Search Java Classes and Packages
#Fiji.plugin Classes and Interfaces - 380 results found.
| Name | Description | Type | Package | Framework |
| AbstractFeatureGrapher | Class | fiji.plugin.trackmate.features | Fiji | |
| AbstractProvider | Class | fiji.plugin.trackmate.providers | Fiji | |
| AbstractSemiAutoTracker | A class made to perform semi-automated tracking of spots in TrackMate & The user has to select one spot, one a meaningful location. | Class | fiji.plugin.trackmate.detection.semiauto | Fiji |
| AbstractSemiAutoTracker .SearchRegion | A utility class made to return the information on a neighborhood generated from a source around a Spot. | Class | fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker | Fiji |
| AbstractTMAction | Class | fiji.plugin.trackmate.action | Fiji | |
| AbstractTrackMateModelView | An abstract class for spot displayers, that can overlay detected spots and tracks on top of the image data. | Class | fiji.plugin.trackmate.visualization | Fiji |
| ActionChooserDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| ActionChooserPanel | Class | fiji.plugin.trackmate.gui.panels | Fiji | |
| ActionListenablePanel | Class | fiji.plugin.trackmate.gui.panels | Fiji | |
| ActionProvider | Class | fiji.plugin.trackmate.providers | Fiji | |
| AlphanumComparator | The Alphanum Algorithm is an improved sorting algorithm for strings containing numbers. | Class | fiji.plugin.trackmate.util | Fiji |
| Apply_External_Transformation | Class | fiji.plugin | Fiji | |
| Apply_Transformation | Class | spim.fiji.plugin | Fiji | |
| ApplyParameters | Class | spim.fiji.plugin.apply | Fiji | |
| AssignmentAlgorithm | Just in case I want to try more than one implementation of the assignment algorithm. | Interface | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
| AssignmentProblem | An implementation of this: http://en. | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
| BasicDetectorConfigurationPanel | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji | |
| Bead_Registration | Class | fiji.plugin | Fiji | |
| BigDataViewerTransformationWindow | Class | spim.fiji.plugin.apply | Fiji | |
| BlockLogDetector | Class | fiji.plugin.trackmate.detection | Fiji | |
| BlockLogDetectorConfigurationPanel | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji | |
| BlockLogDetectorFactory | Class | fiji.plugin.trackmate.detection | Fiji | |
| CaptureOverlayAction | Class | fiji.plugin.trackmate.action | Fiji | |
| CaptureOverlayAction .Factory | Class | fiji.plugin.trackmate.action.CaptureOverlayAction | Fiji | |
| CategoryJComboBox | A JcomboBox that displays categories, and return the category the selectedAuthor:Jean-Yves Tinevez, adapted from | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
| Control | Class | fiji.plugin.volumeviewer | Fiji | |
| ConvexBranchesDecomposition | A class that can decompose the tracks of a Model in convex branches. | Class | fiji.plugin.trackmate.graph | Fiji |
| ConvexBranchesDecomposition .TrackBranchDecomposition | Class | fiji.plugin.trackmate.graph.ConvexBranchesDecomposition | Fiji | |
| CopyOverlayAction | Class | fiji.plugin.trackmate.action | Fiji | |
| CopyOverlayAction .Factory | Class | fiji.plugin.trackmate.action.CopyOverlayAction | Fiji | |
| CostFunction | Interface representing a function that can calculate the cost to link a source object to a target object. | Interface | fiji.plugin.trackmate.tracking.sparselap.costfunction | Fiji |
| CostFunctions | Interface for cost function classes, which take a Matrix and fill in values according to the cost function. | Interface | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
| CostMatrixCreator | Interface for function that can generate a SparseCostMatrix from assignment candidates. | Interface | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji |
| CVMKalmanFilter | A Kalman filter that deals with a single particle motion in 3D with a constant velocity vector. | Class | fiji.plugin.trackmate.tracking.kalman | Fiji |
| Data_Explorer | Class | spim.fiji.plugin | Fiji | |
| Debug | Class | fiji.plugin.trackmate | Fiji | |
| DefaultCostMatrixCreator | A CostMatrixCreator that build a cost matrix from 3 lists containing the sources, the targets and the associated costs. | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji |
| DefaultCostMatrixCreator .Assignment | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix.DefaultCostMatrixCreator | Fiji | |
| DefaultFileFilter | Filter for use in a JFileChooser. | Class | fiji.plugin.trackmate.util | Fiji |
| DefaultFileFilter .EditorFileFilter | Utility file filter to accept editor files, namely . | Class | fiji.plugin.trackmate.util.DefaultFileFilter | Fiji |
| DefaultFileFilter .ImageFileFilter | Utility file filter to accept all image formats supported by image io. | Class | fiji.plugin.trackmate.util.DefaultFileFilter | Fiji |
| Define_Bounding_Box | Class | spim.fiji.plugin | Fiji | |
| Define_Multi_View_Dataset | Class | spim.fiji.plugin | Fiji | |
| DetectionDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| DetectionUtils | Class | fiji.plugin.trackmate.detection | Fiji | |
| DetectorChoiceDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| DetectorConfigurationDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| DetectorKeys | Class | fiji.plugin.trackmate.detection | Fiji | |
| DetectorProvider | Class | fiji.plugin.trackmate.providers | Fiji | |
| DifferenceOf | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| DifferenceOfGaussian | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| DifferenceOfMean | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| Dimension | Class | fiji.plugin.trackmate | Fiji | |
| Display_View | Class | spim.fiji.plugin | Fiji | |
| DisplaySettingsEvent | An event object fired when the user changes one of the display settings through this GUI panel. | Class | fiji.plugin.trackmate.gui | Fiji |
| DisplaySettingsListener | Interface for classes that listen to display settings changes on a GUI. | Interface | fiji.plugin.trackmate.gui | Fiji |
| DogDetector | Class | fiji.plugin.trackmate.detection | Fiji | |
| DogDetectorConfigurationPanel | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji | |
| DogDetectorFactory | Class | fiji.plugin.trackmate.detection | Fiji | |
| DownsampleLogDetector | Class | fiji.plugin.trackmate.detection | Fiji | |
| DownSampleLogDetectorConfigurationPanel | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji | |
| DownsampleLogDetectorFactory | Class | fiji.plugin.trackmate.detection | Fiji | |
| DummySpotColorGenerator | A dummy spot color generator that always return the default color. | Class | fiji.plugin.trackmate.visualization | Fiji |
| DummyTrackColorGenerator | A dummy track color generator that always return the default color. | Class | fiji.plugin.trackmate.visualization | Fiji |
| Duplicate_Transformation | Class | spim.fiji.plugin | Fiji | |
| EdgeAnalyzer | Interface for analyzers that can compute scalar numerical features for an edge of a TrackMate model. | Interface | fiji.plugin.trackmate.features.edges | Fiji |
| EdgeAnalyzerProvider | A provider for the edge analyzers provided in the GUI. | Class | fiji.plugin.trackmate.providers | Fiji |
| EdgeFeatureCalculator | A class dedicated to centralizing the calculation of the numerical features of spots, through EdgeAnalyzers. | Class | fiji.plugin.trackmate.features | Fiji |
| EdgeFeatureGrapher | Class | fiji.plugin.trackmate.features | Fiji | |
| EdgeTargetAnalyzer | Class | fiji.plugin.trackmate.features.edges | Fiji | |
| EdgeTimeLocationAnalyzer | Class | fiji.plugin.trackmate.features.edges | Fiji | |
| EdgeVelocityAnalyzer | Class | fiji.plugin.trackmate.features.edges | Fiji | |
| ExportableChartPanel | Class | fiji.plugin.trackmate.util | Fiji | |
| ExportStatsToIJAction | Class | fiji.plugin.trackmate.action | Fiji | |
| ExportStatsToIJAction .Factory | Class | fiji.plugin.trackmate.action.ExportStatsToIJAction | Fiji | |
| ExportTracksToXML | Class | fiji.plugin.trackmate.action | Fiji | |
| ExportTracksToXML .Factory | Class | fiji.plugin.trackmate.action.ExportTracksToXML | Fiji | |
| ExtractTrackStackAction | Class | fiji.plugin.trackmate.action | Fiji | |
| ExtractTrackStackAction .Factory | Class | fiji.plugin.trackmate.action.ExtractTrackStackAction | Fiji | |
| FastLAPTracker | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji | |
| FastLAPTrackerFactory | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji | |
| FeatureAnalyzer | Interface | fiji.plugin.trackmate.features | Fiji | |
| FeatureColorGenerator | Interface for color generator that can color objects based on a feature identified by a String. | Interface | fiji.plugin.trackmate.visualization | Fiji |
| FeatureFilter | A helper class to store a feature filter. | Class | fiji.plugin.trackmate.features | Fiji |
| FeatureModel | This class represents the part of the Model that is in charge of dealing with spot features and track features. | Class | fiji.plugin.trackmate | Fiji |
| FeaturePenaltyCostFunction | A cost function that tempers a square distance cost by difference in feature This cost is calculated as follow: | Class | fiji.plugin.trackmate.tracking.sparselap.costfunction | Fiji |
| FeaturePlotSelectionPanel | A simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum. | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
| FeaturePlotSelectionPanel | A simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum. | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
| FileOpenMenuEntry | Class | fiji.plugin.timelapsedisplay | Fiji | |
| FilterGuiPanel | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| FilterPanel | Class | fiji.plugin.trackmate.gui.panels | Fiji | |
| FlagNode | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji | |
| FromContinuousBranches | Class | fiji.plugin.trackmate.graph | Fiji | |
| Function1 | Interface for function that compute values from a single input and store it in Author:Jean-Yves Inevez | Interface | fiji.plugin.trackmate.graph | Fiji |
| Function2 | Interface for function that compute values from a two inputs and store it in Author:Jean-Yves Inevez | Interface | fiji.plugin.trackmate.graph | Fiji |
| Fusion | Class | spim.fiji.plugin.fusion | Fiji | |
| GapClosingCostFunction | Gap closing cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
| Generic_Resave_HDF5 | Class | spim.fiji.plugin.resave | Fiji | |
| Generic_Resave_HDF5 .Parameters | Class | spim.fiji.plugin.resave.Generic_Resave_HDF5 | Fiji | |
| GenericDialogAppender | Interface | spim.fiji.plugin.util | Fiji | |
| GenericLoadParseQueryXML | Interface for interactive parsing of spimdata XMLsAuthor:Stephan Preibisch (stephan. | Class | spim.fiji.plugin.queryXML | Fiji |
| Gradient | Class | fiji.plugin.volumeviewer | Fiji | |
| GrapherDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| GrapherPanel | Class | fiji.plugin.trackmate.gui | Fiji | |
| GraphFrame | Class | fiji.plugin.timelapsedisplay | Fiji | |
| GraphSegmentSplitter | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji | |
| GraphUtils | Class | fiji.plugin.trackmate.graph | Fiji | |
| Gui | Class | fiji.plugin.volumeviewer | Fiji | |
| GUIHelper | Class | spim.fiji.plugin.util | Fiji | |
| GuiUtils | Class | fiji.plugin.trackmate.gui | Fiji | |
| Histogram | Class | spim.fiji.plugin.thinout | Fiji | |
| HungarianAlgorithm | An implementation of the classic Hungarian algorithm for the assignment problem. | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
| HyperStackDisplayer | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji | |
| HyperStackDisplayerFactory | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji | |
| IcyTrackExporter | Class | fiji.plugin.trackmate.action | Fiji | |
| IcyTrackExporter .Factory | Class | fiji.plugin.trackmate.action.IcyTrackExporter | Fiji | |
| IcyTrackFormatWriter | Class | fiji.plugin.trackmate.io | Fiji | |
| IcyXmlReader | A 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 proper | Class | fiji.plugin.trackmate.io | Fiji |
| Image_Fusion | Class | spim.fiji.plugin | Fiji | |
| ImagePlusChooser | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| IndependentSpotFeatureAnalyzer | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| InfoPane | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| InitFilterDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| InitFilterPanel | Class | fiji.plugin.trackmate.gui.panels | Fiji | |
| Interactive_Remove_Detections | Class | spim.fiji.plugin | Fiji | |
| InteractiveProjections | Class | spim.fiji.plugin.removedetections | Fiji | |
| Interest_Point_Detection | Plugin 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 the | Class | spim.fiji.plugin | Fiji |
| Interest_Point_Registration | Class | spim.fiji.plugin | Fiji | |
| Interest_Point_Registration .RegistrationType | Class | spim.fiji.plugin.Interest_Point_Registration | Fiji | |
| InterestPointDetection | Class | spim.fiji.plugin.interestpointdetection | Fiji | |
| InterestPointRegistration | Class | spim.fiji.plugin.interestpointregistration | Fiji | |
| Interpolation | Class | fiji.plugin.volumeviewer | Fiji | |
| IOUtils | A collection of static utilities for the input/output of xml files. | Class | fiji.plugin.trackmate.io | Fiji |
| ISBIChallengeExporter | Class | fiji.plugin.trackmate.action | Fiji | |
| ISBIChallengeExporter .Factory | Class | fiji.plugin.trackmate.action.ISBIChallengeExporter | Fiji | |
| JaqamanLinker | Links two lists of objects based on the LAP framework described in Jaqaman et al. | Class | fiji.plugin.trackmate.tracking.sparselap.linker | Fiji |
| JaqamanLinkingCostMatrixCreator | A CostMatrixCreator that can generate a cost matrix from a list of sources, a list of targets and a CostFunction that can generate a | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji |
| JaqamanSegmentCostMatrixCreator | This class generates the top-left quadrant of the LAP segment linking cost matrix, following Jaqaman et al. | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji |
| JGraphXAdapter | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| JLabelLogger | Class | fiji.plugin.trackmate.util | Fiji | |
| JNumericTextField | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| JonkerVolgenantAlgorithm | Based on: Jonker, R. | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
| JPanelColorByFeatureGUI | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| JPanelFeaturePenalty | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| JPanelFeatureSelectionGui | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| JPanelTrackerSettingsMain | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji | |
| KalmanTracker | Class | fiji.plugin.trackmate.tracking.kalman | Fiji | |
| KalmanTrackerConfigPanel | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji | |
| KalmanTrackerFactory | Class | fiji.plugin.trackmate.tracking.kalman | Fiji | |
| LAPJV | tailored for sparse cost matrices. | Class | fiji.plugin.trackmate.tracking.sparselap.linker | Fiji |
| LAPTracker | This class tracks objects by formulating the problem as a Linear Assignment For reference, see: Jaqaman, K. | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji |
| LAPTrackerCostMatrixCreator | Contains the mutually shared fields and private functions used by the two cost matrix classes LinkingCostMatrixCreator and TrackSegmentCostMatrixCreator | Class | fiji.plugin.trackmate.tracking.oldlap.costmatrix | Fiji |
| LAPTrackerFactory | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji | |
| LAPTrackerSettingsPanel | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji | |
| LAPUtils | Class | fiji.plugin.trackmate.tracking | Fiji | |
| LinkingCostFunction | Linking cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
| LinkingCostMatrixCreator | Creates the cost matrix described in Figure 1b in the paper. | Class | fiji.plugin.trackmate.tracking.oldlap.costmatrix | Fiji |
| LinkNew3DViewerAction | Class | fiji.plugin.trackmate.action | Fiji | |
| LinkNew3DViewerAction .Factory | Class | fiji.plugin.trackmate.action.LinkNew3DViewerAction | Fiji | |
| ListChooserPanel | A panel to let the user choose what displayer he wants to use. | Class | fiji.plugin.trackmate.gui.panels | Fiji |
| LoadDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| LoadICYTrackPlugIn_ | Class | fiji.plugin.trackmate | Fiji | |
| LoadParseQueryXML | Class | spim.fiji.plugin.queryXML | Fiji | |
| LoadTrackMatePlugIn_ | Class | fiji.plugin.trackmate | Fiji | |
| LogDetector | Class | fiji.plugin.trackmate.detection | Fiji | |
| LogDetectorConfigurationPanel | Configuration panel for spot detectors based on LoG detector. | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji |
| LogDetectorFactory | Class | fiji.plugin.trackmate.detection | Fiji | |
| Logger | This class is used to log messages occurring during TrackMate execution. | Class | fiji.plugin.trackmate | Fiji |
| Logger .SlaveLogger | A logger that wraps a master logger and uses it to echo any received message. | Class | fiji.plugin.trackmate.Logger | Fiji |
| Logger .StringBuilderLogger | This Logger outputs to a StringBuilder given at construction. | Class | fiji.plugin.trackmate.Logger | Fiji |
| LogPanel | A panel using s JTextPane to log events. | Class | fiji.plugin.trackmate.gui | Fiji |
| LogPanelDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| LookupTable | Class | fiji.plugin.volumeviewer | Fiji | |
| ManualDetectorFactory | Class | fiji.plugin.trackmate.detection | Fiji | |
| ManualEdgeColorAnalyzer | Class | fiji.plugin.trackmate.features.manual | Fiji | |
| ManualEdgeColorGenerator | Class | fiji.plugin.trackmate.visualization | Fiji | |
| ManualSpotColorAnalyzerFactory | Class | fiji.plugin.trackmate.features.manual | Fiji | |
| ManualSpotColorGenerator | Class | fiji.plugin.trackmate.visualization | Fiji | |
| ManualTrackerFactory | Class | fiji.plugin.trackmate.tracking | Fiji | |
| ManualTrackingGUIController | Class | fiji.plugin.trackmate.gui | Fiji | |
| ManualTrackingPlugIn_ | Class | fiji.plugin.trackmate | Fiji | |
| Max_Project | Class | spim.fiji.plugin | Fiji | |
| MedianFilter2D | A simple median filter that operates on 1D, 2D or 3D images. | Class | fiji.plugin.trackmate.detection.util | Fiji |
| Merge_Cluster_Jobs | Class | spim.fiji.plugin | Fiji | |
| MergeClusterJobs | Class | spim.fiji.plugin.cluster | Fiji | |
| MergeFileAction | Class | fiji.plugin.trackmate.action | Fiji | |
| MergeFileAction .Factory | Class | fiji.plugin.trackmate.action.MergeFileAction | Fiji | |
| MergingCostFunction | Merging cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
| MinMaxAdjustable | Simple interface for objects whose effects depend on a minimal and maximal double value that can be adjusted manually or automatically. | Interface | fiji.plugin.trackmate.visualization | Fiji |
| Model | The model for the data managed by TrackMate trackmate. | Class | fiji.plugin.trackmate | Fiji |
| ModelChangeEvent | Class | fiji.plugin.trackmate | Fiji | |
| ModelChangeListener | An interface for listeners that will be notified when a ModelAuthor:Jean-Yves Tinevez | Interface | fiji.plugin.trackmate | Fiji | |
| ModelFeatureUpdater | A utility class that listens to the change occurring in a model, and updates its spot, edge and track features accordingly. | Class | fiji.plugin.trackmate.features | Fiji |
| ModelLink | Class | spim.fiji.plugin.apply | Fiji | |
| ModelTools | A collection of static utilities made to ease the manipulation of a TrackMate Model and SelectionModel. | Class | fiji.plugin.trackmate.util | Fiji |
| MouseListenerTimelapse | Class | fiji.plugin.timelapsedisplay | Fiji | |
| MouseListenerValue | Class | spim.fiji.plugin.thinout | Fiji | |
| Multi_View_Deconvolution | Class | fiji.plugin | Fiji | |
| Multi_View_Fusion | Class | fiji.plugin | Fiji | |
| MunkresKuhnAlgorithm | This implements optimal matching between two sets given a weight matrix (where the goal is to minimize the cumulative weight of the matches). | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
| mxScaledLabelShape | This is a shape that is made to display a cell in a way that suits for our spots objects. | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
| mxSideTextShape | A text shape that draws edge label along the edge line and parallel to it. | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
| MyMultiLineLabel | Class | spim.fiji.plugin.util | Fiji | |
| NearestNeighborFlagSearchOnKDTree | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji | |
| NearestNeighborTracker | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji | |
| NearestNeighborTrackerFactory | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji | |
| NearestNeighborTrackerSettingsPanel | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji | |
| OnRequestUpdater | This class extends Thread and is suited to call methods that are typically called often, but takes time to complete, such as display refreshing. | Class | fiji.plugin.trackmate.util | Fiji |
| OnRequestUpdater .Refreshable | Interface | fiji.plugin.trackmate.util.OnRequestUpdater | Fiji | |
| OpenImg | Class | spim.fiji.plugin.util | Fiji | |
| OutputFunction | Interface for functions that return a new object, computed from two input arguments. | Interface | fiji.plugin.trackmate.graph | Fiji |
| PerEdgeFeatureColorGenerator | Class | fiji.plugin.trackmate.visualization | Fiji | |
| PerTrackFeatureColorGenerator | A TrackColorGenerator that generate colors based on the whole trackAuthor:Jean-Yves Tinevez | Class | fiji.plugin.trackmate.visualization | Fiji |
| Pic | Class | fiji.plugin.volumeviewer | Fiji | |
| PlotNSpotsVsTimeAction | Class | fiji.plugin.trackmate.action | Fiji | |
| PlotNSpotsVsTimeAction .Factory | Class | fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction | Fiji | |
| PluginHelper | Class | spim.fiji.plugin.resave | Fiji | |
| PluginHelper .ChooseXmlFileListener | Class | spim.fiji.plugin.resave.PluginHelper | Fiji | |
| PlugInInstaller | Class | fiji | Fiji | |
| ProgressWriterIJ | Class | spim.fiji.plugin.resave | Fiji | |
| RadiusToEstimatedAction | Class | fiji.plugin.trackmate.action | Fiji | |
| RadiusToEstimatedAction .Factory | Class | fiji.plugin.trackmate.action.RadiusToEstimatedAction | Fiji | |
| RecalculateFeatureAction | Class | fiji.plugin.trackmate.action | Fiji | |
| RecalculateFeatureAction .Factory | Class | fiji.plugin.trackmate.action.RecalculateFeatureAction | Fiji | |
| RecursiveCumSum | Class | fiji.plugin.trackmate.graph | Fiji | |
| RegistrationStatistics | Class | fiji.plugin.timelapsedisplay | Fiji | |
| Resave_HDF5 | Class | spim.fiji.plugin.resave | Fiji | |
| Resave_TIFF | Class | spim.fiji.plugin.resave | Fiji | |
| Resave_TIFF .Parameters | Class | spim.fiji.plugin.resave.Resave_TIFF | Fiji | |
| ResetRadiusAction | Class | fiji.plugin.trackmate.action | Fiji | |
| ResetRadiusAction .Factory | Class | fiji.plugin.trackmate.action.ResetRadiusAction | Fiji | |
| ResetSpotTimeFeatureAction | Class | fiji.plugin.trackmate.action | Fiji | |
| ResetSpotTimeFeatureAction .Factory | Class | fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction | Fiji | |
| ResizableDoubleArray | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji | |
| SaveAction | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| SaveDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| SearchBar | Class | fiji.plugin.trackmate.visualization.trackscheme.utils | Fiji | |
| SelectionChangeEvent | An event that characterizes a change in the current selection. | Class | fiji.plugin.trackmate | Fiji |
| SelectionChangeListener | Interface | fiji.plugin.trackmate | Fiji | |
| SelectionModel | A component of Model that handles spot and edges selection. | Class | fiji.plugin.trackmate | Fiji |
| SemiAutoTracker | Class | fiji.plugin.trackmate.detection.semiauto | Fiji | |
| SetColorScaleDialog | Class | fiji.plugin.trackmate.gui.panels.components | Fiji | |
| Settings | This class is used to store user settings for the TrackMate trackmate. | Class | fiji.plugin.trackmate | Fiji |
| SimpleFastLAPTrackerFactory | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji | |
| SimpleLAPTrackerFactory | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji | |
| SimpleLAPTrackerSettingsPanel | A simplified configuration panel for the LAPTracker. | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji |
| SimpleSparseLAPTrackerFactory | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji | |
| SomeDialogDescriptor | An abstract class made for describing panels that generate a dialog, like save and load panels. | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
| SortedDepthFirstIterator | A depth-first iterator, that - when branching - chooses the next vertex according to a specified comparator. | Class | fiji.plugin.trackmate.graph | Fiji |
| SparseCostMatrix | A class to represent a sparse cost matrix. | Class | fiji.plugin.trackmate.tracking.sparselap.linker | Fiji |
| SparseLAPFrameToFrameTracker | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji | |
| SparseLAPSegmentTracker | This class tracks deals with the second step of tracking according to the LAP tracking framework formulated by Jaqaman, K. | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji |
| SparseLAPTracker | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji | |
| SparseLAPTrackerFactory | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji | |
| Specify_Calibration | Class | spim.fiji.plugin | Fiji | |
| Specify_Calibration .Cal | Class | spim.fiji.plugin.Specify_Calibration | Fiji | |
| SplittingCostFunction | Splitting cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
| Spot | A RealLocalizable implementation, used in TrackMate to represent a On top of being a RealLocalizable, it can store additional numerical | Class | fiji.plugin.trackmate | Fiji |
| SpotAnalyzer | Interface for a class that can compute feature on a collection of spots. | Interface | fiji.plugin.trackmate.features.spot | Fiji |
| SpotAnalyzerFactory | Interface for factories that can generate a SpotAnalyzer configured to operate on a specific frame of a model. | Interface | fiji.plugin.trackmate.features.spot | Fiji |
| SpotAnalyzerProvider | A provider for the spot analyzer factories provided in the GUI. | Class | fiji.plugin.trackmate.providers | Fiji |
| SpotCollection | A utility class that wrap the SortedMap we use to store the spots contained in each frame with a few utility methods. | Class | fiji.plugin.trackmate | Fiji |
| SpotColorGenerator | Class | fiji.plugin.trackmate.visualization | Fiji | |
| SpotColorGeneratorPerTrackFeature | Class | fiji.plugin.trackmate.visualization | Fiji | |
| SpotContrastAnalyzer | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotContrastAnalyzerFactory | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotContrastAndSNRAnalyzer | This FeatureAnalyzer computes both the Michelson contrast and the SNR for each spot: | Class | fiji.plugin.trackmate.features.spot | Fiji |
| SpotContrastAndSNRAnalyzerFactory | A factory for SpotContrastAndSNRAnalyzers. | Class | fiji.plugin.trackmate.features.spot | Fiji |
| SpotDetector | Interface for Spot detector classes, that are able to segment spots of a given estimated radius within a 2D or 3D image. | Interface | fiji.plugin.trackmate.detection | Fiji |
| SpotDetectorFactory | Mother interface for SpotDetector factories. | Interface | fiji.plugin.trackmate.detection | Fiji |
| SpotDisplayer3D | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji | |
| SpotDisplayer3DFactory | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji | |
| SpotEditTool | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji | |
| SpotEditToolConfigPanel | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji | |
| SpotFeatureCalculator | A class dedicated to centralizing the calculation of the numerical features of spots, through SpotAnalyzers. | Class | fiji.plugin.trackmate.features | Fiji |
| SpotFeatureGrapher | Class | fiji.plugin.trackmate.features | Fiji | |
| SpotFilterDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| SpotGroupNode | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji | |
| SpotIconGrabber | This class is used to take a snapshot of a Spot object (or collection) from its coordinates and an ImagePlus that contain the | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
| SpotImageUpdater | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| SpotIntensityAnalyzer | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotIntensityAnalyzerFactory | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotMorphologyAnalyzer | This SpotAnalyzer computes morphology features for the given spots. | Class | fiji.plugin.trackmate.features.spot | Fiji |
| SpotMorphologyAnalyzerFactory | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotNeighborhood | Class | fiji.plugin.trackmate.util | Fiji | |
| SpotNeighborhoodCursor | Class | fiji.plugin.trackmate.util | Fiji | |
| SpotOverlay | The overlay class in charge of drawing the spot images on the hyperstackAuthor:Jean-Yves Tinevez | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji | |
| SpotRadiusEstimator | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotRadiusEstimatorFactory | Class | fiji.plugin.trackmate.features.spot | Fiji | |
| SpotTracker | This interface should be used when creating algorithms for linking objects across multiple frames in time-lapse images. | Interface | fiji.plugin.trackmate.tracking | Fiji |
| SpotTrackerFactory | Interface | fiji.plugin.trackmate.tracking | Fiji | |
| SquareDistCostFunction | A cost function that returns cost equal to the square distance. | Class | fiji.plugin.trackmate.tracking.sparselap.costfunction | Fiji |
| SquareNeighborhood3x3 | Class | fiji.plugin.trackmate.detection.util | Fiji | |
| SquareNeighborhoodCursor3x3 | Class | fiji.plugin.trackmate.detection.util | Fiji | |
| StartDialogDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| StartDialogPanel | Class | fiji.plugin.trackmate.gui.panels | Fiji | |
| StringFormater | Interface for function that can build a human-readable string representation of an object | Interface | fiji.plugin.trackmate.graph | Fiji |
| TFalpha1 | Class | fiji.plugin.volumeviewer | Fiji | |
| TFalpha2 | Class | fiji.plugin.volumeviewer | Fiji | |
| TFalpha3 | Class | fiji.plugin.volumeviewer | Fiji | |
| TFalpha4 | Class | fiji.plugin.volumeviewer | Fiji | |
| TFrgb | Class | fiji.plugin.volumeviewer | Fiji | |
| TGMMImporter | Class | fiji.plugin.trackmate.io | Fiji | |
| ThinOut_Detections | Class | spim.fiji.plugin | Fiji | |
| TimeDirectedDepthFirstIterator | Class | fiji.plugin.trackmate.graph | Fiji | |
| TimeDirectedNeighborIndex | Class | fiji.plugin.trackmate.graph | Fiji | |
| TimeDirectedSortedDepthFirstIterator | Class | fiji.plugin.trackmate.graph | Fiji | |
| TimeLapseDisplay | Class | fiji.plugin.timelapsedisplay | Fiji | |
| TMUtils | Class | fiji.plugin.trackmate.util | Fiji | |
| TmXmlKeys | Contains the key string used for xml marshaling. | Class | fiji.plugin.trackmate.io | Fiji |
| TmXmlReader | Class | fiji.plugin.trackmate.io | Fiji | |
| TmXmlReader_v12 | A compatibility xml loader than can load TrackMate xml file saved for version prior to 2. | Class | fiji.plugin.trackmate.io | Fiji |
| TmXmlReader_v20 | Class | fiji.plugin.trackmate.io | Fiji | |
| TmXmlWriter | Class | fiji.plugin.trackmate.io | Fiji | |
| Toggle_Cluster_Options | Class | spim.fiji.plugin | Fiji | |
| TrackAnalyzer | Mother interface for the classes that can compute the feature of tracks. | Interface | fiji.plugin.trackmate.features.track | Fiji |
| TrackAnalyzerProvider | A provider for the track analyzers provided in the GUI. | Class | fiji.plugin.trackmate.providers | Fiji |
| TrackBranchAnalysis | Class | fiji.plugin.trackmate.action | Fiji | |
| TrackBranchAnalysis .Factory | Class | fiji.plugin.trackmate.action.TrackBranchAnalysis | Fiji | |
| TrackBranchingAnalyzer | Class | fiji.plugin.trackmate.features.track | Fiji | |
| TrackColorGenerator | Interface for functions that can generate track colors, with a different color for each vertex and edge. | Interface | fiji.plugin.trackmate.visualization | Fiji |
| TrackDisplayNode | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji | |
| TrackDurationAnalyzer | Class | fiji.plugin.trackmate.features.track | Fiji | |
| TrackerChoiceDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| TrackerConfigurationDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| TrackerKeys | Class | fiji.plugin.trackmate.tracking | Fiji | |
| TrackerProvider | Class | fiji.plugin.trackmate.providers | Fiji | |
| TrackFeatureCalculator | A class dedicated to centralizing the calculation of the numerical features of tracks, through TrackAnalyzers. | Class | fiji.plugin.trackmate.features | Fiji |
| TrackFeatureGrapher | Class | fiji.plugin.trackmate.features | Fiji | |
| TrackFilterDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| TrackIndexAnalyzer | Class | fiji.plugin.trackmate.features.track | Fiji | |
| TrackingDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| TrackLocationAnalyzer | Class | fiji.plugin.trackmate.features.track | Fiji | |
| TrackMate | The TrackMate_ class runs on the currently active time-lapse image (2D or 3D) and both identifies and tracks bright spots over time. | Class | fiji.plugin.trackmate | Fiji |
| TrackMateAction | This interface describe a track mate action, that can be run on a TrackMate object to change its content or properties. | Interface | fiji.plugin.trackmate.action | Fiji |
| TrackMateActionFactory | Interface | fiji.plugin.trackmate.action | Fiji | |
| TrackMateBatch | Class | fiji.plugin.trackmate | Fiji | |
| TrackMateGUIController | Class | fiji.plugin.trackmate.gui | Fiji | |
| TrackMateGUIModel | Class | fiji.plugin.trackmate.gui | Fiji | |
| TrackMateModelView | Interface | fiji.plugin.trackmate.visualization | Fiji | |
| TrackMateModule | Interface for TrackMate modules. | Interface | fiji.plugin.trackmate | Fiji |
| TrackMatePlugIn_ | Class | fiji.plugin.trackmate | Fiji | |
| TrackMateWizard | Class | fiji.plugin.trackmate.gui | Fiji | |
| TrackModel | A component of Model specialized for tracksAuthor:Jean-Yves Tinevez | Class | fiji.plugin.trackmate | Fiji |
| TrackNavigator | Class | fiji.plugin.trackmate.util | Fiji | |
| TrackOverlay | The overlay class in charge of drawing the tracks on the hyperstack window. | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji |
| TrackScheme | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeActions | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeActions .EditAction | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji | |
| TrackSchemeActions .EndAction | Centers the view to the last cell in selection, sorted by frame number. | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji |
| TrackSchemeActions .HomeAction | Centers the view to the first cell in selection. | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji |
| TrackSchemeActions .ResetZoomAction | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji | |
| TrackSchemeFactory | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeFrame | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeGraphComponent | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeGraphLayout | This mxGraphLayout arranges cells on a graph in lanes corresponding to tracks. | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
| TrackSchemeKeyboardHandler | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemePopupMenu | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeStylist | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeSvgCanvas | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSchemeToolbar | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji | |
| TrackSegmentCostMatrixCreator | Creates the cost matrix roughly described in Figure 1c in the paper: Jaqaman, K. | Class | fiji.plugin.trackmate.tracking.oldlap.costmatrix | Fiji |
| TrackSpeedStatisticsAnalyzer | Class | fiji.plugin.trackmate.features.track | Fiji | |
| TrackSpotQualityFeatureAnalyzer | Class | fiji.plugin.trackmate.features.track | Fiji | |
| TrimNotVisibleAction | Class | fiji.plugin.trackmate.action | Fiji | |
| TrimNotVisibleAction .Factory | Class | fiji.plugin.trackmate.action.TrimNotVisibleAction | Fiji | |
| Version | A utility class to deal with version numbers. | Class | fiji.plugin.trackmate.util | Fiji |
| ViewChoiceDescriptor | Class | fiji.plugin.trackmate.gui.descriptors | Fiji | |
| ViewFactory | Interface | fiji.plugin.trackmate.visualization | Fiji | |
| ViewProvider | Class | fiji.plugin.trackmate.providers | Fiji | |
| ViewUtils | A collection of static utilities related to TrackMateModelViews. | Class | fiji.plugin.trackmate.visualization | Fiji |
| Visualize_Detections | Class | spim.fiji.plugin | Fiji | |
| Visualize_Detections .Params | Class | spim.fiji.plugin.Visualize_Detections | Fiji | |
| Volume | Class | fiji.plugin.volumeviewer | Fiji | |
| Volume_Viewer | Class | fiji.plugin.volumeviewer | Fiji | |
| WizardPanelDescriptor | A 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. | Interface | fiji.plugin.trackmate.gui.descriptors | Fiji |
| WrapLayout | FlowLayout subclass that fully supports wrapping of components. | Class | fiji.plugin.trackmate.gui.panels | Fiji |
| XYEdgeRenderer | Class | fiji.plugin.trackmate.util | Fiji | |
| XYEdgeSeries | Class | fiji.plugin.trackmate.util | Fiji | |
| XYEdgeSeriesCollection | Class | fiji.plugin.trackmate.util | Fiji | |