Name | Description | Type | Package | Framework |
AbstractFeatureGrapher | | Class | fiji.plugin.trackmate.features | Fiji |
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AbstractProvider | | Class | fiji.plugin.trackmate.providers | Fiji |
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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 |
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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 |
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AbstractTMAction | | Class | fiji.plugin.trackmate.action | Fiji |
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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 |
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ActionChooserDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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ActionChooserPanel | | Class | fiji.plugin.trackmate.gui.panels | Fiji |
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ActionListenablePanel | | Class | fiji.plugin.trackmate.gui.panels | Fiji |
|
ActionProvider | | Class | fiji.plugin.trackmate.providers | Fiji |
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AlphanumComparator | The Alphanum Algorithm is an improved sorting algorithm for strings containing numbers. | Class | fiji.plugin.trackmate.util | Fiji |
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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 |
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AssignmentProblem | An implementation of this: http://en. | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
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BasicDetectorConfigurationPanel | | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji |
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Bead_Registration | | Class | fiji.plugin | Fiji |
|
BigDataViewerTransformationWindow | | Class | spim.fiji.plugin.apply | Fiji |
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BlockLogDetector | | Class | fiji.plugin.trackmate.detection | Fiji |
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BlockLogDetectorConfigurationPanel | | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji |
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BlockLogDetectorFactory | | Class | fiji.plugin.trackmate.detection | Fiji |
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CaptureOverlayAction | | Class | fiji.plugin.trackmate.action | Fiji |
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CaptureOverlayAction .Factory | | Class | fiji.plugin.trackmate.action.CaptureOverlayAction | Fiji |
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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 |
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ConvexBranchesDecomposition | A class that can decompose the tracks of a Model in convex branches. | Class | fiji.plugin.trackmate.graph | Fiji |
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ConvexBranchesDecomposition .TrackBranchDecomposition | | Class | fiji.plugin.trackmate.graph.ConvexBranchesDecomposition | Fiji |
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CopyOverlayAction | | Class | fiji.plugin.trackmate.action | Fiji |
|
CopyOverlayAction .Factory | | Class | fiji.plugin.trackmate.action.CopyOverlayAction | Fiji |
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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 |
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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 |
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CostMatrixCreator | Interface for function that can generate a SparseCostMatrix from assignment candidates. | Interface | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji |
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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 |
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Data_Explorer | | Class | spim.fiji.plugin | Fiji |
|
Debug | | Class | fiji.plugin.trackmate | Fiji |
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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 |
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DefaultFileFilter | Filter for use in a JFileChooser. | Class | fiji.plugin.trackmate.util | Fiji |
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DefaultFileFilter .EditorFileFilter | Utility file filter to accept editor files, namely . | Class | fiji.plugin.trackmate.util.DefaultFileFilter | Fiji |
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DefaultFileFilter .ImageFileFilter | Utility file filter to accept all image formats supported by image io. | Class | fiji.plugin.trackmate.util.DefaultFileFilter | Fiji |
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Define_Bounding_Box | | Class | spim.fiji.plugin | Fiji |
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Define_Multi_View_Dataset | | Class | spim.fiji.plugin | Fiji |
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DetectionDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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DetectionUtils | | Class | fiji.plugin.trackmate.detection | Fiji |
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DetectorChoiceDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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DetectorConfigurationDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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DetectorKeys | | Class | fiji.plugin.trackmate.detection | Fiji |
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DetectorProvider | | Class | fiji.plugin.trackmate.providers | Fiji |
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DifferenceOf | | Class | spim.fiji.plugin.interestpointdetection | Fiji |
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DifferenceOfGaussian | | Class | spim.fiji.plugin.interestpointdetection | Fiji |
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DifferenceOfMean | | Class | spim.fiji.plugin.interestpointdetection | Fiji |
|
Dimension | | Class | fiji.plugin.trackmate | Fiji |
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Display_View | | Class | spim.fiji.plugin | Fiji |
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DisplaySettingsEvent | An event object fired when the user changes one of the display settings through this GUI panel. | Class | fiji.plugin.trackmate.gui | Fiji |
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DisplaySettingsListener | Interface for classes that listen to display settings changes on a GUI. | Interface | fiji.plugin.trackmate.gui | Fiji |
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DogDetector | | Class | fiji.plugin.trackmate.detection | Fiji |
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DogDetectorConfigurationPanel | | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji |
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DogDetectorFactory | | Class | fiji.plugin.trackmate.detection | Fiji |
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DownsampleLogDetector | | Class | fiji.plugin.trackmate.detection | Fiji |
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DownSampleLogDetectorConfigurationPanel | | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji |
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DownsampleLogDetectorFactory | | Class | fiji.plugin.trackmate.detection | Fiji |
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DummySpotColorGenerator | A dummy spot color generator that always return the default color. | Class | fiji.plugin.trackmate.visualization | Fiji |
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DummyTrackColorGenerator | A dummy track color generator that always return the default color. | Class | fiji.plugin.trackmate.visualization | Fiji |
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Duplicate_Transformation | | Class | spim.fiji.plugin | Fiji |
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EdgeAnalyzer | Interface for analyzers that can compute scalar numerical features for an edge of a TrackMate model. | Interface | fiji.plugin.trackmate.features.edges | Fiji |
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EdgeAnalyzerProvider | A provider for the edge analyzers provided in the GUI. | Class | fiji.plugin.trackmate.providers | Fiji |
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EdgeFeatureCalculator | A class dedicated to centralizing the calculation of the numerical features of spots, through EdgeAnalyzers. | Class | fiji.plugin.trackmate.features | Fiji |
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EdgeFeatureGrapher | | Class | fiji.plugin.trackmate.features | Fiji |
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EdgeTargetAnalyzer | | Class | fiji.plugin.trackmate.features.edges | Fiji |
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EdgeTimeLocationAnalyzer | | Class | fiji.plugin.trackmate.features.edges | Fiji |
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EdgeVelocityAnalyzer | | Class | fiji.plugin.trackmate.features.edges | Fiji |
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ExportableChartPanel | | Class | fiji.plugin.trackmate.util | Fiji |
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ExportStatsToIJAction | | Class | fiji.plugin.trackmate.action | Fiji |
|
ExportStatsToIJAction .Factory | | Class | fiji.plugin.trackmate.action.ExportStatsToIJAction | Fiji |
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ExportTracksToXML | | Class | fiji.plugin.trackmate.action | Fiji |
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ExportTracksToXML .Factory | | Class | fiji.plugin.trackmate.action.ExportTracksToXML | Fiji |
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ExtractTrackStackAction | | Class | fiji.plugin.trackmate.action | Fiji |
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ExtractTrackStackAction .Factory | | Class | fiji.plugin.trackmate.action.ExtractTrackStackAction | Fiji |
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FastLAPTracker | | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji |
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FastLAPTrackerFactory | | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji |
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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 |
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FeatureFilter | A helper class to store a feature filter. | Class | fiji.plugin.trackmate.features | Fiji |
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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 |
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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 |
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Generic_Resave_HDF5 | | Class | spim.fiji.plugin.resave | Fiji |
|
Generic_Resave_HDF5 .Parameters | | Class | spim.fiji.plugin.resave.Generic_Resave_HDF5 | Fiji |
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GenericDialogAppender | | Interface | spim.fiji.plugin.util | Fiji |
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GenericLoadParseQueryXML | Interface for interactive parsing of spimdata XMLsAuthor:Stephan Preibisch (stephan. | Class | spim.fiji.plugin.queryXML | Fiji |
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Gradient | | Class | fiji.plugin.volumeviewer | Fiji |
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GrapherDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
|
GrapherPanel | | Class | fiji.plugin.trackmate.gui | Fiji |
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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 |
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GuiUtils | | Class | fiji.plugin.trackmate.gui | Fiji |
|
Histogram | | Class | spim.fiji.plugin.thinout | Fiji |
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HungarianAlgorithm | An implementation of the classic Hungarian algorithm for the assignment problem. | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
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HyperStackDisplayer | | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji |
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HyperStackDisplayerFactory | | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji |
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IcyTrackExporter | | Class | fiji.plugin.trackmate.action | Fiji |
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IcyTrackExporter .Factory | | Class | fiji.plugin.trackmate.action.IcyTrackExporter | Fiji |
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IcyTrackFormatWriter | | Class | fiji.plugin.trackmate.io | Fiji |
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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 |
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Image_Fusion | | Class | spim.fiji.plugin | Fiji |
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ImagePlusChooser | | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
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IndependentSpotFeatureAnalyzer | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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InfoPane | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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InitFilterDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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InitFilterPanel | | Class | fiji.plugin.trackmate.gui.panels | Fiji |
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Interactive_Remove_Detections | | Class | spim.fiji.plugin | Fiji |
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InteractiveProjections | | Class | spim.fiji.plugin.removedetections | Fiji |
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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 |
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Interest_Point_Registration | | Class | spim.fiji.plugin | Fiji |
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Interest_Point_Registration .RegistrationType | | Class | spim.fiji.plugin.Interest_Point_Registration | Fiji |
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InterestPointDetection | | Class | spim.fiji.plugin.interestpointdetection | Fiji |
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InterestPointRegistration | | Class | spim.fiji.plugin.interestpointregistration | Fiji |
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Interpolation | | Class | fiji.plugin.volumeviewer | Fiji |
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IOUtils | A collection of static utilities for the input/output of xml files. | Class | fiji.plugin.trackmate.io | Fiji |
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ISBIChallengeExporter | | Class | fiji.plugin.trackmate.action | Fiji |
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ISBIChallengeExporter .Factory | | Class | fiji.plugin.trackmate.action.ISBIChallengeExporter | Fiji |
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JaqamanLinker | Links two lists of objects based on the LAP framework described in Jaqaman et al. | Class | fiji.plugin.trackmate.tracking.sparselap.linker | Fiji |
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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 |
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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 |
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JGraphXAdapter | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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JLabelLogger | | Class | fiji.plugin.trackmate.util | Fiji |
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JNumericTextField | | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
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JonkerVolgenantAlgorithm | Based on: Jonker, R. | Class | fiji.plugin.trackmate.tracking.oldlap.hungarian | Fiji |
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JPanelColorByFeatureGUI | | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
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JPanelFeaturePenalty | | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
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JPanelFeatureSelectionGui | | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
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JPanelTrackerSettingsMain | | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji |
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KalmanTracker | | Class | fiji.plugin.trackmate.tracking.kalman | Fiji |
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KalmanTrackerConfigPanel | | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji |
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KalmanTrackerFactory | | Class | fiji.plugin.trackmate.tracking.kalman | Fiji |
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LAPJV | tailored for sparse cost matrices. | Class | fiji.plugin.trackmate.tracking.sparselap.linker | Fiji |
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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 |
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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 |
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LAPTrackerFactory | | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji |
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LAPTrackerSettingsPanel | | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji |
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LAPUtils | | Class | fiji.plugin.trackmate.tracking | Fiji |
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LinkingCostFunction | Linking cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
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LinkingCostMatrixCreator | Creates the cost matrix described in Figure 1b in the paper. | Class | fiji.plugin.trackmate.tracking.oldlap.costmatrix | Fiji |
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LinkNew3DViewerAction | | Class | fiji.plugin.trackmate.action | Fiji |
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LinkNew3DViewerAction .Factory | | Class | fiji.plugin.trackmate.action.LinkNew3DViewerAction | Fiji |
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ListChooserPanel | A panel to let the user choose what displayer he wants to use. | Class | fiji.plugin.trackmate.gui.panels | Fiji |
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LoadDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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LoadICYTrackPlugIn_ | | Class | fiji.plugin.trackmate | Fiji |
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LoadParseQueryXML | | Class | spim.fiji.plugin.queryXML | Fiji |
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LoadTrackMatePlugIn_ | | Class | fiji.plugin.trackmate | Fiji |
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LogDetector | | Class | fiji.plugin.trackmate.detection | Fiji |
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LogDetectorConfigurationPanel | Configuration panel for spot detectors based on LoG detector. | Class | fiji.plugin.trackmate.gui.panels.detector | Fiji |
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LogDetectorFactory | | Class | fiji.plugin.trackmate.detection | Fiji |
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Logger | This class is used to log messages occurring during TrackMate execution. | Class | fiji.plugin.trackmate | Fiji |
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Logger .SlaveLogger | A logger that wraps a master logger and uses it to echo any received message. | Class | fiji.plugin.trackmate.Logger | Fiji |
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Logger .StringBuilderLogger | This Logger outputs to a StringBuilder given at construction. | Class | fiji.plugin.trackmate.Logger | Fiji |
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LogPanel | A panel using s JTextPane to log events. | Class | fiji.plugin.trackmate.gui | Fiji |
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LogPanelDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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LookupTable | | Class | fiji.plugin.volumeviewer | Fiji |
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ManualDetectorFactory | | Class | fiji.plugin.trackmate.detection | Fiji |
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ManualEdgeColorAnalyzer | | Class | fiji.plugin.trackmate.features.manual | Fiji |
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ManualEdgeColorGenerator | | Class | fiji.plugin.trackmate.visualization | Fiji |
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ManualSpotColorAnalyzerFactory | | Class | fiji.plugin.trackmate.features.manual | Fiji |
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ManualSpotColorGenerator | | Class | fiji.plugin.trackmate.visualization | Fiji |
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ManualTrackerFactory | | Class | fiji.plugin.trackmate.tracking | Fiji |
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ManualTrackingGUIController | | Class | fiji.plugin.trackmate.gui | Fiji |
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ManualTrackingPlugIn_ | | Class | fiji.plugin.trackmate | Fiji |
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Max_Project | | Class | spim.fiji.plugin | Fiji |
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MedianFilter2D | A simple median filter that operates on 1D, 2D or 3D images. | Class | fiji.plugin.trackmate.detection.util | Fiji |
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Merge_Cluster_Jobs | | Class | spim.fiji.plugin | Fiji |
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MergeClusterJobs | | Class | spim.fiji.plugin.cluster | Fiji |
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MergeFileAction | | Class | fiji.plugin.trackmate.action | Fiji |
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MergeFileAction .Factory | | Class | fiji.plugin.trackmate.action.MergeFileAction | Fiji |
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MergingCostFunction | Merging cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
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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 |
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Model | The model for the data managed by TrackMate trackmate. | Class | fiji.plugin.trackmate | Fiji |
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ModelChangeEvent | | Class | fiji.plugin.trackmate | Fiji |
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ModelChangeListener | An interface for listeners that will be notified when a ModelAuthor:Jean-Yves Tinevez Interface | fiji.plugin.trackmate | Fiji | |
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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 |
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ModelLink | | Class | spim.fiji.plugin.apply | Fiji |
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ModelTools | A collection of static utilities made to ease the manipulation of a TrackMate Model and SelectionModel. | Class | fiji.plugin.trackmate.util | Fiji |
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MouseListenerTimelapse | | Class | fiji.plugin.timelapsedisplay | Fiji |
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MouseListenerValue | | Class | spim.fiji.plugin.thinout | Fiji |
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Multi_View_Deconvolution | | Class | fiji.plugin | Fiji |
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Multi_View_Fusion | | Class | fiji.plugin | Fiji |
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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 |
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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 |
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mxSideTextShape | A text shape that draws edge label along the edge line and parallel to it. | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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MyMultiLineLabel | | Class | spim.fiji.plugin.util | Fiji |
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NearestNeighborFlagSearchOnKDTree | | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji |
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NearestNeighborTracker | | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji |
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NearestNeighborTrackerFactory | | Class | fiji.plugin.trackmate.tracking.kdtree | Fiji |
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NearestNeighborTrackerSettingsPanel | | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji |
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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 |
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OnRequestUpdater .Refreshable | | Interface | fiji.plugin.trackmate.util.OnRequestUpdater | Fiji |
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OpenImg | | Class | spim.fiji.plugin.util | Fiji |
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OutputFunction | Interface for functions that return a new object, computed from two input arguments. | Interface | fiji.plugin.trackmate.graph | Fiji |
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PerEdgeFeatureColorGenerator | | Class | fiji.plugin.trackmate.visualization | Fiji |
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PerTrackFeatureColorGenerator | A TrackColorGenerator that generate colors based on the whole trackAuthor:Jean-Yves Tinevez | Class | fiji.plugin.trackmate.visualization | Fiji |
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Pic | | Class | fiji.plugin.volumeviewer | Fiji |
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PlotNSpotsVsTimeAction | | Class | fiji.plugin.trackmate.action | Fiji |
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PlotNSpotsVsTimeAction .Factory | | Class | fiji.plugin.trackmate.action.PlotNSpotsVsTimeAction | Fiji |
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PluginHelper | | Class | spim.fiji.plugin.resave | Fiji |
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PluginHelper .ChooseXmlFileListener | | Class | spim.fiji.plugin.resave.PluginHelper | Fiji |
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PlugInInstaller | | Class | fiji | Fiji |
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ProgressWriterIJ | | Class | spim.fiji.plugin.resave | Fiji |
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RadiusToEstimatedAction | | Class | fiji.plugin.trackmate.action | Fiji |
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RadiusToEstimatedAction .Factory | | Class | fiji.plugin.trackmate.action.RadiusToEstimatedAction | Fiji |
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RecalculateFeatureAction | | Class | fiji.plugin.trackmate.action | Fiji |
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RecalculateFeatureAction .Factory | | Class | fiji.plugin.trackmate.action.RecalculateFeatureAction | Fiji |
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RecursiveCumSum | | Class | fiji.plugin.trackmate.graph | Fiji |
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RegistrationStatistics | | Class | fiji.plugin.timelapsedisplay | Fiji |
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Resave_HDF5 | | Class | spim.fiji.plugin.resave | Fiji |
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Resave_TIFF | | Class | spim.fiji.plugin.resave | Fiji |
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Resave_TIFF .Parameters | | Class | spim.fiji.plugin.resave.Resave_TIFF | Fiji |
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ResetRadiusAction | | Class | fiji.plugin.trackmate.action | Fiji |
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ResetRadiusAction .Factory | | Class | fiji.plugin.trackmate.action.ResetRadiusAction | Fiji |
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ResetSpotTimeFeatureAction | | Class | fiji.plugin.trackmate.action | Fiji |
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ResetSpotTimeFeatureAction .Factory | | Class | fiji.plugin.trackmate.action.ResetSpotTimeFeatureAction | Fiji |
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ResizableDoubleArray | | Class | fiji.plugin.trackmate.tracking.sparselap.costmatrix | Fiji |
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SaveAction | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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SaveDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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SearchBar | | Class | fiji.plugin.trackmate.visualization.trackscheme.utils | Fiji |
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SelectionChangeEvent | An event that characterizes a change in the current selection. | Class | fiji.plugin.trackmate | Fiji |
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SelectionChangeListener | | Interface | fiji.plugin.trackmate | Fiji |
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SelectionModel | A component of Model that handles spot and edges selection. | Class | fiji.plugin.trackmate | Fiji |
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SemiAutoTracker | | Class | fiji.plugin.trackmate.detection.semiauto | Fiji |
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SetColorScaleDialog | | Class | fiji.plugin.trackmate.gui.panels.components | Fiji |
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Settings | This class is used to store user settings for the TrackMate trackmate. | Class | fiji.plugin.trackmate | Fiji |
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SimpleFastLAPTrackerFactory | | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji |
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SimpleLAPTrackerFactory | | Class | fiji.plugin.trackmate.tracking.oldlap | Fiji |
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SimpleLAPTrackerSettingsPanel | A simplified configuration panel for the LAPTracker. | Class | fiji.plugin.trackmate.gui.panels.tracker | Fiji |
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SimpleSparseLAPTrackerFactory | | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji |
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SomeDialogDescriptor | An abstract class made for describing panels that generate a dialog, like save and load panels. | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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SortedDepthFirstIterator | A depth-first iterator, that - when branching - chooses the next vertex according to a specified comparator. | Class | fiji.plugin.trackmate.graph | Fiji |
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SparseCostMatrix | A class to represent a sparse cost matrix. | Class | fiji.plugin.trackmate.tracking.sparselap.linker | Fiji |
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SparseLAPFrameToFrameTracker | | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji |
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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 |
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SparseLAPTracker | | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji |
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SparseLAPTrackerFactory | | Class | fiji.plugin.trackmate.tracking.sparselap | Fiji |
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Specify_Calibration | | Class | spim.fiji.plugin | Fiji |
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Specify_Calibration .Cal | | Class | spim.fiji.plugin.Specify_Calibration | Fiji |
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SplittingCostFunction | Splitting cost function used with LAPTracker. | Class | fiji.plugin.trackmate.tracking.oldlap.costfunction | Fiji |
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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 |
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SpotAnalyzer | Interface for a class that can compute feature on a collection of spots. | Interface | fiji.plugin.trackmate.features.spot | Fiji |
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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 |
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SpotAnalyzerProvider | A provider for the spot analyzer factories provided in the GUI. | Class | fiji.plugin.trackmate.providers | Fiji |
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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 |
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SpotColorGenerator | | Class | fiji.plugin.trackmate.visualization | Fiji |
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SpotColorGeneratorPerTrackFeature | | Class | fiji.plugin.trackmate.visualization | Fiji |
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SpotContrastAnalyzer | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotContrastAnalyzerFactory | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotContrastAndSNRAnalyzer | This FeatureAnalyzer computes both the Michelson contrast and the SNR for each spot: | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotContrastAndSNRAnalyzerFactory | A factory for SpotContrastAndSNRAnalyzers. | Class | fiji.plugin.trackmate.features.spot | Fiji |
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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 |
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SpotDetectorFactory | Mother interface for SpotDetector factories. | Interface | fiji.plugin.trackmate.detection | Fiji |
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SpotDisplayer3D | | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji |
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SpotDisplayer3DFactory | | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji |
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SpotEditTool | | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji |
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SpotEditToolConfigPanel | | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji |
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SpotFeatureCalculator | A class dedicated to centralizing the calculation of the numerical features of spots, through SpotAnalyzers. | Class | fiji.plugin.trackmate.features | Fiji |
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SpotFeatureGrapher | | Class | fiji.plugin.trackmate.features | Fiji |
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SpotFilterDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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SpotGroupNode | | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji |
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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 |
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SpotImageUpdater | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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SpotIntensityAnalyzer | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotIntensityAnalyzerFactory | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotMorphologyAnalyzer | This SpotAnalyzer computes morphology features for the given spots. | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotMorphologyAnalyzerFactory | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotNeighborhood | | Class | fiji.plugin.trackmate.util | Fiji |
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SpotNeighborhoodCursor | | Class | fiji.plugin.trackmate.util | Fiji |
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SpotOverlay | The overlay class in charge of drawing the spot images on the hyperstackAuthor:Jean-Yves Tinevez Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji | |
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SpotRadiusEstimator | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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SpotRadiusEstimatorFactory | | Class | fiji.plugin.trackmate.features.spot | Fiji |
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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 |
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SpotTrackerFactory | | Interface | fiji.plugin.trackmate.tracking | Fiji |
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SquareDistCostFunction | A cost function that returns cost equal to the square distance. | Class | fiji.plugin.trackmate.tracking.sparselap.costfunction | Fiji |
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SquareNeighborhood3x3 | | Class | fiji.plugin.trackmate.detection.util | Fiji |
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SquareNeighborhoodCursor3x3 | | Class | fiji.plugin.trackmate.detection.util | Fiji |
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StartDialogDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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StartDialogPanel | | Class | fiji.plugin.trackmate.gui.panels | Fiji |
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StringFormater | Interface for function that can build a human-readable string representation of an object | Interface | fiji.plugin.trackmate.graph | Fiji |
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TFalpha1 | | Class | fiji.plugin.volumeviewer | Fiji |
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TFalpha2 | | Class | fiji.plugin.volumeviewer | Fiji |
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TFalpha3 | | Class | fiji.plugin.volumeviewer | Fiji |
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TFalpha4 | | Class | fiji.plugin.volumeviewer | Fiji |
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TFrgb | | Class | fiji.plugin.volumeviewer | Fiji |
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TGMMImporter | | Class | fiji.plugin.trackmate.io | Fiji |
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ThinOut_Detections | | Class | spim.fiji.plugin | Fiji |
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TimeDirectedDepthFirstIterator | | Class | fiji.plugin.trackmate.graph | Fiji |
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TimeDirectedNeighborIndex | | Class | fiji.plugin.trackmate.graph | Fiji |
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TimeDirectedSortedDepthFirstIterator | | Class | fiji.plugin.trackmate.graph | Fiji |
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TimeLapseDisplay | | Class | fiji.plugin.timelapsedisplay | Fiji |
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TMUtils | | Class | fiji.plugin.trackmate.util | Fiji |
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TmXmlKeys | Contains the key string used for xml marshaling. | Class | fiji.plugin.trackmate.io | Fiji |
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TmXmlReader | | Class | fiji.plugin.trackmate.io | Fiji |
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TmXmlReader_v12 | A compatibility xml loader than can load TrackMate xml file saved for version prior to 2. | Class | fiji.plugin.trackmate.io | Fiji |
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TmXmlReader_v20 | | Class | fiji.plugin.trackmate.io | Fiji |
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TmXmlWriter | | Class | fiji.plugin.trackmate.io | Fiji |
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Toggle_Cluster_Options | | Class | spim.fiji.plugin | Fiji |
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TrackAnalyzer | Mother interface for the classes that can compute the feature of tracks. | Interface | fiji.plugin.trackmate.features.track | Fiji |
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TrackAnalyzerProvider | A provider for the track analyzers provided in the GUI. | Class | fiji.plugin.trackmate.providers | Fiji |
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TrackBranchAnalysis | | Class | fiji.plugin.trackmate.action | Fiji |
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TrackBranchAnalysis .Factory | | Class | fiji.plugin.trackmate.action.TrackBranchAnalysis | Fiji |
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TrackBranchingAnalyzer | | Class | fiji.plugin.trackmate.features.track | Fiji |
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TrackColorGenerator | Interface for functions that can generate track colors, with a different color for each vertex and edge. | Interface | fiji.plugin.trackmate.visualization | Fiji |
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TrackDisplayNode | | Class | fiji.plugin.trackmate.visualization.threedviewer | Fiji |
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TrackDurationAnalyzer | | Class | fiji.plugin.trackmate.features.track | Fiji |
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TrackerChoiceDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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TrackerConfigurationDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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TrackerKeys | | Class | fiji.plugin.trackmate.tracking | Fiji |
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TrackerProvider | | Class | fiji.plugin.trackmate.providers | Fiji |
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TrackFeatureCalculator | A class dedicated to centralizing the calculation of the numerical features of tracks, through TrackAnalyzers. | Class | fiji.plugin.trackmate.features | Fiji |
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TrackFeatureGrapher | | Class | fiji.plugin.trackmate.features | Fiji |
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TrackFilterDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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TrackIndexAnalyzer | | Class | fiji.plugin.trackmate.features.track | Fiji |
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TrackingDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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TrackLocationAnalyzer | | Class | fiji.plugin.trackmate.features.track | Fiji |
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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 |
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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 |
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TrackMateActionFactory | | Interface | fiji.plugin.trackmate.action | Fiji |
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TrackMateBatch | | Class | fiji.plugin.trackmate | Fiji |
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TrackMateGUIController | | Class | fiji.plugin.trackmate.gui | Fiji |
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TrackMateGUIModel | | Class | fiji.plugin.trackmate.gui | Fiji |
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TrackMateModelView | | Interface | fiji.plugin.trackmate.visualization | Fiji |
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TrackMateModule | Interface for TrackMate modules. | Interface | fiji.plugin.trackmate | Fiji |
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TrackMatePlugIn_ | | Class | fiji.plugin.trackmate | Fiji |
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TrackMateWizard | | Class | fiji.plugin.trackmate.gui | Fiji |
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TrackModel | A component of Model specialized for tracksAuthor:Jean-Yves Tinevez | Class | fiji.plugin.trackmate | Fiji |
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TrackNavigator | | Class | fiji.plugin.trackmate.util | Fiji |
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TrackOverlay | The overlay class in charge of drawing the tracks on the hyperstack window. | Class | fiji.plugin.trackmate.visualization.hyperstack | Fiji |
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TrackScheme | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeActions | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeActions .EditAction | | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji |
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TrackSchemeActions .EndAction | Centers the view to the last cell in selection, sorted by frame number. | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji |
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TrackSchemeActions .HomeAction | Centers the view to the first cell in selection. | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji |
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TrackSchemeActions .ResetZoomAction | | Class | fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions | Fiji |
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TrackSchemeFactory | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeFrame | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeGraphComponent | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeGraphLayout | This mxGraphLayout arranges cells on a graph in lanes corresponding to tracks. | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeKeyboardHandler | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemePopupMenu | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeStylist | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeSvgCanvas | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSchemeToolbar | | Class | fiji.plugin.trackmate.visualization.trackscheme | Fiji |
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TrackSegmentCostMatrixCreator | Creates the cost matrix roughly described in Figure 1c in the paper: Jaqaman, K. | Class | fiji.plugin.trackmate.tracking.oldlap.costmatrix | Fiji |
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TrackSpeedStatisticsAnalyzer | | Class | fiji.plugin.trackmate.features.track | Fiji |
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TrackSpotQualityFeatureAnalyzer | | Class | fiji.plugin.trackmate.features.track | Fiji |
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TrimNotVisibleAction | | Class | fiji.plugin.trackmate.action | Fiji |
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TrimNotVisibleAction .Factory | | Class | fiji.plugin.trackmate.action.TrimNotVisibleAction | Fiji |
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Version | A utility class to deal with version numbers. | Class | fiji.plugin.trackmate.util | Fiji |
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ViewChoiceDescriptor | | Class | fiji.plugin.trackmate.gui.descriptors | Fiji |
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ViewFactory | | Interface | fiji.plugin.trackmate.visualization | Fiji |
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ViewProvider | | Class | fiji.plugin.trackmate.providers | Fiji |
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ViewUtils | A collection of static utilities related to TrackMateModelViews. | Class | fiji.plugin.trackmate.visualization | Fiji |
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Visualize_Detections | | Class | spim.fiji.plugin | Fiji |
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Visualize_Detections .Params | | Class | spim.fiji.plugin.Visualize_Detections | Fiji |
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Volume | | Class | fiji.plugin.volumeviewer | Fiji |
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Volume_Viewer | | Class | fiji.plugin.volumeviewer | Fiji |
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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 |
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WrapLayout | FlowLayout subclass that fully supports wrapping of components. | Class | fiji.plugin.trackmate.gui.panels | Fiji |
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XYEdgeRenderer | | Class | fiji.plugin.trackmate.util | Fiji |
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XYEdgeSeries | | Class | fiji.plugin.trackmate.util | Fiji |
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XYEdgeSeriesCollection | | Class | fiji.plugin.trackmate.util | Fiji |