Constant Field Values

Contents

• sc.fiji.*

sc.fiji.*

sc.fiji.snt.FillManagerUI

Modifier and Type	Constant Field	Value
protected static final String	FILLING_URI	"https://imagej.net/plugins/snt/walkthroughs#filling"

sc.fiji.snt.Path

Modifier and Type	Constant Field	Value
protected static final int	DEFAULT_SAMPLING_INTERVAL	2
protected static final int	noMoreThanOneEvery	2
public static final int	SWC_APICAL_DENDRITE	4
public static final String	SWC_APICAL_DENDRITE_LABEL	"apical dendrite"
public static final int	SWC_AXON	2
public static final String	SWC_AXON_LABEL	"axon"
public static final int	SWC_CUSTOM	5
public static final String	SWC_CUSTOM_LABEL	"custom"
public static final int	SWC_CUSTOM2	8
public static final String	SWC_CUSTOM2_LABEL	"custom (2)"
public static final int	SWC_DENDRITE	3
public static final String	SWC_DENDRITE_LABEL	"(basal) dendrite"
public static final int	SWC_END_POINT	-6
public static final int	SWC_FORK_POINT	-5
public static final int	SWC_GLIA_PROCESS	7
public static final String	SWC_GLIA_PROCESS_LABEL	"glia process"
public static final int	SWC_SOMA	1
public static final String	SWC_SOMA_LABEL	"soma"
public static final int	SWC_UNDEFINED	0
public static final String	SWC_UNDEFINED_LABEL	"undefined"
public static final int	SWC_UNSPECIFIED	6
public static final String	SWC_UNSPECIFIED_LABEL	"unspecified neurite"

sc.fiji.snt.PathAndFillManager

Modifier and Type	Constant Field	Value
protected static final int	TRACES_FILE_TYPE_COMPRESSED_XML	1
protected static final int	TRACES_FILE_TYPE_ML_JSON	4
protected static final int	TRACES_FILE_TYPE_NDF	5
protected static final int	TRACES_FILE_TYPE_NEUROLUCIDA	6
protected static final int	TRACES_FILE_TYPE_SWC	3
protected static final int	TRACES_FILE_TYPE_UNCOMPRESSED_XML	2

sc.fiji.snt.PathFitter

Modifier and Type	Constant Field	Value
public static final int	FALLBACK_MIN_SEP	16
public static final int	FALLBACK_MODE	32
public static final int	FALLBACK_NAN	8
public static final int	MIDPOINTS	2
public static final int	RADII	1
public static final int	RADII_AND_MIDPOINTS	4

sc.fiji.snt.PathManagerUI

Modifier and Type	Constant Field	Value
protected static final String	TABLE_TITLE	"SNT Measurements"

sc.fiji.snt.PathNodeCanvas

Modifier and Type	Constant Field	Value
public static final int	END	2
public static final int	HERMIT	5
public static final int	JOINT	3
public static final int	SLAB	4
public static final int	SOMA_RENDER_DEFAULT	0
public static final int	SOMA_RENDER_TRIANGLE	1
public static final int	START	1

sc.fiji.snt.SNT

Modifier and Type	Constant Field	Value
protected static final int	ballRadiusMultiplier	5
protected static final int	DISPLAY_PATHS_LINES	2
protected static final int	DISPLAY_PATHS_LINES_AND_DISCS	3
protected static final int	DISPLAY_PATHS_SURFACE	1
protected static final int	MAX_SNAP_CURSOR_WINDOW_XY	40
protected static final int	MAX_SNAP_CURSOR_WINDOW_Z	10
protected static final int	MIN_SNAP_CURSOR_WINDOW_XY	2
protected static final int	MIN_SNAP_CURSOR_WINDOW_Z	0
protected static final String	startBallName	"Start point"
protected static final String	targetBallName	"Target point"

sc.fiji.snt.SNTPrefs

Modifier and Type	Constant Field	Value
public static final String	AUTOSAVE_KEY	"tracespath"
public static final String	BVV_MAX_RENDER_MILLIS	"bvv.maxRenderMillis"
public static final String	BVV_MAX_STEP_IN_VOXELS	"bvv.maxStepInVoxels"
public static final String	BVV_RENDER_HEIGHT	"bvv.renderHeight"
public static final String	BVV_RENDER_WIDTH	"bvv.renderWidth"
public static final String	NO_IMAGE_ASSOCIATED_DATA	"noImgData"
public static final String	RESIZE_REQUIRED	"resizeNeeded"
public static final String	RESTORE_LOADED_IMGS	"restoreLoadedImgs"
public static final String	SPLIT_FILLS_KEY	"splitfills"

sc.fiji.snt.SNTUI

Modifier and Type	Constant Field	Value
public static final int	EDITING	15
public static final int	FITTING_PATHS	14
public static final int	LOADING	13
public static final int	READY	0
public static final int	RUNNING_CMD	4
public static final int	SNT_PAUSED	16
public static final int	TRACING_PAUSED	17
public static final int	WAITING_FOR_SIGMA_POINT_I	9

sc.fiji.snt.SNTUtils

Modifier and Type	Constant Field	Value
public static final String	TIMESTAMP_REGEX	"(.+?)_D(\\d{4}-\\d{2}-\\d{2})T(\\d{2}-\\d{2}-\\d{2})"

sc.fiji.snt.Tree

Modifier and Type	Constant Field	Value
public static final int	X_AXIS	1
public static final int	Y_AXIS	2
public static final int	Z_AXIS	4

sc.fiji.snt.TreeProperties

Modifier and Type	Constant Field	Value
public static final String	AXONAL	"axonal"
public static final String	DENDRITIC	"dendritic"
public static final String	KEY_COLOR	"color"
public static final String	KEY_COMPARTMENT	"compartment"
public static final String	KEY_FRAME_POS	"frame"
public static final String	KEY_ID	"id"
public static final String	KEY_IMG	"img"
public static final String	KEY_IMG_CHANNEL	"channel"
public static final String	KEY_IMG_FRAME	"frame"
public static final String	KEY_LABEL	"label"
public static final String	KEY_SOURCE	"source"
public static final String	KEY_SPATIAL_UNIT	"unit"
public static final String	SOMATIC	"somatic"
public static final String	UNSET	"?"

sc.fiji.snt.analysis.ConvexHullAnalyzer

Modifier and Type	Constant Field	Value
public static final String	BOUNDARY_SIZE	"Boundary size"
public static final String	BOXIVITY	"Boxivity"
public static final String	COMPACTNESS_3D	"Compactness"
public static final String	ECCENTRICITY_2D	"Eccentricity"
public static final String	ELONGATION	"Elongation"
public static final String	ROUNDNESS	"Roundness"
public static final String	SIZE	"Size"

sc.fiji.snt.analysis.MultiTreeColorMapper

Modifier and Type	Constant Field	Value
public static final String	ASSIGNED_VALUE	"Assigned value"
public static final String	CABLE_LENGTH	"Cable length"
public static final String	HIGHEST_PATH_ORDER	"Highest path order"
public static final String	ID	"Cell/id"
public static final String	N_BRANCHES	"No. of branches"
public static final String	N_TIPS	"No. of tips"
public static final String	STRAHLER_NUMBER	"Horton-Strahler root number"

sc.fiji.snt.analysis.MultiTreeStatistics

Modifier and Type	Constant Field	Value
public static final String	ASSIGNED_VALUE	"Assigned value"
public static final String	AVG_BRANCH_LENGTH	"Average branch length"
public static final String	AVG_CONTRACTION	"Average contraction"
public static final String	AVG_FRACTAL_DIMENSION	"Average fractal dimension"
public static final String	AVG_FRAGMENTATION	"Average fragmentation"
public static final String	AVG_PARTITION_ASYMMETRY	"Average partition asymmetry"
public static final String	AVG_REMOTE_ANGLE	"Average remote bif. angle"
public static final String	HIGHEST_PATH_ORDER	"Highest path order"
public static final String	INNER_LENGTH	"Length of inner branches (sum)"
public static final String	MEAN_RADIUS	"Mean radius"
public static final String	PRIMARY_LENGTH	"Length of primary branches (sum)"
public static final String	TERMINAL_LENGTH	"Length of terminal branches (sum)"

sc.fiji.snt.analysis.NodeColorMapper

Modifier and Type	Constant Field	Value
public static final String	BRANCH_LENGTH	"Branch length"
public static final String	BRANCH_ORDER	"Branch order"
public static final String	NEAREST_NEIGHBOR_DISTANCE	"Nearest neighbor distance"
public static final String	RADIUS	"Node radius"
public static final String	VALUES	"Node intensity values"
public static final String	X_COORDINATES	"X coordinates"
public static final String	Y_COORDINATES	"Y coordinates"
public static final String	Z_COORDINATES	"Z coordinates"

sc.fiji.snt.analysis.NodeStatistics<T>

Modifier and Type	Constant Field	Value
public static final String	BRANCH_LENGTH	"Branch length"
public static final String	BRANCH_ORDER	"Branch order"
public static final String	NEAREST_NEIGHBOR_DISTANCE	"Nearest neighbor distance"
public static final String	RADIUS	"Node radius"
public static final String	VALUES	"Node intensity values"
public static final String	X_COORDINATES	"X coordinates"
public static final String	Y_COORDINATES	"Y coordinates"
public static final String	Z_COORDINATES	"Z coordinates"

sc.fiji.snt.analysis.PathProfiler

Modifier and Type	Constant Field	Value
protected static final String	CIRCLE2D	"Circle (hollow)"
protected static final String	CIRCLE3D	"Circle (hollow, in orthogonal plane)"
protected static final String	DISK2D	"Disk (filled)"
protected static final String	DISK3D	"Disk (filled, in orthogonal plane)"
protected static final String	LINE2D	"Line (orthoghonal)"
protected static final String	LINE3D	"2D Line (orthoghonal, in node\'s plane)"
protected static final String	NONE	"None. Path centerline only"
protected static final String	SPHERE	"Sphere (filled)"
public static final String	X_VALUES	"x-values"
public static final String	Y_VALUES	"y-values"

sc.fiji.snt.analysis.PathStatistics

Modifier and Type	Constant Field	Value
public static final String	N_CHILDREN	"No. of children"

sc.fiji.snt.analysis.PersistenceAnalyzer

Modifier and Type	Constant Field	Value
protected static final int	FUNC_0_GEODESIC	0
protected static final int	FUNC_1_RADIAL	1
protected static final int	FUNC_2_CENTRIFUGAL	2
protected static final int	FUNC_3_PATH_ORDER	3
protected static final int	FUNC_4_X	4
protected static final int	FUNC_5_Y	5
protected static final int	FUNC_6_Z	6
protected static final int	FUNC_UNKNOWN	-1

sc.fiji.snt.analysis.RoiConverter

Modifier and Type	Constant Field	Value
public static final int	XY_PLANE	0
public static final int	XZ_PLANE	1
public static final int	ZY_PLANE	2

sc.fiji.snt.analysis.RootAngleAnalyzer

Modifier and Type	Constant Field	Value
public static final String	BALANCING_FACTOR	"Balancing factor"
public static final String	CENTRIPETAL_BIAS	"Centripetal bias"
public static final String	MEAN_DIRECTION	"Mean direction"

sc.fiji.snt.analysis.ShollAnalyzer

Modifier and Type	Constant Field	Value
public static final String	DECAY	"Decay"
public static final String	MAX	"Max"
public static final String	MAX_FITTED	"Max (fitted)"
public static final String	MAX_FITTED_RADIUS	"Max (fitted) radius"
public static final String	MEAN	"Mean"
public static final String	N_MAX	"No. maxima"
public static final String	N_SECONDARY_MAX	"No. secondary maxima"
public static final String	POLY_FIT_DEGREE	"Degree of Polynomial fit"
public static final String	RAMIFICATION_INDEX	"Ramification index"
public static final String	SUM	"Sum"

sc.fiji.snt.analysis.TreeColorMapper

Modifier and Type	Constant Field	Value
public static final String	INTER_NODE_ANGLE	"Internode angle"
public static final String	INTER_NODE_DISTANCE	"Internode distance"
public static final String	N_BRANCH_POINTS	"No. of branch points"
public static final String	N_NODES	"No. of nodes"
public static final String	N_SPINES	"No. of spines/varicosities"
public static final String	NODE_RADIUS	"Node radius"
public static final String	PATH_AVG_SPINE_DENSITY	"Path spine/varicosity density"
public static final String	PATH_DISTANCE	"Path distance to soma"
public static final String	PATH_EXT_ANGLE	"Path extension angle"
public static final String	PATH_EXT_ANGLE_REL	"Path extension angle (Rel.)"
public static final String	PATH_EXT_ANGLE_XY	"Path extension angle XY"
public static final String	PATH_EXT_ANGLE_XZ	"Path extension angle XZ"
public static final String	PATH_EXT_ANGLE_ZY	"Path extension angle ZY"
public static final String	PATH_FRAME	"Path frame"
public static final String	PATH_LENGTH	"Path length"
public static final String	PATH_MEAN_RADIUS	"Path mean radius"
public static final String	PATH_ORDER	"Path order"
public static final String	SHOLL_COUNTS	"Sholl inters. (root centered)"
public static final String	STRAHLER_ORDERS	"Horton-Strahler orders"
public static final String	TAG_FILENAME	"Tags/filename"
public static final String	VALUES	"Node intensity values"
public static final String	X_COORDINATES	"X coordinates"
public static final String	Y_COORDINATES	"Y coordinates"
public static final String	Z_COORDINATES	"Z coordinates"

sc.fiji.snt.analysis.TreeStatistics

Modifier and Type	Constant Field	Value
public static final String	AVG_SPINE_DENSITY	"Average spine/varicosity density"
public static final String	BRANCH_CONTRACTION	"Branch contraction"
public static final String	BRANCH_EXTENSION_ANGLE	"Branch extension angle"
public static final String	BRANCH_EXTENSION_ANGLE_REL	"Branch extension angle (Rel.)"
public static final String	BRANCH_EXTENSION_ANGLE_XY	"Branch extension angle XY"
public static final String	BRANCH_EXTENSION_ANGLE_XZ	"Branch extension angle XZ"
public static final String	BRANCH_EXTENSION_ANGLE_ZY	"Branch extension angle ZY"
public static final String	BRANCH_FRACTAL_DIMENSION	"Branch fractal dimension"
public static final String	BRANCH_LENGTH	"Branch length"
public static final String	BRANCH_MEAN_RADIUS	"Branch mean radius"
public static final String	BRANCH_SURFACE_AREA	"Branch surface area"
public static final String	BRANCH_VOLUME	"Branch volume"
public static final String	COMPLEXITY_INDEX_ACI	"Complexity index: ACI"
public static final String	COMPLEXITY_INDEX_DCI	"Complexity index: DCI"
public static final String	CONTRACTION	"Contraction"
public static final String	CONVEX_HULL_BOUNDARY_SIZE	"Convex hull: Boundary size"
public static final String	CONVEX_HULL_BOXIVITY	"Convex hull: Boxivity"
public static final String	CONVEX_HULL_CENTROID_ROOT_DISTANCE	"Convex hull: Centroid-root distance"
public static final String	CONVEX_HULL_COMPACTNESS_3D	"Convex hull: Compactness"
public static final String	CONVEX_HULL_ECCENTRICITY_2D	"Convex hull: Eccentricity"
public static final String	CONVEX_HULL_ELONGATION	"Convex hull: Elongation"
public static final String	CONVEX_HULL_ROUNDNESS	"Convex hull: Roundness"
public static final String	CONVEX_HULL_SIZE	"Convex hull: Size"
public static final String	DEPTH	"Depth"
public static final String	FRACTAL_DIMENSION	"Fractal dimension"
public static final String	GRAPH_DIAMETER	"Longest shortest path: Length"
public static final String	GRAPH_DIAMETER_ANGLE	"Longest shortest path: Extension angle"
public static final String	GRAPH_DIAMETER_ANGLE_XY	"Longest shortest path: Extension angle XY"
public static final String	GRAPH_DIAMETER_ANGLE_XZ	"Longest shortest path: Extension angle XZ"
public static final String	GRAPH_DIAMETER_ANGLE_ZY	"Longest shortest path: Extension angle ZY"
public static final String	HEIGHT	"Height"
public static final String	INNER_EXTENSION_ANGLE	"Inner branches: Extension angle"
public static final String	INNER_EXTENSION_ANGLE_REL	"Inner branches: Extension angle (Rel.)"
public static final String	INNER_EXTENSION_ANGLE_XY	"Inner branches: Extension angle XY"
public static final String	INNER_EXTENSION_ANGLE_XZ	"Inner branches: Extension angle XZ"
public static final String	INNER_EXTENSION_ANGLE_ZY	"Inner branches: Extension angle ZY"
public static final String	INNER_LENGTH	"Inner branches: Length"
public static final String	INTER_NODE_ANGLE	"Internode angle"
public static final String	INTER_NODE_DISTANCE	"Internode distance"
public static final String	INTER_NODE_DISTANCE_SQUARED	"Internode distance (squared)"
public static final String	LENGTH	"Cable length"
public static final String	MEAN_RADIUS	"Path mean radius"
public static final String	N_BRANCH_NODES	"No. of branch nodes (branch fragmentation)"
public static final String	N_BRANCH_POINTS	"No. of branch points"
public static final String	N_BRANCHES	"No. of branches"
public static final String	N_FITTED_PATHS	"No. of fitted paths"
public static final String	N_INNER_BRANCHES	"No. of inner branches"
public static final String	N_NODES	"No. of nodes"
public static final String	N_PATH_NODES	"No. of path nodes (path fragmentation)"
public static final String	N_PATHS	"No. of paths"
public static final String	N_PRIMARY_BRANCHES	"No. of primary branches"
public static final String	N_SPINES	"No. of spines/varicosities"
public static final String	N_TERMINAL_BRANCHES	"No. of terminal branches"
public static final String	N_TIPS	"No. of tips"
public static final String	NODE_RADIUS	"Node radius"
public static final String	PARTITION_ASYMMETRY	"Partition asymmetry"
public static final String	PATH_CHANNEL	"Path channel"
public static final String	PATH_CONTRACTION	"Path contraction"
public static final String	PATH_EXT_ANGLE	"Path extension angle"
public static final String	PATH_EXT_ANGLE_REL	"Path extension angle (Rel.)"
public static final String	PATH_EXT_ANGLE_XY	"Path extension angle XY"
public static final String	PATH_EXT_ANGLE_XZ	"Path extension angle XZ"
public static final String	PATH_EXT_ANGLE_ZY	"Path extension angle ZY"
public static final String	PATH_FRACTAL_DIMENSION	"Path fractal dimension"
public static final String	PATH_FRAME	"Path frame"
public static final String	PATH_LENGTH	"Path length"
public static final String	PATH_MEAN_RADIUS	"Path mean radius"
public static final String	PATH_N_SPINES	"No. of spines/varicosities per path"
public static final String	PATH_ORDER	"Path order"
public static final String	PATH_SPINE_DENSITY	"Path spine/varicosity density"
public static final String	PATH_SURFACE_AREA	"Path surface area"
public static final String	PATH_VOLUME	"Path volume"
public static final String	PRIMARY_EXTENSION_ANGLE	"Primary branches: Extension angle"
public static final String	PRIMARY_EXTENSION_ANGLE_XY	"Primary branches: Extension angle XY"
public static final String	PRIMARY_EXTENSION_ANGLE_XZ	"Primary branches: Extension angle XZ"
public static final String	PRIMARY_EXTENSION_ANGLE_ZY	"Primary branches: Extension angle ZY"
public static final String	PRIMARY_LENGTH	"Primary branches: Length"
public static final String	REMOTE_BIF_ANGLES	"Remote bif. angles"
public static final String	ROOT_ANGLE_B_FACTOR	"Root angles: Balancing factor"
public static final String	ROOT_ANGLE_C_BIAS	"Root angles: Centripetal bias"
public static final String	ROOT_ANGLE_M_DIRECTION	"Root angles: Mean direction"
public static final String	SHOLL_DECAY	"Sholl: Decay"
public static final String	SHOLL_KURTOSIS	"Sholl: Kurtosis"
public static final String	SHOLL_MAX_FITTED	"Sholl: Max (fitted)"
public static final String	SHOLL_MAX_FITTED_RADIUS	"Sholl: Max (fitted) radius"
public static final String	SHOLL_MAX_VALUE	"Sholl: Max"
public static final String	SHOLL_MEAN_VALUE	"Sholl: Mean"
public static final String	SHOLL_N_MAX	"Sholl: No. maxima"
public static final String	SHOLL_N_SECONDARY_MAX	"Sholl: No. secondary maxima"
public static final String	SHOLL_POLY_FIT_DEGREE	"Sholl: Degree of Polynomial fit"
public static final String	SHOLL_RAMIFICATION_INDEX	"Sholl: Ramification index"
public static final String	SHOLL_SKEWNESS	"Sholl: Skeweness"
public static final String	SHOLL_SUM_VALUE	"Sholl: Sum"
public static final String	STRAHLER_NUMBER	"Horton-Strahler root number"
public static final String	STRAHLER_RATIO	"Horton-Strahler bifurcation ratio"
public static final String	SURFACE_AREA	"Surface area"
public static final String	TERMINAL_EXTENSION_ANGLE	"Terminal branches: Extension angle"
public static final String	TERMINAL_EXTENSION_ANGLE_REL	"Terminal branches: Extension angle (Rel.)"
public static final String	TERMINAL_EXTENSION_ANGLE_XY	"Terminal branches: Extension angle XY"
public static final String	TERMINAL_EXTENSION_ANGLE_XZ	"Terminal branches: Extension angle XZ"
public static final String	TERMINAL_EXTENSION_ANGLE_ZY	"Terminal branches: Extension angle ZY"
public static final String	TERMINAL_LENGTH	"Terminal branches: Length"
public static final String	VALUES	"Node intensity values"
public static final String	VOLUME	"Volume"
public static final String	WIDTH	"Width"
public static final String	X_COORDINATES	"X coordinates"
public static final String	Y_COORDINATES	"Y coordinates"
public static final String	Z_COORDINATES	"Z coordinates"

sc.fiji.snt.analysis.curation.CurationTags

Modifier and Type	Constant Field	Value
public static final String	NEGATIVE	"cur:reject"
public static final String	POSITIVE	"cur:accept"
public static final String	UNSURE	"cur:unsure"

sc.fiji.snt.analysis.curation.PlausibilityCalibrator

Modifier and Type	Constant Field	Value
public static final String	CURATION_EXTENSION	"curation"

sc.fiji.snt.analysis.curation.PlausibilityCheck.SignalQuality

Modifier and Type	Constant Field	Value
public static final double	AUTO_THRESHOLD	-1.0

sc.fiji.snt.analysis.graph.AnnotationGraph

Modifier and Type	Constant Field	Value
public static final String	BRANCH_POINTS	"No. of branch points"
public static final String	EDGES	"edges"
public static final String	LENGTH	"Cable length"
public static final String	TIPS	"No. of tips"

sc.fiji.snt.analysis.graph.GraphColorMapper<V,E>

Modifier and Type	Constant Field	Value
public static final String	BETWEENNESS_CENTRALITY	"Betweenness centrality"
public static final String	CONNECTIVITY	"Connected components"
public static final String	ECCENTRICITY	"Eccentricity"
public static final String	EDGE_WEIGHT	"Edge weight"
public static final int	EDGES	2
public static final String	HEAVY_PATH_DECOMPOSITION	"Heavy path decomposition"
public static final String	IN_DEGREE	"In degree"
public static final String	INCOMING_WEIGHT	"Incoming weight"
public static final String	OUT_DEGREE	"Out degree"
public static final String	OUTGOING_WEIGHT	"Outgoing weight"
public static final String	PAGE_RANK	"Page rank"
public static final int	VERTICES	1
public static final int	VERTICES_AND_EDGES	4

sc.fiji.snt.analysis.growth.GrowthAnalyzer

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_ABSOLUTE_WINDOW_SIZE	3
public static final double	DEFAULT_BASE_THRESHOLD_FRACTION	0.3
public static final double	DEFAULT_MIN_PATH_LENGTH	5.0
public static final int	DEFAULT_MIN_TIME_POINTS	3
public static final double	DEFAULT_PHASE_SENSITIVITY	0.5
public static final double	DEFAULT_RAPID_THRESHOLD_MULTIPLE	1.5
public static final double	DEFAULT_RETRACTION_THRESHOLD	0.05
public static final boolean	DEFAULT_USE_ABSOLUTE_WINDOW_SIZE	true
public static final boolean	DEFAULT_USE_GLOBAL_THRESHOLDS	true
public static final double	DEFAULT_WINDOW_SIZE_FRACTION	0.125
public static final String	TAG_REGEX_PATTERN	"\\{([Nn]eurite\\s*#\\d+)}"

sc.fiji.snt.analysis.sholl.ProfileProperties

Modifier and Type	Constant Field	Value
public static final String	HEMI_EAST	"east"
public static final String	HEMI_NONE	"none"
public static final String	HEMI_NORTH	"north"
public static final String	HEMI_SOUTH	"south"
public static final String	HEMI_WEST	"west"
public static final String	INTG_MEAN	"mean"
public static final String	INTG_MEDIAN	"median"
public static final String	INTG_MODE	"mode"
public static final String	KEY_2D3D	"n-dimensions"
public static final String	KEY_CALIBRATION	"calibration"
public static final String	KEY_CENTER	"center"
public static final String	KEY_CHANNEL_POS	"channel"
public static final String	KEY_EFFECTIVE_STEP_SIZE	"effective.step.size"
public static final String	KEY_EXTRA_MEASUREMENT	"extra-measurement"
public static final String	KEY_FRAME_POS	"frame"
public static final String	KEY_HEMISHELLS	"hemishells"
public static final String	KEY_ID	"id"
public static final String	KEY_NSAMPLES	"samples-per-radius"
public static final String	KEY_NSAMPLES_INTG	"samples-integration"
public static final String	KEY_SLICE_POS	"slice"
public static final String	KEY_SOURCE	"source"
public static final String	KEY_THRESHOLD_RANGE	"threshold-range"
public static final String	SRC_IMG	"image"
public static final String	SRC_TABLE	"table"
public static final String	SRC_TRACES	"tracings"
public static final String	UNSET	"?"

sc.fiji.snt.analysis.sholl.ShollUtils

Modifier and Type	Constant Field	Value
public static final String	URL	"https://imagej.net/plugins/snt/sholl"

sc.fiji.snt.analysis.sholl.gui.ShollOverlay

Modifier and Type	Constant Field	Value
public static final String	COUNT	"sholl-count"
public static final String	POINTS	"points"
public static final String	PROP	"sholl-prop"
public static final String	RADIUS	"sholl-radius"
public static final String	SHELL	"shell"

sc.fiji.snt.analysis.sholl.gui.ShollPlot

Modifier and Type	Constant Field	Value
public static final int	THICK_LINE	-1

sc.fiji.snt.analysis.sholl.math.LinearProfileStats

Modifier and Type	Constant Field	Value
protected static final double	UNASSIGNED_VALUE	4.9E-324

sc.fiji.snt.analysis.sholl.math.NormalizedProfileStats

Modifier and Type	Constant Field	Value
protected static final double	UNASSIGNED_VALUE	4.9E-324

sc.fiji.snt.analysis.sholl.math.ShollStats

Modifier and Type	Constant Field	Value
public static final int	ANNULUS	8
public static final int	AREA	2
public static final int	GUESS_SLOG	512
public static final int	LOG_LOG	256
public static final int	PERIMETER	4
public static final int	S_SHELL	64
public static final int	SEMI_LOG	128
public static final int	SURFACE	32
public static final int	VOLUME	16

sc.fiji.snt.analysis.sholl.parsers.ImageParser2D

Modifier and Type	Constant Field	Value
public final int	MAX_N_SPANS	10
public static final int	MEAN	0
public static final int	MEDIAN	1
public static final int	MODE	2

sc.fiji.snt.analysis.sholl.parsers.TreeParser

Modifier and Type	Constant Field	Value
public static final int	ROOT_NODES_ANY	0
public static final int	ROOT_NODES_APICAL_DENDRITE	1
public static final int	ROOT_NODES_AXON	2
public static final int	ROOT_NODES_CUSTOM	3
public static final int	ROOT_NODES_DENDRITE	4
public static final int	ROOT_NODES_SOMA	5
public static final int	ROOT_NODES_SOMA_ANY	7
public static final int	ROOT_NODES_UNDEFINED	6

sc.fiji.snt.annotation.AllenUtils

Modifier and Type	Constant Field	Value
public static final int	BRAIN_ROOT_ID	997
public static final String	VERSION	"3"

sc.fiji.snt.annotation.BrainAnnotation

Modifier and Type	Constant Field	Value
public static final char	ANY_HEMISPHERE	'\u0000'
public static final char	LEFT_HEMISPHERE	'l'
public static final char	RIGHT_HEMISPHERE	'r'

sc.fiji.snt.annotation.DrosophilaUtils

Modifier and Type	Constant Field	Value
public static final int	BRAIN_ROOT_ID	3624

sc.fiji.snt.event.SNTEvent

Modifier and Type	Constant Field	Value
public static final int	NO_EVENT	0
public static final int	QUIT	1
public static final int	SEND_TO_TRAKEM2	2

sc.fiji.snt.gui.FilePicker

Modifier and Type	Constant Field	Value
public static final int	OPEN_DIALOG	0
public static final int	SAVE_DIALOG	1

sc.fiji.snt.gui.GuiUtils

Modifier and Type	Constant Field	Value
public static final String	LAF_DARCULA	"FlatLaf Darcula"
public static final String	LAF_DARK	"FlatLaf Dark"
public static final String	LAF_DEFAULT	"FlatLaf Light"
public static final String	LAF_LIGHT	"FlatLaf Light"
public static final String	LAF_LIGHT_INTJ	"FlatLaf IntelliJ"

sc.fiji.snt.gui.GuiUtils.JTables.VisitingZoom

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PERCENT	600
public static final int	MAX_PERCENT	3200
public static final int	MIN_PERCENT	25

sc.fiji.snt.gui.OntologyBrowser

Modifier and Type	Constant Field	Value
public static final String	SEPARATOR	"::"

sc.fiji.snt.gui.ScriptRecorder

Modifier and Type	Constant Field	Value
public static final String	IGNORED_CMD	"rec-off"

sc.fiji.snt.gui.SearchField

Modifier and Type	Constant Field	Value
public static final int	CASE_BUTTON	2
public static final int	OPTIONS_MENU	1
public static final int	REGEX_BUTTON	8
public static final int	WORD_BUTTON	4

sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd

Modifier and Type	Constant Field	Value
public static final String	COLOR_SOMA_MESH	"Soma compartment (graph color)"
public static final String	COLOR_UNIQUE	"Unique colors"

sc.fiji.snt.gui.cmds.CommonDynamicCmd

Modifier and Type	Constant Field	Value
protected static final String	EMPTY_LABEL	"<html>&nbsp;"
protected static final String	HEADER_HTML	"<html><body><div style=\'font-weight:bold;\'>"

sc.fiji.snt.gui.cmds.ImportSeedPointsCmd

Modifier and Type	Constant Field	Value
public static final String	UNITS_PHYSICAL	"Physical (image-calibrated)"

sc.fiji.snt.gui.cmds.MultiSpectralRefinerCmd

Modifier and Type	Constant Field	Value
public static final String	AUTO_INTENSITY_KEY	"autoIntensity"
public static final String	AUTO_TUNE_KEY	"autoTune"
public static final String	BACKGROUND_THRESHOLD_KEY	"backgroundThreshold"
public static final String	COLOR_WEIGHT_KEY	"colorWeight"
public static final String	COS_SIMILARITY_KEY	"cosSimilarity"
public static final String	INTENSITY_WEIGHT_KEY	"intensityWeight"
public static final String	MAX_INTENSITY_KEY	"maxIntensity"
public static final String	MAX_PERCENT_C_KEY	"maxPercentC"
public static final String	MAX_RADIUS_KEY	"maxRadius"
public static final String	MIN_INTENSITY_KEY	"minIntensity"
public static final String	MIN_PERCENT_C_KEY	"minPercentC"
public static final String	RADIUS_WEIGHT_KEY	"radiusWeight"
public static final String	REF_WINDOW_KEY	"referenceWindowRadius"

sc.fiji.snt.gui.cmds.PathFitterCmd

Modifier and Type	Constant Field	Value
public static final String	FALLBACK_CHOICE_KEY	"fallback"
public static final String	FIT_CHOICE_KEY	"choice"
public static final String	FIT_IN_PLACE_KEY	"inplace"
public static final String	MAX_SEARCH_RADIUS_PX_KEY	"maxsearchpx"
public static final String	MIN_ANGLE_KEY	"minang"
public static final String	SEC_LAYER_KEY	"secondary"

sc.fiji.snt.hyperpanes.MultiDThreePanes

Modifier and Type	Constant Field	Value
protected static final String	MIP_OVERLAY_IDENTIFIER_PREFIX	"SNT-MIP-OVERLAY"
public static final int	XY_PLANE	0
public static final int	XZ_PLANE	1
public static final int	ZY_PLANE	2

sc.fiji.snt.io.MouseLightLoader

Modifier and Type	Constant Field	Value
public static final String	AXON	"axon"
public static final String	DENDRITE	"dendrite"
public static final String	SOMA	"soma"

sc.fiji.snt.io.OmeAxisUtils

Modifier and Type	Constant Field	Value
public static final String	LAYOUT_BIOFORMATS2RAW	"bioformats2raw"
public static final String	LAYOUT_OME_NGFF	"ome-ngff"
public static final String	LAYOUT_UNKNOWN	"unknown"

sc.fiji.snt.plugin.AutotraceFromBinarySeedsCmd

Modifier and Type	Constant Field	Value
public static final String	SOURCE_SELECTION	"Selection only"

sc.fiji.snt.plugin.AutotraceFromBinaryTipsCmd

Modifier and Type	Constant Field	Value
public static final String	SOURCE_SELECTION	"Selection only"

sc.fiji.snt.plugin.AutotraceFromSeedsCmd

Modifier and Type	Constant Field	Value
public static final String	SOURCE_SELECTION	"Selection only"

sc.fiji.snt.plugin.AutotraceFromTipsCmd

Modifier and Type	Constant Field	Value
protected static final String	SOURCE_ALL	"All seeds"
public static final String	SOURCE_SELECTION	"Selection only"
protected static final String	SOURCE_VISIBLE	"Visible (within confidence range)"

sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

Modifier and Type	Constant Field	Value
public static final String	SOURCE_SELECTION	"Selection only"

sc.fiji.snt.plugin.BinaryTracerCommonCmd

Modifier and Type	Constant Field	Value
public static final String	ROI_AUTO_DETECT	"None. Use auto-detection"
public static final String	ROI_CENTROID	"Path(s) branch out from ROI simple centroid"
public static final String	ROI_CENTROID_WEIGHTED	"Path(s) branch out from ROI weighted centroid"
public static final String	ROI_CONTAINED	"ROI marks a single root"
public static final String	ROI_EDGE	"Path(s) branch out from ROI edge"
public static final String	ROI_UNSET	"None. Ignore any ROIs"

sc.fiji.snt.plugin.PathMatcherCmd

Modifier and Type	Constant Field	Value
public static final String	TAG_REGEX_PATTERN	"\\{([Nn]eurite\\s*#\\d+)}"
public static final String	TAG_REGEX_PATTERN_LEGACY	"\\{Group \\d+\\}"

sc.fiji.snt.plugin.ShollAnalysisImgCommonCmd

Modifier and Type	Constant Field	Value
protected static final String	EMPTY_LABEL	"<html>&nbsp;"
protected static final String	HEADER_HTML	"<html><body><div style=\'font-weight:bold;\'>"
protected static final String	HEADER_TOOLTIP	"<HTML><div WIDTH=650>"

sc.fiji.snt.plugin.ShollAnalysisPrefsCmd

Modifier and Type	Constant Field	Value
public static final int	ALLOWED_MAX_DEGREE	60
public static final int	ALLOWED_MIN_DEGREE	2
public static final int	DEF_ANGLE_STEP_SIZE	10
public static final boolean	DEF_DEBUG_MODE	false
public static final boolean	DEF_DETAILED_METRICS	false
public static final int	DEF_ENCLOSING_RADIUS_CUTOFF	1
public static final boolean	DEF_INCLUDE_ZERO_COUNTS	true
public static final boolean	DEF_KS_TESTING	false
public static final int	DEF_MAX_DEGREE	30
public static final int	DEF_MIN_DEGREE	2
public static final String	DEF_ROI_SIZE	"Medium"
public static final double	DEF_RSQUARED	0.7
public static final boolean	DEF_SKIP_SINGLE_VOXELS	true
public static final boolean	DEF_SKIP_SOMATIC_SEGMENTS	true
protected static final String	DESCRIPTION_HTML	"<html><body><div style=\'width:500px\'>"
protected static final String	HEADER_HTML	"<html><body><div style=\'font-weight:bold;\'>"

sc.fiji.snt.plugin.ij1.Strahler

Modifier and Type	Constant Field	Value
protected static final String	URL	"https://imagej.net/plugins/snt/strahler"

sc.fiji.snt.seed.SeedOverlay

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_COLOR_TABLE_NAME	"Viridis"

sc.fiji.snt.seed.SeedPoint

Modifier and Type	Constant Field	Value
public static final int	CT_UNSET	-1
public static final String	TAG_UNSET	""

sc.fiji.snt.seed.SeedTableModel

Modifier and Type	Constant Field	Value
public static final int	COL_CONFIDENCE	3
public static final int	COL_RADIUS	4
public static final int	COL_SOURCE	6
public static final int	COL_STATUS	7
public static final int	COL_TYPE	5
public static final int	COL_X	0
public static final int	COL_Y	1
public static final int	COL_Z	2
public static final String	STATUS_COVERED	"covered"
public static final String	STATUS_UNCOVERED	"uncovered"
public static final String	STATUS_UNKNOWN	"-"

sc.fiji.snt.tracing.SearchThread

Modifier and Type	Constant Field	Value
public static final int	CANCELLED	1
public static final byte	CLOSED_FROM_GOAL	0x4
public static final byte	CLOSED_FROM_START	0x2
public static final byte	FREE	0x5
public static final byte	OPEN_FROM_GOAL	0x3
public static final byte	OPEN_FROM_START	0x1
public static final int	OUT_OF_MEMORY	4
public static final int	POINTS_EXHAUSTED	3
public static final int	SUCCESS	0
public static final int	TIMED_OUT	2

sc.fiji.snt.tracing.auto.AbstractGWDTTracer<T>

Modifier and Type	Constant Field	Value
public static final byte	ALIVE	0x2
public static final byte	FAR	0x0
public static final byte	TRIAL	0x1

sc.fiji.snt.tracing.auto.AutoTracer

Modifier and Type	Constant Field	Value
public static final int	ROI_CENTROID	2
public static final int	ROI_CENTROID_WEIGHTED	3
public static final int	ROI_CONTAINED	4
public static final int	ROI_EDGE	1
public static final int	ROI_UNSET	0

sc.fiji.snt.tracing.auto.BinaryTracer

Modifier and Type	Constant Field	Value
public static final int	LOWEST_INTENSITY_BRANCH	3
public static final int	LOWEST_INTENSITY_VOXEL	2
public static final int	MOST_DISTAL	-3
public static final int	PERIPHERAL_SEGMENTS	-2
public static final int	SHORTEST_BRANCH	1
public static final int	SHORTEST_EDGE	-1

sc.fiji.snt.tracing.auto.SomaUtils

Modifier and Type	Constant Field	Value
public static final String	OUTPUT_CIRCLE	"Circle"
public static final String	OUTPUT_CONTOUR	"Contour"
public static final String	OUTPUT_POINT	"Point"

sc.fiji.snt.tracing.cost.DifferenceSq

Modifier and Type	Constant Field	Value
public static final double	MIN_COST_PER_UNIT_DISTANCE	1.0

sc.fiji.snt.tracing.cost.Reciprocal

Modifier and Type	Constant Field	Value
public static final double	CONST_8	255.0
public static final double	MIN_COST_PER_UNIT_DISTANCE	0.00392156862745098
public static final double	RECIPROCAL_FUDGE	1.0E-6

sc.fiji.snt.util.SNTColor

Modifier and Type	Constant Field	Value
protected static final int	SWC_TYPE_IGNORED	-1

sc.fiji.snt.viewer.Annotation3D

Modifier and Type	Constant Field	Value
protected static final int	MERGE	4
protected static final int	PLANE	6
protected static final int	Q_TIP	3
protected static final int	SCATTER	0
protected static final int	STRIP	2
protected static final int	SURFACE	1
protected static final int	SURFACE_AND_VOLUME	5

sc.fiji.snt.viewer.Bvv.Keyframe

Modifier and Type	Constant Field	Value
public static final int	ACCEL_SLOW_END	2
public static final int	ACCEL_SLOW_START	1
public static final int	ACCEL_SOFT_SLOW_END	5
public static final int	ACCEL_SOFT_SLOW_START	4
public static final int	ACCEL_SOFT_SYMMETRIC	3
public static final int	ACCEL_SYMMETRIC	0

sc.fiji.snt.viewer.OBJMesh

Modifier and Type	Constant Field	Value
public static final int	SHADING_DEFAULT	0
public static final int	SHADING_SMOOTH	1

sc.fiji.snt.viewer.Viewer3D

Modifier and Type	Constant Field	Value
protected static final float	DEF_NODE_RADIUS	3.0f