Index

_

__init__() (AnnotationGraph method) (DirectedWeightedGraph method) (DirectedWeightedSubgraph method) (EnhancedJavaObject method) (ImageParser2D method) (ImageParser3D method) (LinearProfileStats method) (NormalizedProfileStats method) (PolarProfileStats method) (Profile method) (ProfileEntry method) (ProfileProperties method) (ShollOverlay method) (ShollPlot method) (ShollStats method) (ShollTable method) (SNTGraph method) (TreeParser method)

A

accept(), [1], [2], [3] accessToValidImageData(), [1] acronym(), [1], [2], [3] action(), [1], [2], [3], [4], [5], [6], [7], [8], [9] actionPerformed(), [1] add(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] addAll(), [1] addAncestorListener(), [1] addAsLinesTo3DViewer() addChartMouseListener(), [1] addColorBarLegend(), [1], [2], [3], [4], [5], [6], [7] addColumn(), [1] addComponentListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addContainerListener(), [1], [2], [3], [4], [5] addDiscsTo3DViewer() addFillerThread(), [1] addFirst(), [1] addFocusListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addGenericColumn(), [1] addGroup(), [1] addHierarchyBoundsListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addHierarchyListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addInput(), [1], [2], [3], [4], [5] addInputMethodListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addKeyListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addLabel(), [1] addLast(), [1] addListener(), [1] addMesh(), [1] addMouseListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addMouseMotionListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addMouseWheelListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addNode(), [1], [2], [3], [4], [5], [6], [7] addNodes(), [1] addNotify(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addOutput(), [1], [2], [3], [4], [5] addOverlay(), [1] addPath(), [1] addPathAndFillListener(), [1] addPointDouble(), [1] addPolygon(), [1], [2], [3] addProgressListener(), [1], [2], [3], [4], [5], [6], [7] addPropertyChangeListener(), [1], [2], [3], [4], [5], [6], [7], [8], [9] addTo3DViewer() addTree(), [1], [2], [3], [4], [5], [6] addTrees(), [1], [2], [3] addVetoableChangeListener(), [1] addWindowFocusListener(), [1], [2], [3] addWindowListener(), [1], [2], [3] addWindowStateListener(), [1], [2], [3]

aliases(), [1], [2], [3] AllenCompartment (class in pysnt.annotation) AllenUtils (class in pysnt.annotation) allPointsIterator(), [1] andThen(), [1], [2], [3] annotate(), [1] annotateCategory(), [1] annotateLine(), [1] annotateMidPlane(), [1] annotatePlane(), [1] annotatePoint(), [1], [2], [3] annotatePoints(), [1] annotateSurface(), [1] annotateXline(), [1] annotateYline(), [1] Annotation3D (class in pysnt.viewer) AnnotationGraph (class in pysnt.analysis.graph) AnnotationWeightedEdgeExtractor (class in pysnt.converters.extractors) anovaPValue(), [1] anySelected(), [1] append(), [1] appendColumn(), [1] appendColumns(), [1] appendRow(), [1] appendRows(), [1] appendToLastRow(), [1] applyCanvasOffset(), [1] applyComponentOrientation(), [1], [2], [3], [4], [5], [6], [7], [8], [9] applyDefaultTags(), [1] applyFit(), [1] applyProperties(), [1] applyResourceBundle(), [1], [2], [3] applySelectionFilter(), [1] applySettings(), [1] applyStyle(), [1] applyTag(), [1] areFocusTraversalKeysSet(), [1], [2], [3], [4], [5], [6], [7], [8], [9] ArraySearchImage (class in pysnt.tracing.image) asPath(), [1] asPathReversed(), [1] assignBranches(), [1] assignImage(), [1] assignSpatialSettings(), [1] assignUniqueColors(), [1] assignValue(), [1] assignValues(), [1], [2], [3] auto_detect_and_configure() (in module pysnt.setup_utils) auto_enhance_java_objects() (in module pysnt.converters) (in module pysnt.converters.enhancement) autoTrace(), [1]

B

balancingFactor(), [1] BiSearchArtist (class in pysnt.tracing.artist)

boundarySize(), [1], [2], [3] bounds(), [1], [2], [3], [4], [5], [6], [7], [8], [9] BrainAnnotationExtractor (class in pysnt.converters.extractors)

C

call(), [1] cancel(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] cancelPath(), [1] cancelSearch(), [1] cancelTemporary(), [1] canvasResized() captureView(), [1] centripetalBias(), [1] changeState(), [1] changeUIState(), [1] characters(), [1] chartChanged(), [1] chartProgress(), [1] chebyshevDxTo(), [1], [2], [3] chebyshevXYdxTo(), [1], [2], [3] chebyshevZdxTo(), [1], [2], [3] check_fiji_installation() (in module pysnt.setup_utils) check_java_installation() (in module pysnt.java_utils) checkImage(), [1], [2], [3], [4], [5], [6], [7], [8], [9] clear(), [1], [2], [3] clear_fiji_path() (in module pysnt.setup_utils) clearSelection(), [1] clone(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] closeAndResetAllPanes(), [1] color(), [1], [2], [3], [4], [5] colorCode(), [1], [2], [3] combine(), [1] compareTo(), [1], [2], [3], [4], [5], [6], [7] compute(), [1], [2], [3], [4], [5], [6], [7], [8], [9]

configure_gui_safety() (in module pysnt.gui_utils) configure_java_logging() (in module pysnt.java_utils) confirmTemporary(), [1] contains(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] contains2D(), [1] containsAll(), [1] contentAdded() contentChanged() contentRemoved() contentSelected() context(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] convert(), [1] convertBinary(), [1] convertDistance(), [1] convertLabels(), [1] ConvexHull2D (class in pysnt.analysis) ConvexHull3D (class in pysnt.analysis) ConvexHullAnalyzer (class in pysnt.analysis) countComponents(), [1], [2], [3] create_dynamic_placeholder_class() (in module pysnt.common_module) createBufferStrategy(), [1], [2], [3], [4], [5], [6], [7] createCanvas(), [1] createCircles() createImage(), [1], [2], [3], [4], [5], [6], [7] createNewNode(), [1], [2], [3], [4], [5] createOrUpdateDisplay(), [1] createPath(), [1] createVolatileImage(), [1], [2], [3], [4], [5], [6], [7] cursorOverImage(), [1], [2], [3]

D

data (SNTObject attribute), [1], [2], [3] declaration(), [1] deletePath(), [1] deletePaths(), [1] deliverEvent(), [1], [2], [3], [4], [5], [6], [7] demoImage(), [1] demoTree(), [1] demoTreeImage() demoTrees(), [1] depth(), [1] describe_option() (in module pysnt.config) detachFromParent(), [1] detect_zarr_layout() (in module pysnt.io.images) Difference (class in pysnt.tracing.cost) DifferenceSq (class in pysnt.tracing.cost) Dijkstra (class in pysnt.tracing.heuristic) DirectedWeightedGraph (class in pysnt.analysis.graph) DirectedWeightedSubgraph (class in pysnt.analysis.graph) disable(), [1], [2], [3], [4], [5], [6], [7]

disableEvents(), [1], [2], [3] disableEventsAllPanes(), [1] disablePopupMenu(), [1], [2], [3] disableZoomAllPanes(), [1] discover_java_classes() (in module pysnt.java_utils) dispatchEvent(), [1], [2], [3], [4], [5], [6], [7] display() (in module pysnt.converters) (in module pysnt.display) (in module pysnt.display.core) dispose(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (in module pysnt.core) distanceSquaredTo(), [1], [2], [3] distanceTo(), [1], [2], [3] doLayout(), [1], [2], [3], [4], [5], [6], [7] downSample() downsample(), [1], [2], [3] downsampleAll(), [1] drawPathAsPoints(), [1] dump(), [1] duplicate(), [1]

E

EdgeExtractor (class in pysnt.converters.extractors) editModeAllowed(), [1] enable(), [1], [2], [3], [4], [5] enableAstar(), [1] enableAutoActivation(), [1] enableAutoSelectionOfFinishedPath(), [1] enableSecondaryLayerTracing(), [1] enableSnapCursor(), [1] enableSourceVersion(), [1] endDocument(), [1] endElement(), [1] endPrefixMapping(), [1] enhance_java_object() (in module pysnt.converters) (in module pysnt.converters.enhancement) EnhancedJavaObject (class in pysnt.converters.enhancement) ensure_java_available() (in module pysnt.java_utils)

ensureCapacity(), [1] error (SNTObject attribute), [1], [2], [3] error(), [1], [2], [3] Euclidean (class in pysnt.tracing.heuristic) euclideanDxTo(), [1], [2], [3] exportAllPathsAsSWC(), [1] exportFillsAsCSV(), [1] exportToCSV(), [1] exportTree(), [1] extract_attributes() (AnnotationWeightedEdgeExtractor method) (BrainAnnotationExtractor method) (EdgeExtractor method) (SWCPointExtractor method) (SWCWeightedEdgeExtractor method) (VertexExtractor method) extract_figure() (in module pysnt.core)

F

fatalError(), [1] FigCreatorCmd (class in pysnt.gui) (class in pysnt.gui.cmds) FijiNotFoundError fillEmptyCells(), [1] FillerThreadArtist (class in pysnt.tracing.artist) filter(), [1] find_fiji_installations() (in module pysnt.setup_utils) find_members() (in module pysnt.java_utils) findComponentAt(), [1] findJunctionIndices(), [1] findJunctions(), [1] findMaxima(), [1]

findMinima(), [1] findPointInStack(), [1] findPointInStackPrecise(), [1] finished(), [1] firePropertyChange(), [1], [2], [3] firstNode(), [1] fitToWindow(), [1], [2], [3] flushSecondaryData(), [1] FlyCircuitLoader (class in pysnt.io) forEach(), [1] Frangi (class in pysnt.filter) freeze(), [1] from_java() (in module pysnt.core)

G

geColumnHeaders(), [1] geColumnStats(), [1] geRowStats(), [1] get(), [1], [2], [3], [4], [5], [6], [7] get_available_classes() (in module pysnt) (in module pysnt.analysis) (in module pysnt.analysis.graph) (in module pysnt.analysis.growth) (in module pysnt.analysis.sholl) (in module pysnt.analysis.sholl.gui) (in module pysnt.analysis.sholl.math) (in module pysnt.analysis.sholl.parsers) (in module pysnt.annotation) (in module pysnt.filter) (in module pysnt.gui) (in module pysnt.gui.cmds) (in module pysnt.io) (in module pysnt.tracing) (in module pysnt.tracing.artist) (in module pysnt.tracing.cost) (in module pysnt.tracing.heuristic) (in module pysnt.tracing.image) (in module pysnt.util) (in module pysnt.viewer) get_available_levels() (in module pysnt.io.images) get_class() (in module pysnt) (in module pysnt.analysis) (in module pysnt.analysis.graph) (in module pysnt.analysis.growth) (in module pysnt.analysis.sholl) (in module pysnt.analysis.sholl.gui) (in module pysnt.analysis.sholl.math) (in module pysnt.analysis.sholl.parsers) (in module pysnt.annotation) (in module pysnt.filter) (in module pysnt.gui) (in module pysnt.gui.cmds) (in module pysnt.io) (in module pysnt.tracing) (in module pysnt.tracing.artist) (in module pysnt.tracing.cost) (in module pysnt.tracing.heuristic) (in module pysnt.tracing.image) (in module pysnt.util) (in module pysnt.viewer) get_config_dir() (in module pysnt.setup_utils) get_config_info() (in module pysnt.setup_utils) get_curated_classes() (in module pysnt) (in module pysnt.analysis) (in module pysnt.analysis.graph) (in module pysnt.analysis.growth) (in module pysnt.analysis.sholl) (in module pysnt.analysis.sholl.gui) (in module pysnt.analysis.sholl.math) (in module pysnt.analysis.sholl.parsers) (in module pysnt.annotation) (in module pysnt.filter) (in module pysnt.gui) (in module pysnt.gui.cmds) (in module pysnt.io) (in module pysnt.tracing) (in module pysnt.tracing.artist) (in module pysnt.tracing.cost) (in module pysnt.tracing.heuristic) (in module pysnt.tracing.image) (in module pysnt.util) (in module pysnt.viewer) get_dataset_path() (in module pysnt.io.images) get_dataset_path_from_metadata() (in module pysnt.io.images) get_default_attributes() (AnnotationWeightedEdgeExtractor method) (BrainAnnotationExtractor method) (EdgeExtractor method) (SWCPointExtractor method) (SWCWeightedEdgeExtractor method) (VertexExtractor method) get_display_position() (SWCPointExtractor method) (VertexExtractor method) get_extended_classes() (in module pysnt) (in module pysnt.analysis) (in module pysnt.analysis.graph) (in module pysnt.analysis.growth) (in module pysnt.analysis.sholl) (in module pysnt.analysis.sholl.gui) (in module pysnt.analysis.sholl.math) (in module pysnt.analysis.sholl.parsers) (in module pysnt.annotation) (in module pysnt.filter) (in module pysnt.gui) (in module pysnt.gui.cmds) (in module pysnt.io) (in module pysnt.tracing) (in module pysnt.tracing.artist) (in module pysnt.tracing.cost) (in module pysnt.tracing.heuristic) (in module pysnt.tracing.image) (in module pysnt.util) (in module pysnt.viewer) get_fields() (in module pysnt.java_utils) get_fiji_path() (in module pysnt.setup_utils) get_fiji_status() (in module pysnt.setup_utils) get_inner_classes() (in module pysnt.java_utils) get_methods() (in module pysnt.java_utils) get_mode() (in module pysnt.core) get_option() (in module pysnt.config) get_zattrs_path() (in module pysnt.io.images) getAccessibleContext(), [1], [2], [3] getAlignmentX(), [1], [2], [3] getAlignmentY(), [1], [2], [3] getAnalysis(), [1], [2], [3] getAnalyzer() getAncestor(), [1], [2], [3] getAncestors(), [1] getAngle(), [1] getAngles(), [1] getAnnotatedFrequencies(), [1] getAnnotatedFrequenciesByHemisphere(), [1] getAnnotatedFrequencyHistogram(), [1] getAnnotatedHistogram(), [1] getAnnotatedLength(), [1], [2], [3], [4], [5] getAnnotatedLengthHistogram(), [1], [2], [3], [4], [5] getAnnotatedLengthsByHemisphere(), [1], [2], [3], [4], [5] getAnnotatedNodes(), [1] getAnnotation(), [1], [2], [3], [4], [5], [6], [7] getAnnotations(), [1], [2], [3], [4], [5], [6], [7], [8], [9] getAnnotationsColor(), [1], [2], [3] getApproximatedSurface(), [1], [2], [3] getApproximatedVolume(), [1], [2], [3] getArity(), [1], [2], [3] getAssignedValue(), [1] getAvailableLuts(), [1], [2], [3], [4], [5], [6], [7] getAverageSeparation(), [1] getAvgBifurcationRatio(), [1] getAvgBranchLength(), [1], [2], [3], [4], [5] getAvgContraction(), [1], [2], [3], [4], [5] getAvgContractions(), [1] getAvgExtensionAngle(), [1] getAvgExtensionAngles(), [1] getAvgFractalDimension(), [1], [2], [3], [4], [5] getAvgFragmentation(), [1], [2], [3], [4], [5] getAvgFragmentations(), [1] getAvgPartitionAsymmetry(), [1], [2], [3], [4], [5] getAvgRemoteBifAngle(), [1], [2], [3], [4], [5] getBackground(), [1], [2], [3] getBarcode(), [1] getBarycentre(), [1] getBaseline(), [1], [2], [3] getBifurcationRatios(), [1] getBoundarySize(), [1] getBoundingBox(), [1], [2], [3] getBoxivity(), [1] getBoxPlot(), [1], [2], [3] getBPs(), [1] getBranchCounts(), [1] getBranches(), [1], [2], [3], [4], [5], [6], [7] getBranchPoint(), [1] getBranchPointCounts(), [1] getBranchPointIndex(), [1] getBranchPoints(), [1], [2], [3], [4], [5], [6], [7] getCableLength(), [1], [2], [3], [4], [5] getCableLengthNorm(), [1], [2], [3], [4], [5] getCalibration(), [1], [2], [3] getCancelReason(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] getCanvasOffset(), [1] getCentroid(), [1], [2], [3] getChannel(), [1], [2], [3] getChart(), [1] getChildren(), [1], [2], [3] getColor(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] getColorRGB(), [1], [2], [3], [4], [5], [6], [7], [8], [9] getColorTable(), [1], [2], [3], [4], [5], [6], [7] getColumnCount(), [1] getColumnHeader(), [1] getColumnIndex(), [1] getCompactness(), [1] getContext(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] getContraction(), [1] getConvexAnalyzer(), [1], [2], [3], [4], [5] getConvexHull(), [1] getConvexHullMetric(), [1], [2], [3], [4], [5] getCoordinateOnAxis(), [1], [2], [3], [4], [5] getCorrespondences(), [1] getCostType(), [1] getCramerVonMisesStatistic(), [1] getCurrentPath(), [1] getDataset(), [1] getDelegateObject(), [1], [2], [3], [4], [5] getDensityPlot(), [1] getDepth(), [1], [2], [3], [4], [5], [6], [7] getDescriptiveStatistics(), [1], [2], [3] getDescriptiveStats(), [1], [2], [3], [4], [5] getDiagonal(), [1]

getDiagram(), [1] getDiagramNodes(), [1] getDimensions(), [1] getDistanceAtPoint(), [1] getDOI(), [1] getDrawable(), [1] getDrawDiameters(), [1] getEccentricity(), [1] getEditableNodeIndex(), [1] getElongation(), [1] getErrorMessage(), [1] getEstimatedMeanRadius(), [1] getExitReason(), [1], [2], [3], [4], [5] getExtensionAngle3D(), [1] getExtensionAngleFromHorizontal(), [1] getExtensionAngleFromVertical(), [1] getExtensionAngles(), [1] getExtensionAngles3D(), [1] getExtensionAngleXY(), [1] getExtensionAngleXZ(), [1] getExtensionAngleZY(), [1] getExtensionDirection3D(), [1] getF(), [1] getFFromGoal(), [1] getFFromStart(), [1] getFill(), [1] getFilledBinaryImp(), [1] getFilledDistanceImp(), [1] getFilledImp(), [1] getFilledLabelImp(), [1] getFillerStack(), [1] getFilterType(), [1] getFirst(), [1] getFitted(), [1] getFlowPlot(), [1], [2], [3], [4], [5], [6], [7] getFractalDimension(), [1], [2], [3], [4], [5], [6], [7] getFrame(), [1], [2], [3], [4], [5] getG(), [1] getGFromGoal(), [1] getGFromStart(), [1] getGraph(), [1], [2], [3] getGraphs(), [1] getGroup(), [1] getGroups(), [1] getGroupStats(), [1] getHandle(), [1] getHeapHandle(), [1] getHeapHandleFromGoal(), [1] getHeapHandleFromStart(), [1] getHeight(), [1], [2], [3], [4], [5], [6], [7] getHemisphere(), [1], [2], [3], [4], [5] getHeuristicType(), [1] getHighestBranchOrder(), [1] getHighestPathOrder(), [1], [2], [3], [4], [5] getHistogram(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] getHull(), [1] getID(), [1], [2], [3] getIdentifier(), [1] getImagePlus(), [1] getImpContainer(), [1] getIndependentInstance(), [1], [2], [3] getInfo(), [1], [2], [3], [4], [5], [6], [7] getInnerBranches(), [1], [2], [3], [4], [5] getInnerLength(), [1], [2], [3], [4], [5] getInput(), [1], [2], [3], [4], [5] getInputs(), [1], [2], [3], [4], [5] getInstance(), [1] getJFreeChart(), [1] getJSON(), [1] getLabel(), [1], [2], [3] getLandscape(), [1] getLast(), [1] getLengths(), [1] getLinearStats(), [1] getLoadedData(), [1] getLoadedDataAsImp(), [1] getLoadedFills(), [1] getLoadedIterable(), [1] getLocation(), [1] getManagerPanel(), [1] getMaximaRadii(), [1] getMesh(), [1], [2], [3], [4], [5], [6], [7] getMeshes(), [1], [2], [3] getMetric(), [1], [2], [3], [4], [5], [6], [7] getMinMax(), [1], [2], [3], [4], [5], [6], [7] getMultiViewer(), [1], [2], [3], [4], [5] getN(), [1] getNaNColor(), [1], [2], [3], [4], [5], [6], [7] getNBranchPoints(), [1] getNeuronInfo(), [1] getNextPoints(), [1] getNodeList(), [1] getNodes(), [1], [2], [3], [4], [5] getNodesAsImage(), [1], [2], [3] getNodesAsImageFromGoal(), [1], [2], [3], [4], [5] getNodesAsImageFromStart(), [1], [2], [3], [4], [5] getNodesAsSWCPoints(), [1] getNodesByColor(), [1] getNodesCount(), [1] getNormStats(), [1] getNumberOfPoints(), [1] getOntologyDepth(), [1], [2], [3] getOrCreateSciViewSNT(), [1] getOutput(), [1], [2], [3], [4], [5] getOutputs(), [1], [2], [3], [4], [5] getParent(), [1], [2], [3] getPath(), [1], [2], [3], [4], [5], [6], [7], [8], [9] getPathAndFillManager(), [1] getPathFromID(), [1] getPathFromName(), [1] getPaths(), [1], [2], [3] getPathsFiltered(), [1] getPathsInROI(), [1] getPathsStructured(), [1] getPlot(), [1], [2], [3], [4], [5] getPlugin(), [1], [2] getPolarHistogram(), [1] getPolygon(), [1] getPredecessor(), [1] getPredecessorFromGoal(), [1] getPredecessorFromStart(), [1] getPriority(), [1] getProperties(), [1] getPruneMode(), [1] getReader(), [1], [2], [3], [4], [5] getReconstructionURL(), [1], [2], [3], [4], [5] getRecorder(), [1] getRecViewer(), [1] getRelativeExtensionAngle(), [1] getResult(), [1], [2], [3], [4], [5], [6], [7] getRoot(), [1] getRootAssociatedBranches(), [1] getRootNumber(), [1] getRootRoiStrategy(), [1] getRoundness(), [1] getRowCount(), [1] getRowHeader(), [1] getRowIndex(), [1] getSampleInfo(), [1] getSciView(), [1] getSciViewSNT(), [1] getSecondaryMaxima(), [1] getSelectedPaths(), [1], [2], [3] getSingleGraph(), [1] getSingleTree(), [1] getSingleValueMetrics(), [1] getSize(), [1] getSkeleton(), [1] getSkeleton2D(), [1] getSomaCompartment(), [1] getSomaLocation(), [1] getSomaNodes(), [1] getSourcePaths(), [1] getSourcePathsStringHuman(), [1] getSourcePathsStringMachine(), [1] getState(), [1] getStateFromGoal(), [1] getStateFromStart(), [1] getStatistics(), [1] getSucceeded(), [1] getSuccess(), [1] getSummaryRow(), [1] getSWC(), [1] getSWCFor(), [1] getSWCTypeNames(), [1] getSWCTypes(), [1] getTable(), [1], [2], [3] getTaggedGraph(), [1] getTaggedTree(), [1] getTags(), [1] getThreshold(), [1], [2], [3] getTips(), [1] getTitle(), [1] getTree(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] getTreeAsSceneryNode(), [1] getTreePath(), [1] getTrees(), [1], [2], [3], [4], [5] getType(), [1] getUI(), [1] getUnit(), [1], [2], [3] getUnscaledPoint(), [1], [2], [3] getUUID(), [1] getValues(), [1], [2], [3] getVersion(), [1] getVolume(), [1], [2], [3] getX(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] getXYPlot(), [1] getY(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] getZ(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] GroupedTreeStatistics (class in pysnt.analysis) GrowthAnalysisResults (class in pysnt.analysis.growth) GrowthAnalyzer (class in pysnt.analysis.growth)

H

handle_display_errors() (in module pysnt.display.core) has_class_name() (JavaTypeDetector static method) has_methods() (JavaTypeDetector static method) has_pandasgui() (in module pysnt.converters.core)

hasDimensions(), [1] heapDecreaseKey(), [1] heapInsert(), [1] height(), [1] Heuristic (class in pysnt.tracing.heuristic)

I

id(), [1], [2], [3] idExists(), [1], [2], [3] ij() (in module pysnt.core) ImageParser2D (class in pysnt.analysis.sholl.parsers) ImageParser3D (class in pysnt.analysis.sholl.parsers) imgplus_from_zarr() (in module pysnt.io.images) in(), [1], [2], [3] includes(), [1] indexOf(), [1] inferSpacing(), [1] initialize(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] (in module pysnt.core) InsectBrainCompartment (class in pysnt.annotation) InsectBrainLoader (class in pysnt.io) InsectBrainUtils (class in pysnt.annotation) inspect() (in module pysnt.java_utils) inspect_zarr() (in module pysnt.io.images) install_openjdk() (in module pysnt.java_utils) interactive_fiji_setup() (in module pysnt.setup_utils) intersection(), [1], [2], [3], [4], [5] intersectionBox(), [1], [2], [3] is3D(), [1] is_fiji_valid() (in module pysnt.setup_utils) is_initialized() (in module pysnt.core)

is_instance_of() (in module pysnt.java_utils) is_macos() (in module pysnt.gui_utils) is_main_thread() (in module pysnt.gui_utils) isActive(), [1], [2], [3] isAnnotated(), [1] isCanceled(), [1], [2], [3], [4], [5], [6], [7] isChildOf(), [1], [2], [3] isColorCodeAllowed(), [1] isDarkModeOn(), [1] isDatabaseAvailable(), [1], [2], [3], [4], [5] isEmpty(), [1] isInputResolved(), [1], [2], [3], [4], [5] isIntegerScale(), [1], [2], [3], [4], [5], [6], [7] isMeshAvailable(), [1], [2], [3] isNodeMapping(), [1], [2], [3], [4], [5] isOutputResolved(), [1], [2], [3], [4], [5] isParentOf(), [1], [2], [3] isReal(), [1], [2], [3] isResolved(), [1], [2], [3], [4], [5] isSameLocation(), [1], [2], [3] isScaled(), [1] isSNTInstance(), [1] isSplitDendritesFromAxons(), [1] isTypeDefined(), [1]

J

JavaTypeDetector (class in pysnt.converters.core)

L

LinearProfileStats (class in pysnt.analysis.sholl.math) list(), [1] list_classes() (in module pysnt) (in module pysnt.analysis) (in module pysnt.analysis.graph) (in module pysnt.analysis.growth) (in module pysnt.analysis.sholl) (in module pysnt.analysis.sholl.gui) (in module pysnt.analysis.sholl.math) (in module pysnt.analysis.sholl.parsers) (in module pysnt.annotation) (in module pysnt.filter) (in module pysnt.gui) (in module pysnt.gui.cmds) (in module pysnt.io) (in module pysnt.tracing) (in module pysnt.tracing.artist) (in module pysnt.tracing.cost) (in module pysnt.tracing.heuristic) (in module pysnt.tracing.image) (in module pysnt.util) (in module pysnt.viewer)

list_converters() (in module pysnt.converters) list_options() (in module pysnt.config) ListSearchImage (class in pysnt.tracing.image) load_config() (in module pysnt.setup_utils) loadGraph(), [1] loadMesh(), [1] loadRefBrain(), [1] loadTracings(), [1] loadTree(), [1] log(), [1] logSceneControls(), [1]

M

main_thread_wrapper() (in module pysnt.gui_utils) map(), [1], [2], [3], [4], [5], [6], [7] mapRootDistanceToCentroid(), [1] MapSearchImage (class in pysnt.tracing.image) mapTrees(), [1], [2], [3], [4], [5] matches_pattern() (JavaTypeDetector static method) max(), [1] mean(), [1] meanDirection(), [1] mergeAnnotations(), [1] metadata (SNTObject attribute), [1], [2], [3] min(), [1] module pysnt pysnt.analysis pysnt.analysis.graph pysnt.analysis.growth pysnt.analysis.sholl pysnt.analysis.sholl.gui pysnt.analysis.sholl.math pysnt.analysis.sholl.parsers pysnt.annotation pysnt.common_module pysnt.config pysnt.converters pysnt.converters.chart_converters pysnt.converters.core pysnt.converters.enhancement pysnt.converters.extractors pysnt.converters.graph_converters pysnt.converters.structured_data_converters pysnt.converters.tree_converters pysnt.core pysnt.display pysnt.display.core pysnt.display.data_display pysnt.display.utils pysnt.display.visual_display pysnt.filter pysnt.gui pysnt.gui.cmds pysnt.gui_utils pysnt.io pysnt.io.images pysnt.java_utils pysnt.setup_utils pysnt.tracing pysnt.tracing.artist pysnt.tracing.cost pysnt.tracing.heuristic pysnt.tracing.image pysnt.util pysnt.viewer

MouseLightLoader (class in pysnt.io) MouseLightQuerier (class in pysnt.io) MultiTreeColorMapper (class in pysnt.analysis) MultiTreeStatistics (class in pysnt.analysis) MultiViewer2D (class in pysnt.viewer) MultiViewer3D (class in pysnt.viewer)

N

name(), [1], [2], [3] NeuroMorphoLoader (class in pysnt.io) newRecViewer(), [1]

NodeColorMapper (class in pysnt.analysis) NodeProfiler (class in pysnt.analysis) NodeStatistics (class in pysnt.analysis) NormalizedProfileStats (class in pysnt.analysis.sholl.math)

O

OneMinusErf (class in pysnt.tracing.cost) ops(), [1], [2], [3] option_context() (in module pysnt.config)

OptionError origin(), [1] originOpposite(), [1] out(), [1], [2], [3]

P

Path (class in pysnt) pathChanged(), [1] PathProfiler (class in pysnt.analysis) PathStatistics (class in pysnt.analysis) PathStraightener (class in pysnt.analysis) PCAnalyzer (class in pysnt.analysis) PersistenceAnalyzer (class in pysnt.analysis) PointInImage (class in pysnt.util) pointsConsideredInSearch(), [1], [2], [3], [4], [5], [6], [7] PolarProfileStats (class in pysnt.analysis.sholl.math) preview(), [1], [2], [3], [4], [5] previous(), [1] print_fiji_status() (in module pysnt.setup_utils) print_java_status() (in module pysnt.java_utils) printStatus(), [1], [2], [3], [4], [5], [6], [7] Profile (class in pysnt.analysis.sholl) ProfileEntry (class in pysnt.analysis.sholl) ProfileProperties (class in pysnt.analysis.sholl) pysnt module pysnt.analysis module pysnt.analysis.graph module pysnt.analysis.growth module pysnt.analysis.sholl module pysnt.analysis.sholl.gui module pysnt.analysis.sholl.math module pysnt.analysis.sholl.parsers module pysnt.annotation module pysnt.common_module module pysnt.config module pysnt.converters module pysnt.converters.chart_converters module pysnt.converters.core module pysnt.converters.enhancement module pysnt.converters.extractors module

pysnt.converters.graph_converters module pysnt.converters.structured_data_converters module pysnt.converters.tree_converters module pysnt.core module pysnt.display module pysnt.display.core module pysnt.display.data_display module pysnt.display.utils module pysnt.display.visual_display module pysnt.filter module pysnt.gui module pysnt.gui.cmds module pysnt.gui_utils module pysnt.io module pysnt.io.images module pysnt.java_utils module pysnt.setup_utils module pysnt.tracing module pysnt.tracing.artist module pysnt.tracing.cost module pysnt.tracing.heuristic module pysnt.tracing.image module pysnt.util module pysnt.viewer module

R

readPreferences(), [1] rebuild(), [1] Reciprocal (class in pysnt.tracing.cost) recordRotation(), [1] reflect_java_object() (in module pysnt.java_utils) register_display_handler() (in module pysnt.converters) (in module pysnt.display) (in module pysnt.display.utils) register_snt_converters() (in module pysnt.converters) registerEventHandlers(), [1]

RemoteSWCLoader (class in pysnt.io) removeInput(), [1], [2], [3], [4], [5] removeOutput(), [1], [2], [3], [4], [5] removeTree(), [1] reportFinished(), [1], [2], [3], [4], [5], [6], [7] reset_fiji_path() (in module pysnt.setup_utils) reset_option() (in module pysnt.config) resolveInput(), [1], [2], [3], [4], [5] resolveOutput(), [1], [2], [3], [4], [5] RootAngleAnalyzer (class in pysnt.analysis) run(), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19]

S

safe_gui_call() (in module pysnt.gui_utils) save(), [1], [2], [3], [4], [5] save_config() (in module pysnt.setup_utils) saveAsJSON(), [1] saveAsSWC(), [1] scale(), [1], [2], [3], [4], [5] SearchArtistFactory (class in pysnt.tracing.artist) SearchImageStack (class in pysnt.tracing.image) SearchThread (class in pysnt.tracing) SearchThreadArtist (class in pysnt.tracing.artist) set_fiji_path() (in module pysnt.setup_utils) set_option() (in module pysnt.config) setAnimationEnabled(), [1] setAnnotation(), [1], [2], [3], [4], [5] setAWTColor(), [1] setAxesVisible(), [1], [2], [3] setBoundingBoxColor(), [1] setColor(), [1], [2], [3] setColorBarLegend(), [1] setConnectComponents(), [1] setContext(), [1], [2], [3], [4], [5], [6], [7], [8], [9] setCrossSectionRadius(), [1] setDefaultColor(), [1] setDimensions(), [1] setEnableCurveFitting(), [1] setEnvironment(), [1], [2], [3] setEqualizeAxes(), [1] setErrorMessage(), [1] setFFromGoal(), [1] setFFromStart(), [1] setFrom(), [1], [2], [3] setFromGoal(), [1] setFromStart(), [1] setGap(), [1] setGFromGoal(), [1] setGFromStart(), [1] setGridlinesVisible(), [1], [2], [3] setHandle(), [1] setHeapHandle(), [1] setHeapHandleFromGoal(), [1] setHeapHandleFromStart(), [1] setHemisphere(), [1], [2], [3], [4], [5] setImage(), [1] setInfo(), [1] setInput(), [1], [2], [3], [4], [5], [6], [7], [8], [9] setInputs(), [1], [2], [3], [4], [5] setLabel(), [1], [2], [3], [4] setLabels(), [1] setLayoutColumns(), [1], [2], [3] setLengthThreshold(), [1] setMaxConnectDist(), [1] setMetric(), [1], [2], [3] setMinMax(), [1], [2], [3], [4], [5], [6], [7] setMinNBins(), [1] setNaNColor(), [1], [2], [3], [4], [5], [6], [7] setNodeIndicesAsDistances(), [1] setNodeRadiusFallback(), [1] setNodeStep(), [1] setOrigin(), [1] setOriginOpposite(), [1] setOrigIP(), [1] setOutlineVisible(), [1], [2], [3] setOutput(), [1], [2], [3], [4], [5], [6], [7], [8], [9] setOutputs(), [1], [2], [3], [4], [5] setPath(), [1], [2], [3], [4], [5] setPolynomialFitRange(), [1] setPosition(), [1] setPredecessor(), [1] setPredecessorFromGoal(), [1] setPredecessorFromStart(), [1]

setPreferredSize(), [1] setPrevious(), [1] setPriority(), [1] setProgressCallback(), [1] setPruneByLength(), [1] setPruneEnds(), [1] setPruneMode(), [1] setRadius(), [1], [2], [3] setReplaceNodes(), [1] setResolved(), [1], [2], [3] setRootRoi(), [1] setSciView(), [1] setScope(), [1] setShape(), [1] setShortestPath(), [1] setShowAnnotatedView(), [1] setSilent(), [1] setSize(), [1] setSourcePaths(), [1], [2], [3] setSpacing(), [1], [2], [3] setState(), [1] setStateFromGoal(), [1] setStateFromStart(), [1] setStopAtThreshold(), [1] setStoreExtraNodes(), [1] setSuccess(), [1] setSWCType(), [1] setTags(), [1] setThreshold(), [1], [2], [3] setTitle(), [1], [2], [3], [4], [5] setTransparency(), [1] setUnit(), [1] setup_dynamic_imports() (in module pysnt.core) setup_fiji_environment() (in module pysnt.setup_utils) setup_java_environment() (in module pysnt.java_utils) setup_module_classes() (in module pysnt.common_module) setVerbose(), [1] setViewMode(), [1] setWidth(), [1] setWireframeColor(), [1] setX(), [1] setXrange(), [1], [2], [3] setY(), [1] setYrange(), [1], [2], [3] setZ(), [1] shift(), [1] ShollAnalyzer (class in pysnt.analysis) ShollOverlay (class in pysnt.analysis.sholl.gui) ShollPlot (class in pysnt.analysis.sholl.gui) ShollStats (class in pysnt.analysis.sholl.math) ShollTable (class in pysnt.analysis.sholl.gui) show(), [1], [2], [3], [4], [5] (in module pysnt.core) show_config_status() (in module pysnt.setup_utils) size(), [1], [2], [3] SkeletonConverter (class in pysnt.analysis) SNTChart (class in pysnt.analysis) SNTGraph (class in pysnt.analysis.graph) SNTObject (class in pysnt.converters) (class in pysnt.converters.core) SNTService (class in pysnt) SNTTable (class in pysnt.analysis) SNTUtils (class in pysnt) sortedMappedTrees(), [1] StrahlerAnalyzer (class in pysnt.analysis) straighten(), [1] SupplierUtil (class in pysnt.tracing.image) SWCPoint (class in pysnt.util) SWCPointExtractor (class in pysnt.converters.extractors) SWCWeightedEdgeExtractor (class in pysnt.converters.extractors) syncPathManagerList(), [1]

T

to_python() (in module pysnt.core) toBoundingBox3d(), [1] TracerThread (class in pysnt.tracing) transform(), [1], [2], [3] Tree (class in pysnt) tree_to_points() (in module pysnt.converters) (in module pysnt.converters.tree_converters)

TreeColorMapper (class in pysnt.analysis) TreeParser (class in pysnt.analysis.sholl.parsers) TreeStatistics (class in pysnt.analysis) tTest(), [1] Tubeness (class in pysnt.filter) type (SNTObject attribute), [1], [2], [3] type(), [1]

U

uncancel(), [1], [2], [3] unresolveInput(), [1], [2], [3] unresolveOutput(), [1], [2], [3]

unscaledOrigin(), [1] unscaledOriginOpposite(), [1] updateViewers(), [1]

V

VertexExtractor (class in pysnt.converters.extractors) VFBUtils (class in pysnt.annotation)

Viewer2D (class in pysnt.viewer) Viewer3D (class in pysnt.viewer) viewers(), [1]

W

WekaModelLoader (class in pysnt.io) width(), [1]

writeNodesXML(), [1] writeXML(), [1]

X

xSeparationFromPreviousPoint(), [1]

Y

ySeparationFromPreviousPoint(), [1]

Z

ZBAtlasUtils (class in pysnt.annotation)

zSeparationFromPreviousPoint(), [1]