiji.plugin.trackmate.tracking.sparselap.costfunctionFiji
CostFunctionsInterface for cost function classes, which take a Matrix and fill in values according to the cost function.Interfacefiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
CostMatrixCreatorInterface for function that can generate a SparseCostMatrix from assignment candidates.Interfacefiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
CVMKalmanFilterA Kalman filter that deals with a single particle motion in 3D with a constant velocity vector.Classfiji.plugin.trackmate.tracking.kalmanFiji
Data_ExplorerClassspim.fiji.pluginFiji
DebugClassfiji.plugin.trackmateFiji
DefaultCostMatrixCreatorA CostMatrixCreator that build a cost matrix from 3 lists containing the sources, the targets and the associated costs.Classfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
DefaultCostMatrixCreator .AssignmentClassfiji.plugin.trackmate.tracking.sparselap.costmatrix.DefaultCostMatrixCreatorFiji
DefaultFileFilterFilter for use in a JFileChooser.Classfiji.plugin.trackmate.utilFiji
DefaultFileFilter .EditorFileFilterUtility file filter to accept editor files, namely .Classfiji.plugin.trackmate.util.DefaultFileFilterFiji
DefaultFileFilter .ImageFileFilterUtility file filter to accept all image formats supported by image io.Classfiji.plugin.trackmate.util.DefaultFileFilterFiji
Define_Bounding_BoxClassspim.fiji.pluginFiji
Define_Multi_View_DatasetClassspim.fiji.pluginFiji
DetectionDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
DetectionUtilsClassfiji.plugin.trackmate.detectionFiji
DetectorChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
DetectorConfigurationDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
DetectorKeysClassfiji.plugin.trackmate.detectionFiji
DetectorProviderClassfiji.plugin.trackmate.providersFiji
DifferenceOfClassspim.fiji.plugin.interestpointdetectionFiji
DifferenceOfGaussianClassspim.fiji.plugin.interestpointdetectionFiji
DifferenceOfMeanClassspim.fiji.plugin.interestpointdetectionFiji
DimensionClassfiji.plugin.trackmateFiji
Display_ViewClassspim.fiji.pluginFiji
DisplaySettingsEventAn event object fired when the user changes one of the display settings through this GUI panel.Classfiji.plugin.trackmate.guiFiji
DisplaySettingsListenerInterface for classes that listen to display settings changes on a GUI.Interfacefiji.plugin.trackmate.guiFiji
DogDetectorClassfiji.plugin.trackmate.detectionFiji
DogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
DogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
DownsampleLogDetectorClassfiji.plugin.trackmate.detectionFiji
DownSampleLogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
DownsampleLogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
DummySpotColorGeneratorA dummy spot color generator that always return the default color.Classfiji.plugin.trackmate.visualizationFiji
DummyTrackColorGeneratorA dummy track color generator that always return the default color.Classfiji.plugin.trackmate.visualizationFiji
Duplicate_TransformationClassspim.fiji.pluginFiji
EdgeAnalyzerInterface for analyzers that can compute scalar numerical features for an edge of a TrackMate model.Interfacefiji.plugin.trackmate.features.edgesFiji
EdgeAnalyzerProviderA provider for the edge analyzers provided in the GUI.Classfiji.plugin.trackmate.providersFiji
EdgeFeatureCalculatorA class dedicated to centralizing the calculation of the numerical features of spots, through EdgeAnalyzers.Classfiji.plugin.trackmate.featuresFiji
EdgeFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
EdgeTargetAnalyzerClassfiji.plugin.trackmate.features.edgesFiji
EdgeTimeLocationAnalyzerClassfiji.plugin.trackmate.features.edgesFiji
EdgeVelocityAnalyzerClassfiji.plugin.trackmate.features.edgesFiji
ExportableChartPanelClassfiji.plugin.trackmate.utilFiji
ExportStatsToIJActionClassfiji.plugin.trackmate.actionFiji
ExportStatsToIJAction .FactoryClassfiji.plugin.trackmate.action.ExportStatsToIJActionFiji
ExportTracksToXMLClassfiji.plugin.trackmate.actionFiji
ExportTracksToXML .FactoryClassfiji.plugin.trackmate.action.ExportTracksToXMLFiji
ExtractTrackStackActionClassfiji.plugin.trackmate.actionFiji
ExtractTrackStackAction .FactoryClassfiji.plugin.trackmate.action.ExtractTrackStackActionFiji
FastLAPTrackerClassfiji.plugin.trackmate.tracking.oldlapFiji
FastLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFiji
FeatureAnalyzerInterfacefiji.plugin.trackmate.featuresFiji
FeatureColorGeneratorInterface for color generator that can color objects based on a feature identified by a String.Interfacefiji.plugin.trackmate.visualizationFiji
FeatureFilterA helper class to store a feature filter.Classfiji.plugin.trackmate.featuresFiji
FeatureModelThis class represents the part of the Model that is in charge of dealing with spot features and track features.Classfiji.plugin.trackmateFiji
FeaturePenaltyCostFunctionA cost function that tempers a square distance cost by difference in feature This cost is calculated as follow:Classfiji.plugin.trackmate.tracking.sparselap.costfunctionFiji
FeaturePlotSelectionPanelA simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum.Classfiji.plugin.trackmate.gui.panels.componentsFiji
FeaturePlotSelectionPanelA simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum.Classfiji.plugin.trackmate.visualization.trackschemeFiji
FileOpenMenuEntryClassfiji.plugin.timelapsedisplayFiji
FilterGuiPanelClassfiji.plugin.trackmate.gui.panels.componentsFiji
FilterPanelClassfiji.plugin.trackmate.gui.panelsFiji
FlagNodeClassfiji.plugin.trackmate.tracking.kdtreeFiji
FromContinuousBranchesClassfiji.plugin.trackmate.graphFiji
Function1Interface for function that compute values from a single input and store it in Author:Jean-Yves InevezInterfacefiji.plugin.trackmate.graphFiji
Function2Interface for function that compute values from a two inputs and store it in Author:Jean-Yves InevezInterfacefiji.plugin.trackmate.graphFiji
FusionClassspim.fiji.plugin.fusionFiji
GapClosingCostFunctionGap closing cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
Generic_Resave_HDF5Classspim.fiji.plugin.resaveFiji
Generic_Resave_HDF5 .ParametersClassspim.fiji.plugin.resave.Generic_Resave_HDF5Fiji
GenericDialogAppenderInterfacespim.fiji.plugin.utilFiji
GenericLoadParseQueryXMLInterface for interactive parsing of spimdata XMLsAuthor:Stephan Preibisch (stephan.Classspim.fiji.plugin.queryXMLFiji
GradientClassfiji.plugin.volumeviewerFiji
GrapherDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
GrapherPanelClassfiji.plugin.trackmate.guiFiji
GraphFrameClassfiji.plugin.timelapsedisplayFiji
GraphSegmentSplitterClassfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
GraphUtilsClassfiji.plugin.trackmate.graphFiji
GuiClassfiji.plugin.volumeviewerFiji
GUIHelperClassspim.fiji.plugin.utilFiji
GuiUtilsClassfiji.plugin.trackmate.guiFiji
HistogramClassspim.fiji.plugin.thinoutFiji
HungarianAlgorithmAn implementation of the classic Hungarian algorithm for the assignment problem.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
HyperStackDisplayerClassfiji.plugin.trackmate.visualization.hyperstackFiji
HyperStackDisplayerFactoryClassfiji.plugin.trackmate.visualization.hyperstackFiji
IcyTrackExporterClassfiji.plugin.trackmate.actionFiji
IcyTrackExporter .FactoryClassfiji.plugin.trackmate.action.IcyTrackExporterFiji
IcyTrackFormatWriterClassfiji.plugin.trackmate.ioFiji
IcyXmlReaderA reader for the XML files generated in the TrackManager of the Icy software The reader requires a calibration s to operate, so as to generate a properClassfiji.plugin.trackmate.ioFiji
Image_FusionClassspim.fiji.pluginFiji
ImagePlusChooserClassfiji.plugin.trackmate.gui.panels.componentsFiji
IndependentSpotFeatureAnalyzerClassfiji.plugin.trackmate.features.spotFiji
InfoPaneClassfiji.plugin.trackmate.visualization.trackschemeFiji
InitFilterDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
InitFilterPanelClassfiji.plugin.trackmate.gui.panelsFiji
Interactive_Remove_DetectionsClassspim.fiji.pluginFiji
InteractiveProjectionsClassspim.fiji.plugin.removedetectionsFiji
Interest_Point_DetectionPlugin to detect interest points, store them on disk, and link them into the XML Different plugins to detect interest points are supported, needs to implement theClassspim.fiji.pluginFiji
Interest_Point_RegistrationClassspim.fiji.pluginFiji
Interest_Point_Registration .RegistrationTypeClassspim.fiji.plugin.Interest_Point_RegistrationFiji
InterestPointDetectionClassspim.fiji.plugin.interestpointdetectionFiji
InterestPointRegistrationClassspim.fiji.plugin.interestpointregistrationFiji
InterpolationClassfiji.plugin.volumeviewerFiji
IOUtilsA collection of static utilities for the input/output of xml files.Classfiji.plugin.trackmate.ioFiji
ISBIChallengeExporterClassfiji.plugin.trackmate.actionFiji
ISBIChallengeExporter .FactoryClassfiji.plugin.trackmate.action.ISBIChallengeExporterFiji
JaqamanLinkerLinks two lists of objects based on the LAP framework described in Jaqaman et al.Classfiji.plugin.trackmate.tracking.sparselap.linkerFiji
JaqamanLinkingCostMatrixCreatorA CostMatrixCreator that can generate a cost matrix from a list of sources, a list of targets and a CostFunction that can generate aClassfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
JaqamanSegmentCostMatrixCreatorThis class generates the top-left quadrant of the LAP segment linking cost matrix, following Jaqaman et al.Classfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
JGraphXAdapterClassfiji.plugin.trackmate.visualization.trackschemeFiji
JLabelLoggerClassfiji.plugin.trackmate.utilFiji
JNumericTextFieldClassfiji.plugin.trackmate.gui.panels.componentsFiji
JonkerVolgenantAlgorithm Based on: Jonker, R.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
JPanelColorByFeatureGUIClassfiji.plugin.trackmate.gui.panels.componentsFiji
JPanelFeaturePenaltyClassfiji.plugin.trackmate.gui.panels.componentsFiji
JPanelFeatureSelectionGuiClassfiji.plugin.trackmate.gui.panels.componentsFiji
JPanelTrackerSettingsMainClassfiji.plugin.trackmate.gui.panels.trackerFiji
KalmanTrackerClassfiji.plugin.trackmate.tracking.kalmanFiji
KalmanTrackerConfigPanelClassfiji.plugin.trackmate.gui.panels.trackerFiji
KalmanTrackerFactoryClassfiji.plugin.trackmate.tracking.kalmanFiji
LAPJV tailored for sparse cost matrices.Classfiji.plugin.trackmate.tracking.sparselap.linkerFiji
LAPTracker This class tracks objects by formulating the problem as a Linear Assignment For reference, see: Jaqaman, K.Classfiji.plugin.trackmate.tracking.oldlapFiji
LAPTrackerCostMatrixCreatorContains the mutually shared fields and private functions used by the two cost matrix classes LinkingCostMatrixCreator and TrackSegmentCostMatrixCreatorClassfiji.plugin.trackmate.tracking.oldlap.costmatrixFiji
LAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFiji
LAPTrackerSettingsPanelClassfiji.plugin.trackmate.gui.panels.trackerFiji
LAPUtilsClassfiji.plugin.trackmate.trackingFiji
LinkingCostFunctionLinking cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
LinkingCostMatrixCreatorCreates the cost matrix described in Figure 1b in the paper.Classfiji.plugin.trackmate.tracking.oldlap.costmatrixFiji
LinkNew3DViewerActionClassfiji.plugin.trackmate.actionFiji
LinkNew3DViewerAction .FactoryClassfiji.plugin.trackmate.action.LinkNew3DViewerActionFiji
ListChooserPanelA panel to let the user choose what displayer he wants to use.Classfiji.plugin.trackmate.gui.panelsFiji
LoadDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
LoadICYTrackPlugIn_Classfiji.plugin.trackmateFiji
LoadParseQueryXMLClassspim.fiji.plugin.queryXMLFiji
LoadTrackMatePlugIn_Classfiji.plugin.trackmateFiji
LogDetectorClassfiji.plugin.trackmate.detectionFiji
LogDetectorConfigurationPanelConfiguration panel for spot detectors based on LoG detector.Classfiji.plugin.trackmate.gui.panels.detectorFiji
LogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
LoggerThis class is used to log messages occurring during TrackMate execution.Classfiji.plugin.trackmateFiji
Logger .SlaveLoggerA logger that wraps a master logger and uses it to echo any received message.Classfiji.plugin.trackmate.LoggerFiji
Logger .StringBuilderLoggerThis Logger outputs to a StringBuilder given at construction.Classfiji.plugin.trackmate.LoggerFiji
LogPanelA panel using s JTextPane to log events.Classfiji.plugin.trackmate.guiFiji
LogPanelDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
LookupTableClassfiji.plugin.volumeviewerFiji
ManualDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
ManualEdgeColorAnalyzerClassfiji.plugin.trackmate.features.manualFiji
ManualEdgeColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
ManualSpotColorAnalyzerFactoryClassfiji.plugin.trackmate.features.manualFiji
ManualSpotColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
ManualTrackerFactoryClassfiji.plugin.trackmate.trackingFiji
ManualTrackingGUIControllerClassfiji.plugin.trackmate.guiFiji
ManualTrackingPlugIn_Classfiji.plugin.trackmateFiji
Max_ProjectClassspim.fiji.pluginFiji
MedianFilter2DA simple median filter that operates on 1D, 2D or 3D images.Classfiji.plugin.trackmate.detection.utilFiji
Merge_Cluster_JobsClassspim.fiji.pluginFiji
MergeClusterJobsClassspim.fiji.plugin.clusterFiji
MergeFileActionClassfiji.plugin.trackmate.actionFiji
MergeFileAction .FactoryClassfiji.plugin.trackmate.action.MergeFileActionFiji
MergingCostFunctionMerging cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
MinMaxAdjustableSimple interface for objects whose effects depend on a minimal and maximal double value that can be adjusted manually or automatically.Interfacefiji.plugin.trackmate.visualizationFiji
ModelThe model for the data managed by TrackMate trackmate.Classfiji.plugin.trackmateFiji
ModelChangeEventClassfiji.plugin.trackmateFiji
ModelChangeListenerAn interface for listeners that will be notified when a ModelAuthor:Jean-Yves Tinevez Interfacefiji.plugin.trackmateFiji
ModelFeatureUpdaterA utility class that listens to the change occurring in a model, and updates its spot, edge and track features accordingly.Classfiji.plugin.trackmate.featuresFiji
ModelLinkClassspim.fiji.plugin.applyFiji
ModelToolsA collection of static utilities made to ease the manipulation of a TrackMate Model and SelectionModel.Classfiji.plugin.trackmate.utilFiji
MouseListenerTimelapseClassfiji.plugin.timelapsedisplayFiji
MouseListenerValueClassspim.fiji.plugin.thinoutFiji
Multi_View_DeconvolutionClassfiji.pluginFiji
Multi_View_FusionClassfiji.pluginFiji
MunkresKuhnAlgorithmThis implements optimal matching between two sets given a weight matrix (where the goal is to minimize the cumulative weight of the matches).Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
mxScaledLabelShapeThis is a shape that is made to display a cell in a way that suits for our spots objects.Classfiji.plugin.trackmate.visualization.trackschemeFiji
mxSideTextShapeA text shape that draws edge label along the edge line and parallel to it.Classfiji.plugin.trackmate.visualization.trackschemeFiji
MyMultiLineLabelClassspim.fiji.plugin.utilFiji
NearestNeighborFlagSearchOnKDTreeClassfiji.plugin.trackmate.tracking.kdtreeFiji
NearestNeighborTrackerClassfiji.plugin.trackmate.tracking.kdtreeFiji
NearestNeighborTrackerFactoryClassfiji.plugin.trackmate.tracking.kdtreeFiji
NearestNeighborTrackerSettingsPanelClassfiji.plugin.trackmate.gui.panels.trackerFiji
OnRequestUpdaterThis class extends Thread and is suited to call methods that are typically called often, but takes time to complete, such as display refreshing.Classfiji.plugin.trackmate.utilFiji
OnRequestUpdater .RefreshableInterfacefiji.plugin.trackmate.util.OnRequestUpdaterFiji
OpenImgClassspim.fiji.plugin.utilFiji
OutputFunctionInterface for functions that return a new object, computed from two input arguments.Interfacefiji.plugin.trackmate.graphFiji
PerEdgeFeatureColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
PerTrackFeatureColorGeneratorA TrackColorGenerator that generate colors based on the whole trackAuthor:Jean-Yves TinevezClassfiji.plugin.trackmate.visualizationFiji
PicClassfiji.plugin.volumeviewerFiji
PlotNSpotsVsTimeActionClassfiji.plugin.trackmate.actionFiji
PlotNSpotsVsTimeAction .FactoryClassfiji.plugin.trackmate.action.PlotNSpotsVsTimeActionFiji
PluginHelperClassspim.fiji.plugin.resaveFiji
PluginHelper .ChooseXmlFileListenerClassspim.fiji.plugin.resave.PluginHelperFiji
PlugInInstallerClassfijiFiji
ProgressWriterIJClassspim.fiji.plugin.resaveFiji
RadiusToEstimatedActionClassfiji.plugin.trackmate.actionFiji
RadiusToEstimatedAction .FactoryClassfiji.plugin.trackmate.action.RadiusToEstimatedActionFiji
RecalculateFeatureActionClassfiji.plugin.trackmate.actionFiji
RecalculateFeatureAction .FactoryClassfiji.plugin.trackmate.action.RecalculateFeatureActionFiji
RecursiveCumSumClassfiji.plugin.trackmate.graphFiji
RegistrationStatisticsClassfiji.plugin.timelapsedisplayFiji
Resave_HDF5Classspim.fiji.plugin.resaveFiji
Resave_TIFFClassspim.fiji.plugin.resaveFiji
Resave_TIFF .ParametersClassspim.fiji.plugin.resave.Resave_TIFFFiji
ResetRadiusActionClassfiji.plugin.trackmate.actionFiji
ResetRadiusAction .FactoryClassfiji.plugin.trackmate.action.ResetRadiusActionFiji
ResetSpotTimeFeatureActionClassfiji.plugin.trackmate.actionFiji
ResetSpotTimeFeatureAction .FactoryClassfiji.plugin.trackmate.action.ResetSpotTimeFeatureActionFiji
ResizableDoubleArrayClassfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
SaveActionClassfiji.plugin.trackmate.visualization.trackschemeFiji
SaveDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
SearchBarClassfiji.plugin.trackmate.visualization.trackscheme.utilsFiji
SelectionChangeEventAn event that characterizes a change in the current selection.Classfiji.plugin.trackmateFiji
SelectionChangeListenerInterfacefiji.plugin.trackmateFiji
SelectionModelA component of Model that handles spot and edges selection.Classfiji.plugin.trackmateFiji
SemiAutoTrackerClassfiji.plugin.trackmate.detection.semiautoFiji
SetColorScaleDialogClassfiji.plugin.trackmate.gui.panels.componentsFiji
SettingsThis class is used to store user settings for the TrackMate trackmate.Classfiji.plugin.trackmateFiji
SimpleFastLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFiji
SimpleLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFiji
SimpleLAPTrackerSettingsPanelA simplified configuration panel for the LAPTracker.Classfiji.plugin.trackmate.gui.panels.trackerFiji
SimpleSparseLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.sparselapFiji
SomeDialogDescriptorAn abstract class made for describing panels that generate a dialog, like save and load panels.Classfiji.plugin.trackmate.gui.descriptorsFiji
SortedDepthFirstIteratorA depth-first iterator, that - when branching - chooses the next vertex according to a specified comparator.Classfiji.plugin.trackmate.graphFiji
SparseCostMatrixA class to represent a sparse cost matrix.Classfiji.plugin.trackmate.tracking.sparselap.linkerFiji
SparseLAPFrameToFrameTrackerClassfiji.plugin.trackmate.tracking.sparselapFiji
SparseLAPSegmentTrackerThis class tracks deals with the second step of tracking according to the LAP tracking framework formulated by Jaqaman, K.Classfiji.plugin.trackmate.tracking.sparselapFiji
SparseLAPTrackerClassfiji.plugin.trackmate.tracking.sparselapFiji
SparseLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.sparselapFiji
Specify_CalibrationClassspim.fiji.pluginFiji
Specify_Calibration .CalClassspim.fiji.plugin.Specify_CalibrationFiji
SplittingCostFunctionSplitting cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
SpotA RealLocalizable implementation, used in TrackMate to represent a On top of being a RealLocalizable, it can store additional numericalClassfiji.plugin.trackmateFiji
SpotAnalyzerInterface for a class that can compute feature on a collection of spots.Interfacefiji.plugin.trackmate.features.spotFiji
SpotAnalyzerFactoryInterface for factories that can generate a SpotAnalyzer configured to operate on a specific frame of a model.Interfacefiji.plugin.trackmate.features.spotFiji
SpotAnalyzerProviderA provider for the spot analyzer factories provided in the GUI.Classfiji.plugin.trackmate.providersFiji
SpotCollectionA utility class that wrap the SortedMap we use to store the spots contained in each frame with a few utility methods.Classfiji.plugin.trackmateFiji
SpotColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
SpotColorGeneratorPerTrackFeatureClassfiji.plugin.trackmate.visualizationFiji
SpotContrastAnalyzerClassfiji.plugin.trackmate.features.spotFiji
SpotContrastAnalyzerFactoryClassfiji.plugin.trackmate.features.spotFiji
SpotContrastAndSNRAnalyzerThis FeatureAnalyzer computes both the Michelson contrast and the SNR for each spot:Classfiji.plugin.trackmate.features.spotFiji
SpotContrastAndSNRAnalyzerFactoryA factory for SpotContrastAndSNRAnalyzers.Classfiji.plugin.trackmate.features.spotFiji
SpotDetectorInterface for Spot detector classes, that are able to segment spots of a given estimated radius within a 2D or 3D image.Interfacefiji.plugin.trackmate.detectionFiji
SpotDetectorFactoryMother interface for SpotDetector factories.Interfacefiji.plugin.trackmate.detectionFiji
SpotDisplayer3DClassfiji.plugin.trackmate.visualization.threedviewerFiji
SpotDisplayer3DFactoryClassfiji.plugin.trackmate.visualization.threedviewerFiji
SpotEditToolClassfiji.plugin.trackmate.visualization.hyperstackFiji
SpotEditToolConfigPanelClassfiji.plugin.trackmate.visualization.hyperstackFiji
SpotFeatureCalculatorA class dedicated to centralizing the calculation of the numerical features of spots, through SpotAnalyzers.Classfiji.plugin.trackmate.featuresFiji
SpotFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
SpotFilterDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
SpotGroupNodeClassfiji.plugin.trackmate.visualization.threedviewerFiji
SpotIconGrabberThis class is used to take a snapshot of a Spot object (or collection) from its coordinates and an ImagePlus that contain theClassfiji.plugin.trackmate.visualization.trackschemeFiji
SpotImageUpdaterClassfiji.plugin.trackmate.visualization.trackschemeFiji
SpotIntensityAnalyzerClassfiji.plugin.trackmate.features.spotFiji
SpotIntensityAnalyzerFactoryClassfiji.plugin.trackmate.features.spotFiji
SpotMorphologyAnalyzerThis SpotAnalyzer computes morphology features for the given spots.Classfiji.plugin.trackmate.features.spotFiji
SpotMorphologyAnalyzerFactoryClassfiji.plugin.trackmate.features.spotFiji
SpotNeighborhoodClassfiji.plugin.trackmate.utilFiji
SpotNeighborhoodCursorClassfiji.plugin.trackmate.utilFiji
SpotOverlayThe overlay class in charge of drawing the spot images on the hyperstackAuthor:Jean-Yves Tinevez Classfiji.plugin.trackmate.visualization.hyperstackFiji
SpotRadiusEstimatorClassfiji.plugin.trackmate.features.spotFiji
SpotRadiusEstimatorFactoryClassfiji.plugin.trackmate.features.spotFiji
SpotTrackerThis interface should be used when creating algorithms for linking objects across multiple frames in time-lapse images.Interfacefiji.plugin.trackmate.trackingFiji
SpotTrackerFactoryInterfacefiji.plugin.trackmate.trackingFiji
SquareDistCostFunctionA cost function that returns cost equal to the square distance.Classfiji.plugin.trackmate.tracking.sparselap.costfunctionFiji
SquareNeighborhood3x3Classfiji.plugin.trackmate.detection.utilFiji
SquareNeighborhoodCursor3x3Classfiji.plugin.trackmate.detection.utilFiji
StartDialogDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
StartDialogPanelClassfiji.plugin.trackmate.gui.panelsFiji
StringFormaterInterface for function that can build a human-readable string representation of an objectInterfacefiji.plugin.trackmate.graphFiji
TFalpha1Classfiji.plugin.volumeviewerFiji
TFalpha2Classfiji.plugin.volumeviewerFiji
TFalpha3Classfiji.plugin.volumeviewerFiji
TFalpha4Classfiji.plugin.volumeviewerFiji
TFrgbClassfiji.plugin.volumeviewerFiji
TGMMImporterClassfiji.plugin.trackmate.ioFiji
ThinOut_DetectionsClassspim.fiji.pluginFiji
TimeDirectedDepthFirstIteratorClassfiji.plugin.trackmate.graphFiji
TimeDirectedNeighborIndexClassfiji.plugin.trackmate.graphFiji
TimeDirectedSortedDepthFirstIteratorClassfiji.plugin.trackmate.graphFiji
TimeLapseDisplayClassfiji.plugin.timelapsedisplayFiji
TMUtilsClassfiji.plugin.trackmate.utilFiji
TmXmlKeysContains the key string used for xml marshaling.Classfiji.plugin.trackmate.ioFiji
TmXmlReaderClassfiji.plugin.trackmate.ioFiji
TmXmlReader_v12A compatibility xml loader than can load TrackMate xml file saved for version prior to 2.Classfiji.plugin.trackmate.ioFiji
TmXmlReader_v20Classfiji.plugin.trackmate.ioFiji
TmXmlWriterClassfiji.plugin.trackmate.ioFiji
Toggle_Cluster_OptionsClassspim.fiji.pluginFiji
TrackAnalyzerMother interface for the classes that can compute the feature of tracks.Interfacefiji.plugin.trackmate.features.trackFiji
TrackAnalyzerProviderA provider for the track analyzers provided in the GUI.Classfiji.plugin.trackmate.providersFiji
TrackBranchAnalysisClassfiji.plugin.trackmate.actionFiji
TrackBranchAnalysis .FactoryClassfiji.plugin.trackmate.action.TrackBranchAnalysisFiji
TrackBranchingAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackColorGeneratorInterface for functions that can generate track colors, with a different color for each vertex and edge.Interfacefiji.plugin.trackmate.visualizationFiji
TrackDisplayNodeClassfiji.plugin.trackmate.visualization.threedviewerFiji
TrackDurationAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackerChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackerConfigurationDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackerKeysClassfiji.plugin.trackmate.trackingFiji
TrackerProviderClassfiji.plugin.trackmate.providersFiji
TrackFeatureCalculatorA class dedicated to centralizing the calculation of the numerical features of tracks, through TrackAnalyzers.Classfiji.plugin.trackmate.featuresFiji
TrackFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
TrackFilterDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackIndexAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackingDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackLocationAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackMate The TrackMate_ class runs on the currently active time-lapse image (2D or 3D) and both identifies and tracks bright spots over time.Classfiji.plugin.trackmateFiji
TrackMateActionThis interface describe a track mate action, that can be run on a TrackMate object to change its content or properties.Interfacefiji.plugin.trackmate.actionFiji
TrackMateActionFactoryInterfacefiji.plugin.trackmate.actionFiji
TrackMateBatchClassfiji.plugin.trackmateFiji
TrackMateGUIControllerClassfiji.plugin.trackmate.guiFiji
TrackMateGUIModelClassfiji.plugin.trackmate.guiFiji
TrackMateModelViewInterfacefiji.plugin.trackmate.visualizationFiji
TrackMateModuleInterface for TrackMate modules.Interfacefiji.plugin.trackmateFiji
TrackMatePlugIn_Classfiji.plugin.trackmateFiji
TrackMateWizardClassfiji.plugin.trackmate.guiFiji
TrackModelA component of Model specialized for tracksAuthor:Jean-Yves TinevezClassfiji.plugin.trackmateFiji
TrackNavigatorClassfiji.plugin.trackmate.utilFiji
TrackOverlayThe overlay class in charge of drawing the tracks on the hyperstack window.Classfiji.plugin.trackmate.visualization.hyperstackFiji
TrackSchemeClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeActionsClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeActions .EditActionClassfiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActionsFiji
TrackSchemeActions .EndActionCenters the view to the last cell in selection, sorted by frame number.Classfiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActionsFiji
TrackSchemeActions .HomeActionCenters the view to the first cell in selection.Classfiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActionsFiji
TrackSchemeActions .ResetZoomActionClassfiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActionsFiji
TrackSchemeFactoryClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeFrameClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeGraphComponentClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeGraphLayoutThis mxGraphLayout arranges cells on a graph in lanes corresponding to tracks.Classfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeKeyboardHandlerClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemePopupMenuClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeStylistClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeSvgCanvasClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeToolbarClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSegmentCostMatrixCreatorCreates the cost matrix roughly described in Figure 1c in the paper: Jaqaman, K.Classfiji.plugin.trackmate.tracking.oldlap.costmatrixFiji
TrackSpeedStatisticsAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackSpotQualityFeatureAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrimNotVisibleActionClassfiji.plugin.trackmate.actionFiji
TrimNotVisibleAction .FactoryClassfiji.plugin.trackmate.action.TrimNotVisibleActionFiji
VersionA utility class to deal with version numbers.Classfiji.plugin.trackmate.utilFiji
ViewChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
ViewFactoryInterfacefiji.plugin.trackmate.visualizationFiji
ViewProviderClassfiji.plugin.trackmate.providersFiji
ViewUtilsA collection of static utilities related to TrackMateModelViews.Classfiji.plugin.trackmate.visualizationFiji
Visualize_DetectionsClassspim.fiji.pluginFiji
Visualize_Detections .ParamsClassspim.fiji.plugin.Visualize_DetectionsFiji
VolumeClassfiji.plugin.volumeviewerFiji
Volume_ViewerClassfiji.plugin.volumeviewerFiji
WizardPanelDescriptorA base descriptor class used to reference a Component panel for the Wizard, as well as provide general rules as to how the panel should behave.Interfacefiji.plugin.trackmate.gui.descriptorsFiji
WrapLayoutFlowLayout subclass that fully supports wrapping of components.Classfiji.plugin.trackmate.gui.panelsFiji
XYEdgeRendererClassfiji.plugin.trackmate.utilFiji
XYEdgeSeriesClassfiji.plugin.trackmate.utilFiji
XYEdgeSeriesCollectionClassfiji.plugin.trackmate.utilFiji