- IconFactory - Class in sc.fiji.snt.gui
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- IconFactory() - Constructor for class sc.fiji.snt.gui.IconFactory
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- IconFactory.GLYPH - Enum in sc.fiji.snt.gui
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- ID - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper
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Mapping property (dummy): Each Tree in the collection is assigned an
incremental LUT entry
- id() - Method in class sc.fiji.snt.annotation.AllenCompartment
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- id() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
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- id - Variable in class sc.fiji.snt.util.SWCPoint
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The sample number of this node
- idExists() - Method in class sc.fiji.snt.io.MouseLightLoader
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Checks whether the neuron to be loaded was found in the database.
- idExists() - Method in class sc.fiji.snt.io.MouseLightQuerier
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Checks whether the neuron to be loaded was found in the database.
- ignoreSWCType(int...) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
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Ignores Paths sharing the specified SWC flag(s).
- imageTypeToString(int) - Static method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
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- importNeurons(Map<String, TreeSet<SWCPoint>>, ColorRGB, String) - Method in class sc.fiji.snt.PathAndFillManager
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Import neuron(s) as a collection of reconstruction nodes (SWC points)
- importSWC(String) - Method in class sc.fiji.snt.PathAndFillManager
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Imports an SWC file using default settings.
- importSWC(String, boolean, double, double, double, double, double, double, boolean) - Method in class sc.fiji.snt.PathAndFillManager
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Imports an SWC file using advanced options.
- importSWCs(Map<String, String>, ColorRGB) - Method in class sc.fiji.snt.PathAndFillManager
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Imports a group of SWC files (Remote URLs supported).
- impRange() - Method in class sc.fiji.snt.HessianCaller
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- indexInPath - Variable in class sc.fiji.snt.NearPoint
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- indexNearestTo(double, double, double, double) - Method in class sc.fiji.snt.Path
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Gets the index of the closest node associated with the specified world
coordinates.
- indexOf(Path) - Method in class sc.fiji.snt.Tree
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Returns the index of the specified Path in this Tree.
- inferSpacing(Collection<SWCPoint>) - Method in class sc.fiji.snt.util.BoundingBox
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Infers the voxel spacing of this box from the inter-node distances of a
Collection of
SWCPoints.
- info - Variable in class sc.fiji.snt.util.BoundingBox
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Used to store information about this bounding box.
- initialize() - Method in class sc.fiji.snt.gui.cmds.SNTLoaderCmd
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- initialize(ImagePlus) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
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- initialize(ImagePlus, int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
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- initialize(ImagePlus) - Method in class sc.fiji.snt.SNT
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- initialize(boolean, int, int) - Method in class sc.fiji.snt.SNT
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Initializes the plugin by assembling all the required tracing views
- initialize(boolean) - Method in class sc.fiji.snt.SNTService
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Initializes SNT.
- initialize(String, boolean) - Method in class sc.fiji.snt.SNTService
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Initializes SNT.
- initialize(ImagePlus, boolean) - Method in class sc.fiji.snt.SNTService
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Initializes SNT.
- insertNode(int, PointInImage) - Method in class sc.fiji.snt.Path
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Inserts a node at a specified position.
- integerSpinner(int, int, int, int) - Static method in class sc.fiji.snt.gui.GuiUtils
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- INTER_NODE_DISTANCE - Static variable in class sc.fiji.snt.analysis.TreeAnalyzer
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Flag for "Inter-node distance" analysis.
- INTER_NODE_DISTANCE_SQUARED - Static variable in class sc.fiji.snt.analysis.TreeAnalyzer
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Flag for "Inter-node distance (squared)" analysis.
- is2D() - Method in class sc.fiji.snt.SNT
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- is3D() - Method in class sc.fiji.snt.Tree
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Assesses whether this Tree has depth.
- isActive() - Method in class sc.fiji.snt.SNTService
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Gets whether SNT is running.
- isAstarEnabled() - Method in class sc.fiji.snt.SNT
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Checks if A* search is enabled
- isColorPairingEnabled() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd
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- isDarkModeOn() - Method in class sc.fiji.snt.viewer.Viewer3D
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Checks if scene is being rendered under dark or light background.
- isDatabaseAvailable() - Static method in class sc.fiji.snt.annotation.VFBUtils
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Checks whether a connection to the Virtual Fly Brain database can be
established.
- isDatabaseAvailable() - Static method in class sc.fiji.snt.annotation.ZBAtlasUtils
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Checks whether a connection to the FishAtlas database can be
established.
- isDatabaseAvailable() - Method in class sc.fiji.snt.io.FlyCircuitLoader
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Checks whether a connection to the FlyCircuit database can be established.
- isDatabaseAvailable() - Static method in class sc.fiji.snt.io.MouseLightLoader
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Checks whether a connection to the MouseLight database can be established.
- isDatabaseAvailable() - Static method in class sc.fiji.snt.io.MouseLightQuerier
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Checks whether a connection to the MouseLight database can be established.
- isDatabaseAvailable() - Method in class sc.fiji.snt.io.NeuroMorphoLoader
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Checks whether a connection to the NeuroMorpho database can be established.
- isDatabaseAvailable() - Method in interface sc.fiji.snt.io.RemoteSWCLoader
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- isDebugMode() - Static method in class sc.fiji.snt.SNTUtils
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Assesses if SNT is running in debug mode
- isEmpty() - Method in class sc.fiji.snt.Tree
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Checks if is empty.
- isEventsDisabled() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
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- isFittedVersionOfAnotherPath() - Method in class sc.fiji.snt.Path
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Checks if this Path is a fitted version of another path.
- isGaussianComputed() - Method in class sc.fiji.snt.HessianCaller
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- isHessianEnabled(String) - Method in class sc.fiji.snt.SNT
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Checks if Hessian analysis is enabled
- isLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
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Checks the hemisphere a neuron belongs to.
- isLeftHemisphere(SNTPoint) - Static method in class sc.fiji.snt.annotation.AllenUtils
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Checks the hemisphere a reconstruction node belongs to.
- isMeshAvailable() - Method in class sc.fiji.snt.annotation.AllenCompartment
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Checks whether a mesh is known to be available for this compartment.
- isOnlySelectedPathsVisible() - Method in class sc.fiji.snt.SNT
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- isPrimary() - Method in class sc.fiji.snt.Path
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Checks if this Path is root.
- isReady() - Method in class sc.fiji.snt.SNTUI
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Assesses whether the UI is blocked.
- isReal() - Method in class sc.fiji.snt.util.PointInImage
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- isSameLocation(PointInImage) - Method in class sc.fiji.snt.util.PointInImage
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- isSaveCompressedTraces() - Method in class sc.fiji.snt.SNTPrefs
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- isSaveWinLocations() - Method in class sc.fiji.snt.SNTPrefs
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- isScaled() - Method in class sc.fiji.snt.util.BoundingBox
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Checks whether this BoundingBox is spatially calibrated, i.e., if voxel
spacing has been specified
- isSecondaryImageLoaded() - Method in class sc.fiji.snt.SNT
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Assesses if the 'secondary image' has been loaded into memory.
- isSelected() - Method in class sc.fiji.snt.Path
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- isSelected(Path) - Method in class sc.fiji.snt.PathAndFillManager
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Checks if a Path is currently selected in the GUI.
- isSNTInstance() - Method in class sc.fiji.snt.viewer.Viewer3D
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Checks whether this instance is SNT's Reconstruction Viewer.
- isTubenessImageCached(String) - Method in class sc.fiji.snt.SNT
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- isTypeDefined() - Method in class sc.fiji.snt.util.SNTColor
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Checks if an SWC type has been defined.
- isZoomAllPanesDisabled() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
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- itemStateChanged(ItemEvent) - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
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