Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
degreeSymbol |
176 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DATE_FORMAT_NOW |
"yyyy-MM-dd HH:mm:ss" |
Modifier and Type | Constant Field | Value |
---|---|---|
public final int |
DELAUNAY |
1 |
public final int |
VORONOI |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CHANNEL |
6 |
public static final int |
T |
5 |
public static final int |
X |
1 |
public static final int |
Y |
2 |
public static final int |
Z |
3 |
public static final int |
ZOOM |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MACRO_CMD |
"var leftClick=16, alt=9;\nmacro \'Fill hole Tool - C111O11ffC100T6c0aF\' {\n while (true) {\n getCursorLoc(x, y, z, flags);\n if (flags&leftClick==0) exit();\n call(\'Fill_holes.fillHoles\', x,y,z,flags);\n exit(); }\n}\n\n" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CLOSE |
3 |
public static final int |
DILATE |
1 |
public static final int |
ERODE |
0 |
public static final int |
FCLOSE |
7 |
public static final int |
FDILATE |
5 |
public static final int |
FERODE |
4 |
public static final int |
FOPEN |
6 |
public static final int |
OPEN |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
EAST |
3 |
public static final int |
HORIZONTAL |
0 |
public static final int |
NORTH |
1 |
public static final int |
SOUTH |
2 |
public static final int |
VERTICAL |
1 |
public static final int |
WEST |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AFFINE |
0 |
public static final int |
RIGID |
2 |
public static final int |
SIMILARITY |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_GAUSSIAN_SCALE |
250 |
public static final int |
MAX_RETINEX_SCALES |
8 |
public static final int |
MIN_GAUSSIAN_SCALE |
16 |
public static final int |
RETINEX_HIGH |
2 |
public static final int |
RETINEX_LOW |
1 |
public static final int |
RETINEX_UNIFORM |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MACRO_CMD |
"var roiBrushWidth = 10;\nvar pollDelay = 10;\nvar leftClick=16, altOrShift=9;\nmacro \'Roi Brush Tool - C111o11ff\' {\n while (true) {\n getCursorLoc(x, y, z, flags);\n if (flags&leftClick==0) exit();\n if (flags&altOrShift==0){\n call(\'ROIBrush_.label\', x,y,z,flags,roiBrushWidth);\n }else{\n call(\'ROIBrush_.unlabel\', x,y,z,flags,roiBrushWidth);\n }\n wait(pollDelay);\n }\n}\n\nmacro \'Roi Brush Tool Options...\' {\n roiBrushWidth = getNumber(\'Roi Brush Width (pixels):\', brushWidth);\n}" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
CUSTOM |
4 |
protected static final int |
LOWER_LEFT |
2 |
protected static final int |
LOWER_RIGHT |
1 |
protected static final int |
UPPER_LEFT |
3 |
protected static final int |
UPPER_RIGHT |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected final String |
COMMON_FIRST_SLICE_BOX |
"CommonFirstSliceBox" |
protected final String |
COMMON_LAST_SLICE_BOX |
"LastSliceBox" |
protected final String |
I_FIRST_SLICE_BOX |
"iFirstSliceBox" |
protected final String |
I_FIRST_SLICE_BUTTON |
"iFirstSliceButton" |
protected final String |
I_LAST_SLICE_BOX |
"iLastSliceBox" |
protected final String |
I_LAST_SLICE_BUTTON |
"iLastSliceButton" |
protected final String |
I_THRESH_SLIDER |
"iThresholdSlider" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
VERSIONSTRING |
"1.7-fiji1" |
Modifier and Type | Constant Field | Value |
---|---|---|
public final int |
ASCII |
3 |
public final int |
RAW |
0 |
public final int |
RLE |
1 |
public final int |
ZLIB |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public final int |
RAW |
0 |
public final int |
RLE |
1 |
public final int |
ZLIB |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO |
"Info" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
iNearestNeighborMethod |
0 |
protected static final int |
iNLinearMethod |
1 |
protected static final int |
numInterpolationMethods |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BRIGHTNESS_SETTINGS |
"brightness settings" |
public static final String |
COLLAPSE_CARDS |
"collapse cards panel" |
public static final String |
CROP |
"crop" |
public static final String |
EXPAND_CARDS |
"expand and focus cards panel" |
public static final String |
GO_TO_BOOKMARK |
"go to bookmark" |
public static final String |
GO_TO_BOOKMARK_ROTATION |
"go to bookmark rotation" |
public static final String |
LOAD_SETTINGS |
"load settings" |
public static final String |
MANUAL_TRANSFORM |
"toggle manual transformation" |
public static final String |
RECORD_MAX_PROJECTION_MOVIE |
"record max projection movie" |
public static final String |
RECORD_MOVIE |
"record movie" |
public static final String |
SAVE_SETTINGS |
"save settings" |
public static final String |
SET_BOOKMARK |
"set bookmark" |
public static final String |
SHOW_HELP |
"help" |
public static final String |
VISIBILITY_AND_GROUPING |
"visibility and grouping" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DRAG_ROTATE |
"2d drag rotate" |
public static final String |
DRAG_TRANSLATE |
"2d drag translate" |
public static final String |
KEY_ZOOM_IN |
"2d zoom in" |
public static final String |
KEY_ZOOM_IN_FAST |
"2d zoom in fast" |
public static final String |
KEY_ZOOM_IN_SLOW |
"2d zoom in slow" |
public static final String |
KEY_ZOOM_OUT |
"2d zoom out" |
public static final String |
KEY_ZOOM_OUT_FAST |
"2d zoom out fast" |
public static final String |
KEY_ZOOM_OUT_SLOW |
"2d zoom out slow" |
public static final String |
ROTATE_LEFT |
"2d rotate left" |
public static final String |
ROTATE_LEFT_FAST |
"2d rotate left fast" |
public static final String |
ROTATE_LEFT_SLOW |
"2d rotate left slow" |
public static final String |
ROTATE_RIGHT |
"2d rotate right" |
public static final String |
ROTATE_RIGHT_FAST |
"2d rotate right fast" |
public static final String |
ROTATE_RIGHT_SLOW |
"2d rotate right slow" |
public static final String |
SCROLL_ROTATE |
"2d scroll rotate" |
public static final String |
SCROLL_ROTATE_FAST |
"2d scroll rotate fast" |
public static final String |
SCROLL_ROTATE_SLOW |
"2d scroll rotate slow" |
public static final String |
SCROLL_TRANSLATE |
"2d scroll translate" |
public static final String |
SCROLL_TRANSLATE_FAST |
"2d scroll translate fast" |
public static final String |
SCROLL_TRANSLATE_SLOW |
"2d scroll translate slow" |
public static final String |
ZOOM_FAST |
"2d scroll zoom fast" |
public static final String |
ZOOM_NORMAL |
"2d scroll zoom" |
public static final String |
ZOOM_SLOW |
"2d scroll zoom slow" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DRAG_ROTATE |
"drag rotate" |
public static final String |
DRAG_ROTATE_FAST |
"drag rotate fast" |
public static final String |
DRAG_ROTATE_SLOW |
"drag rotate slow" |
public static final String |
DRAG_TRANSLATE |
"drag translate" |
public static final String |
KEY_BACKWARD_Z |
"backward z" |
public static final String |
KEY_BACKWARD_Z_FAST |
"backward z fast" |
public static final String |
KEY_BACKWARD_Z_SLOW |
"backward z slow" |
public static final String |
KEY_FORWARD_Z |
"forward z" |
public static final String |
KEY_FORWARD_Z_FAST |
"forward z fast" |
public static final String |
KEY_FORWARD_Z_SLOW |
"forward z slow" |
public static final String |
KEY_ZOOM_IN |
"zoom in" |
public static final String |
KEY_ZOOM_IN_FAST |
"zoom in fast" |
public static final String |
KEY_ZOOM_IN_SLOW |
"zoom in slow" |
public static final String |
KEY_ZOOM_OUT |
"zoom out" |
public static final String |
KEY_ZOOM_OUT_FAST |
"zoom out fast" |
public static final String |
KEY_ZOOM_OUT_SLOW |
"zoom out slow" |
public static final String |
ROTATE_LEFT |
"rotate left" |
public static final String |
ROTATE_LEFT_FAST |
"rotate left fast" |
public static final String |
ROTATE_LEFT_SLOW |
"rotate left slow" |
public static final String |
ROTATE_RIGHT |
"rotate right" |
public static final String |
ROTATE_RIGHT_FAST |
"rotate right fast" |
public static final String |
ROTATE_RIGHT_SLOW |
"rotate right slow" |
public static final String |
SCROLL_Z |
"scroll browse z" |
public static final String |
SCROLL_Z_FAST |
"scroll browse z fast" |
public static final String |
SCROLL_Z_SLOW |
"scroll browse z slow" |
public static final String |
SELECT_AXIS_X |
"axis x" |
public static final String |
SELECT_AXIS_Y |
"axis y" |
public static final String |
SELECT_AXIS_Z |
"axis z" |
public static final String |
ZOOM_NORMAL |
"scroll zoom" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AFFINE |
"Affine" |
public static final String |
ROTATION |
"Rotation" |
public static final String |
SIMILARITY |
"Similarity" |
public static final String |
TPS |
"Thin Plate Spline" |
public static final String |
TRANSLATION |
"Translation" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
LANDMARK_POINT_CUBE_PHYSICAL |
"Landmark point cube (physical units)" |
public static final String |
LANDMARK_POINT_CUBE_PIXEL |
"Landmark point cube (pixel units)" |
public static final String |
LANDMARK_POINTS |
"Landmark points" |
public static final String |
MOVING |
"Moving" |
public static final String |
MOVING_WARPED |
"Moving (warped)" |
public static final String |
SPECIFIED |
"Specified" |
public static final String |
SPECIFIED_PHYSICAL |
"Specified (physical units)" |
public static final String |
SPECIFIED_PIXEL |
"Specified (pixel units)" |
public static final String |
TARGET |
"Target" |
public static final String |
UNION_TARGET_MOVING |
"Union of Target and warped moving image" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
INITIAL_EMPTY_SIZE |
32768 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DATA_TYPE_KEY |
"dataType" |
public static final String |
DOWNSAMPLING_FACTORS_KEY |
"downsamplingFactors" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SOURCETRANSFORM_AFFINE_TAG |
"affine" |
public static final String |
SOURCETRANSFORM_TAG |
"SourceTransform" |
public static final String |
SOURCETRANSFORM_TYPE_ATTRIBUTE_NAME |
"type" |
public static final String |
SOURCETRANSFORM_TYPE_VALUE_AFFINE |
"affine" |
public static final String |
SOURCETRANSFORMS_TAG |
"ManualSourceTransforms" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DEFAULT_SOURCEGROUPS_CARD |
"default bdv groups card" |
public static final String |
DEFAULT_SOURCES_CARD |
"default bdv sources card" |
public static final String |
DEFAULT_VIEWERMODES_CARD |
"default bdv viewer modes card" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
COLOR_COLUMN |
3 |
public static final int |
IS_ACTIVE_COLUMN |
2 |
public static final int |
IS_CURRENT_COLUMN |
1 |
public static final int |
NAME_COLUMN |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MOVING_GROUP_INDEX |
0 |
public static final int |
TARGET_GROUP_INDEX |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_SPOT_SIZE |
4.0 |
public static final String |
KEY_COLOR |
"Color" |
public static final String |
KEY_DISPLAY_SPOT_NAMES |
"DisplaySpotNames" |
public static final String |
KEY_INACTIVE_COLOR |
"InactiveColor" |
public static final String |
KEY_SPOT_RADIUS_RATIO |
"SpotRadiusRatio" |
public static final String |
KEY_SPOT_SIZE |
"SpotSize" |
public static final String |
KEY_SPOTS_VISIBLE |
"SpotsVisible" |
public static final String |
KEY_UNMATCHED_COLOR |
"InactiveColor" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ACTIVATE |
"table activate" |
public static final String |
ACTIVATE_SELECTED |
"table activate selected " |
public static final String |
CLEAR_FIXED |
"table clear fixed" |
public static final String |
CLEAR_MOVING |
"table clear moving" |
public static final String |
CLEAR_SELECTED_FIXED |
"table clear selected fixed" |
public static final String |
CLEAR_SELECTED_MOVING |
"table clear selected moving" |
public static final String |
DELETE |
"table delete" |
public static final String |
DELETE_SELECTED |
"table delete selected " |
public static final boolean |
FIXED |
false |
public static final boolean |
MOVING |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ALIGN_PLANE |
"align %s plane" |
public static final String |
ALIGN_XY_PLANE |
"align XY plane" |
public static final String |
ALIGN_XZ_PLANE |
"align XZ plane" |
public static final String |
ALIGN_ZY_PLANE |
"align ZY plane" |
public static final String |
NEXT_TIMEPOINT |
"next timepoint" |
public static final String |
PREVIOUS_TIMEPOINT |
"previous timepoint" |
public static final String |
SET_CURRENT_SOURCE |
"set current source %d" |
public static final String |
SET_CURRENT_SOURCE_KEYS_FORMAT |
"%s" |
public static final String |
TOGGLE_FUSED_MODE |
"toggle fused mode" |
public static final String |
TOGGLE_GROUPING |
"toggle grouping" |
public static final String |
TOGGLE_INTERPOLATION |
"toggle interpolation" |
public static final String |
TOGGLE_SOURCE_VISIBILITY |
"toggle source visibility %d" |
public static final String |
TOGGLE_SOURCE_VISIBILITY_KEYS_FORMAT |
"shift %s" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CURRENT_GROUP_CHANGED |
1 |
public static final int |
CURRENT_SOURCE_CHANGED |
0 |
public static final int |
DISPLAY_MODE_CHANGED |
4 |
public static final int |
GROUP_ACTIVITY_CHANGED |
3 |
public static final int |
GROUP_NAME_CHANGED |
6 |
public static final int |
NUM_GROUPS_CHANGED |
9 |
public static final int |
NUM_SOURCES_CHANGED |
8 |
public static final int |
SOURCE_ACTVITY_CHANGED |
2 |
public static final int |
SOURCE_TO_GROUP_ASSIGNMENT_CHANGED |
5 |
public static final int |
VISIBILITY_CHANGED |
7 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ALIGN_PLANE |
"align %s plane" |
public static final String |
COLLAPSE_CARDS |
"collapse cards panel" |
public static final String |
DISPLAY_XFMS |
"display transforms" |
public static final String |
EXPAND_CARDS |
"expand and focus cards panel" |
public static final String |
ROTATE_PLANE |
"rotate %s" |
public static final String |
SET_CURRENT_SOURCE |
"set current source %d" |
public static final String |
TOGGLE_FUSED_MODE |
"toggle fused mode" |
public static final String |
TOGGLE_GROUPING |
"toggle grouping" |
public static final String |
TOGGLE_INTERPOLATION |
"toggle interpolation" |
public static final String |
TOGGLE_SOURCE_VISIBILITY |
"toggle source visibility %d" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
DEFAULT_HEIGHT |
400 |
protected static final int |
DEFAULT_WIDTH |
600 |
public static final int |
GRID_SOURCE_ID |
1696993146 |
public static final int |
JACDET_SOURCE_ID |
1006827158 |
public static final int |
WARPMAG_SOURCE_ID |
956736363 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ALIGN_VIEW_TRANSFORMS |
"align view transforms %s" |
public static final String |
BRIGHTNESS_SETTINGS |
"brightness settings" |
public static final String |
CROP |
"crop" |
public static final String |
DEBUG |
"debug" |
public static final String |
ESTIMATE_WARP |
"estimate warp" |
public static final String |
EXPORT_AFFINE |
"export affine" |
public static final String |
EXPORT_IP |
"export imageplus" |
public static final String |
EXPORT_WARP |
"export warp field" |
public static final String |
GARBAGE_COLLECTION |
"garbage collection" |
public static final String |
GO_TO_BOOKMARK |
"go to bookmark" |
public static final String |
GO_TO_BOOKMARK_ROTATION |
"go to bookmark rotation" |
public static final String |
LANDMARK_GRID_DIALOG |
"landmark grid dialog" |
public static final String |
LANDMARK_MODE_OFF |
"landmark mode off" |
public static final String |
LANDMARK_MODE_ON |
"landmark mode on" |
public static final String |
LOAD_LANDMARKS |
"load landmarks" |
public static final String |
LOAD_SETTINGS |
"load settings" |
public static final String |
PRINT_TRANSFORM |
"print transform" |
public static final String |
QUICK_SAVE_LANDMARKS |
"quick save landmarks" |
public static final String |
REDO |
"redo" |
public static final String |
RESET_VIEWER |
"reset active viewer" |
public static final String |
SAVE_LANDMARKS |
"save landmarks" |
public static final String |
SAVE_SETTINGS |
"save settings" |
public static final String |
SAVE_WARPED |
"save warped" |
public static final String |
SAVE_WARPED_XML |
"save warped xml" |
public static final String |
SELECT_TABLE_ROWS |
"select table row %d" |
public static final String |
SET_BOOKMARK |
"set bookmark" |
public static final String |
SET_WARPTYPE_VIS |
"set warp vis type %s" |
public static final String |
SET_WARPTYPE_VIS_P |
"p set warp vis type %s" |
public static final String |
SET_WARPTYPE_VIS_Q |
"q set warp vis type %s" |
public static final String |
SHOW_HELP |
"help" |
public static final String |
SHOW_SOURCE_INFO |
"show source info" |
public static final String |
SHOW_WARPTYPE_DIALOG |
"show warp vis dialog" |
public static final String |
TOGGLE_BOX_AND_TEXT_OVERLAY_VISIBLE |
"toggle box and text overlay visible" |
public static final String |
TOGGLE_ESTIMATE_WARP_ONDRAG |
"toggle estimate warp on drag" |
public static final String |
TOGGLE_LANDMARK_MODE |
"landmark mode toggle" |
public static final String |
TOGGLE_MOVING_IMAGE_DISPLAY |
"toggle moving image display" |
public static final String |
TOGGLE_POINT_NAMES_VISIBLE |
"toggle point names visible" |
public static final String |
TOGGLE_POINTS_VISIBLE |
"toggle points visible" |
public static final String |
UNDO |
"undo" |
public static final String |
VISIBILITY_AND_GROUPING |
"visibility and grouping %s" |
public static final String |
WARP_TO_NEAREST_POINT |
"warp to nearest landmark" |
public static final String |
WARP_TO_NEXT_POINT |
"warp to next landmark %s" |
public static final String |
WARP_TO_SELECTED_POINT |
"warp to selected landmark" |
public static final String |
WARPMAG_BASE |
"set warpmag base %s" |
public static final String |
WARPVISDIALOG |
"warp vis dialog" |
public static final String |
WARPVISGRID |
"set warp vis grid %s" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
defaultGridSpacing |
100 |
public static final int |
defaultGridWidth |
5 |
public static final int |
maxGridSpacing |
400 |
public static final int |
maxGridWidth |
50 |
public static final int |
minGridSpacing |
5 |
public static final int |
minGridWidth |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ACTIVECOLUMN |
1 |
public static final int |
NAMECOLUMN |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AFFINE_TRANSFORM_KEY |
"affineTransform" |
public static final String |
DOWNSAMPLING_FACTORS_KEY |
"downsamplingFactors" |
public static final String |
PIXEL_RESOLUTION_KEY |
"pixelResolution" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
eps |
0.001 |
public static final double |
PI |
3.141592653589793 |
public static final double |
PIo2 |
1.5707963267948966 |
public static final double |
PIo2t3 |
4.71238898038469 |
public static final double |
PIt2 |
6.283185307179586 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_OUTPUT_SIZE |
1024 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ADAPT_COEFFICIENTS |
"adaptCoefficients" |
public static final String |
COMPARE_ELASTIC_RAW |
"compareElasticRawTransforms" |
public static final String |
COMPARE_OPPOSITE_ELASTIC |
"compareOppositeElasticTransforms" |
public static final String |
COMPARE_RAW |
"compareRawTransforms" |
public static final String |
COMPOSE_ELASTIC |
"composeElasticTransforms" |
public static final String |
COMPOSE_RAW |
"composeRawTransforms" |
public static final String |
COMPOSE_RAW_ELASTIC |
"composeRawElasticTransforms" |
public static final String |
CONVERT_TO_ELASTIC |
"convertToElastic" |
public static final String |
CONVERT_TO_RAW |
"convertToRaw" |
public static final String |
EVALUATE_SIMILARITY |
"evaluateImageSimilarity" |
public static final String |
INVERT_RAW |
"invertRawTransform" |
public static final String |
LOAD_ELASTIC_TRANSF |
"loadElasticTransform" |
public static final String |
LOAD_LANDMARKS |
"loadLandmarks" |
public static final String |
LOAD_RAW_TRANSF |
"loadRawTransform" |
public static final String |
LOAD_SOURCE_AFFINE |
"loadSourceAffineMatrix" |
public static final String |
LOAD_SOURCE_MASK |
"loadSourceMask" |
public static final String |
SAVE_LANDMARKS |
"saveLandmarks" |
public static final String |
SHOW_LANDMARKS |
"showLandmarks" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ADD_CROSS |
0 |
public static final int |
FILE |
5 |
public static final int |
INVERTMASK |
4 |
public static final int |
MAGNIFIER |
11 |
public static final int |
MASK |
3 |
public static final int |
MOVE_CROSS |
1 |
public static final int |
REMOVE_CROSS |
2 |
public static final int |
STOP |
7 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_PARALLELS |
12 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CONTINUOUS |
1 |
public static final int |
DASH |
1 |
public static final int |
DASH_DOT |
3 |
public static final float |
DEFAULT_LINEWIDTH |
1.0f |
public static final int |
DEFAULT_MODE |
1 |
public static final int |
DEFAULT_PATTERN |
0 |
public static final int |
DOT |
2 |
public static final int |
PAIRWISE |
0 |
public static final int |
SOLID |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
DEFAULT_POINT_SIZE |
1.0f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_MERIDIANS |
12 |
public static final int |
DEFAULT_PARALLELS |
12 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_PARALLELS |
12 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
Context8 |
0 |
public static final int |
DataSizeInitial |
16 |
public static final int |
HalfMask |
32768 |
public static final int |
MaxRange |
17407 |
public static final int |
NotHalfMask |
32767 |
public static final int |
NotThreeQuarterMask |
16383 |
public static final int |
QuarterMask |
16384 |
public static final int |
SizeBuff |
1024 |
public static final int |
StaticFull |
1024 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PREF_ROOT |
"FijiArchipelago" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MB |
1048576 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
DEFAULT_WAIT |
10000L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DELIM |
" \t\n\r\f" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MONITOR_LOC |
"RoiWatcher.monitor" |
public static final long |
POLL_TIME |
10L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MONITOR_LOC |
"SliceWatcher.monitor" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise absolute value</h3> This function computes the absolute value of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.abs</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise addition</h3>This function adds its two operands, element-wise. The mode depends on the type of the arguments. If A and B are images and alpha and beta are numbers, then: <ul>\t<li><code>A+B</code> will return an image in which each pixel is the sum of the corresponding pixels in A and B. This operation is defined only if A and B have the same number of pixels. \t<li><code>A+alpha</code>will do singleton expansion and return a new image in which each pixel is the sum of the corresponding pixel value in A plus alpha. \t<li><code>alpha+beta</code>simply sums the two numbers. </ul>" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise arc-cosine</h3> This function computes the arc cosine of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.acos</i>. Values returned are in the range [0, \u03c0]." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise arc-sine</h3> This function computes the arc sine of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.asin</i>. Values returned are in the range [-\u03c0/2, \u03c0/2]" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise arc-tangent</h3> This function computes the arc tangent of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.atan</i>. Values returned are in the range [-\u03c0/2, \u03c0/2]." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise arc-tangent</h3> This function computes the two operands arc-tangent of two ImgLib images, taking each pixel of the two images as its two operands. Calculations are done using <i>Math.atan2</i>. Values returned are in the range [-\u03c0, \u03c0]." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise ceiling</h3> This function computes the ceiling of an ImgLib image, by returningthe integer value that is greater than or equal to each pixel valueof its operand. Calculations are done using <i>Math.ceil</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING_EQUAL |
"<h3>Element-wise \'equal\' comparison</h3> This function compares its two operands, element-wise, and return the <i>FloatType</i> value 1 if the first operand is equal to the second, and the <i>FloatType</i> value 0 otherwise.<br> Note the comparison is made with <i>float<i> precision. See \'element-wise greater than\' for more information." |
public static final String |
DOCUMENTATION_STRING_GREATER_OR_EQUAL |
"<h3>Element-wise \'greater or equal\' comparison</h3> This function compares its two operands, element-wise, and return the <i>FloatType</i> value 1 if the first operand is greater than or equal to the second, and the <i>FloatType</i> value 0 otherwise.<br> See \'element-wise greater than\' for more information." |
public static final String |
DOCUMENTATION_STRING_GREATER_THAN |
"<h3>Element-wise \'greater than\' comparison</h3> This function compares its two operands, element-wise,and return the <i>FloatType</i> value 1 if the first operand is greater than the second, and the <i>FloatType</i> value 0 otherwise.<br> Comparisons are made on float.<br>This function does singleton expansion, that is if A and B are images and alpha and beta are numbers, then: <ul> \t<li><code>A>B</code> will compare each pixel of A to the corresponding pixels in B. This operation is defined only if A and B have the same number of pixels. \t<li><code>A+alpha</code>will do singleton expansion and return a new image in which each pixel of A is compared to alpha. \t<li><code>alpha+beta</code>simply compare the two numbers. </ul>" |
public static final String |
DOCUMENTATION_STRING_LOWER_OR_EQUAL |
"<h3>Element-wise \'lower or equal\' comparison</h3> This function compares its two operands, element-wise, and return the <i>FloatType</i> value 1 if the first operand is lower than or equal to the second, and the <i>FloatType</i> value 0 otherwise.<br> See \'element-wise greater than\' for more information." |
public static final String |
DOCUMENTATION_STRING_LOWER_THAN |
"<h3>Element-wise \'lower than\' comparison</h3> This function compares its two operands, element-wise, and return the <i>FloatType</i> value 1 if the first operand is lower than the second, and the <i>FloatType</i> value 0 otherwise.<br> See \'element-wise greater than\' for more information." |
public static final String |
DOCUMENTATION_STRING_NOT_EQUAL |
"<h3>Element-wise \'not equal\' comparison</h3> This function compares its two operands, element-wise, and return the <i>FloatType</i> value 0 if the first operand is equal to the second, and the <i>FloatType</i> value 1 otherwise.<br> Note the comparison is made with <i>float<i> precision. See \'element-wise greater than\' for more information." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise cosine</h3> This function computes the cosine of an ImgLib image, taking each pixel as its operand (must be in radians). Calculations are done using <i>Math.cos</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise division</h3> This function divides its two operands, element-wise. See \'element-wise addition\' for details." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise exponential</h3> This function computes the exponential of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.exp</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise floor</h3> This function computes the floor of an ImgLib image, by returningthe integer value that is less than or equal to each pixel valueof its operand. Calculations are done using <i>Math.floor</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise natural logarithm</h3> This function computes the natural logarithm (base <i>e</i>) of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.log</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING_AND |
"<h3>Element-wise \'AND\' logical operation</h3> This function performs the pixel-wise logical AND operation, extended to real numbers. That is: the value returned by this operation will be the float value 1 if and only if the its operands are non zero, and 0 otherwise." |
public static final String |
DOCUMENTATION_STRING_NOT |
"<h3>Element-wise \'NOT\' logical operation</h3> This function performs the pixel-wise logical NOT operation, extended to real numbers. That is: the value returned by this operation will be the float value 1 if its operand is zero, and will be 0 otherwise." |
public static final String |
DOCUMENTATION_STRING_OR |
"<h3>Element-wise \'OR\' logical operation</h3> This function performs the pixel-wise logical OR operation, extended to real numbers. That is: the value returned by this operation will be the float value 1 if one of its two operands is non zero, and 0 if and only if the two operands are 0." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise modulus</h3> This function computes the modulus of two ImgLib images, with the Java meaning of it, taking each pixel of the two images as its two operands. " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise multiplication</h3> This function multiplies its two operands, element-wise. See \'element-wise\' addition for details." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise power</h3> This function computes the value of the first argument raised to the power of the second argument, pixel by pixel, with singleton exapnsion. Calculations are done using <i>Math.pow</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise round</h3> This function returns a rounded ImgLib image, by rounding each pixel of its operand to the closest integer. Calculations are done using <i>Math.round</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise sine</h3> This function computes the sine of an ImgLib image, taking each pixel as its operand (must be in radians). Calculations are done using <i>Math.sin</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise square root</h3>This function computes the square root of an ImgLib image, taking each pixel as its operand. Calculations are done using <i>Math.sqrt</i>." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STING |
"<h3>Element-wise subtraction</h3> This function subtracts its two operands, element-wise. See \'element-wise addition\' for details." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise tangent</h3> This function computes the tangent of an ImgLib image, taking each pixel as its operand (must be in radians). Calculations are done using Math.tan" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DOCUMENTATION_STRING |
"<h3>Element-wise minus</h3> This function computes the negative of an ImgLib image, by returningthe opposite value of each pixel of its operand." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
url |
"http://fiji.sc/wiki/index.php/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
FEATURES_COMPUTED |
9 |
public static final int |
FLAG_EDGE_ADDED |
4 |
public static final int |
FLAG_EDGE_MODIFIED |
6 |
public static final int |
FLAG_EDGE_REMOVED |
5 |
public static final int |
FLAG_SPOT_ADDED |
0 |
public static final int |
FLAG_SPOT_FRAME_CHANGED |
3 |
public static final int |
FLAG_SPOT_MODIFIED |
2 |
public static final int |
FLAG_SPOT_REMOVED |
1 |
public static final int |
MODEL_MODIFIED |
8 |
public static final int |
SPOTS_COMPUTED |
4 |
public static final int |
SPOTS_FILTERED |
5 |
public static final int |
TRACKS_COMPUTED |
6 |
public static final int |
TRACKS_VISIBILITY_CHANGED |
7 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FRAME |
"FRAME" |
public static final String |
POSITION_T |
"POSITION_T" |
public static final String |
POSITION_X |
"POSITION_X" |
public static final String |
POSITION_Y |
"POSITION_Y" |
public static final String |
POSITION_Z |
"POSITION_Z" |
public static final String |
QUALITY |
"QUALITY" |
public static final String |
RADIUS |
"RADIUS" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
VISIBILITY |
"VISIBILITY" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PLUGIN_NAME_STR |
"TrackMate" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>If the current displayer is the HyperstackDisplayer, this action <br>will capture the TrackMate overlay with current display settings. <br>That is: a new RGB stack will be created (careful with large data) where <br>each frame contains a RGB snapshot of the TrackMate display. <p>It can take long since we pause between each frame to ensure the whole <br>overlay is redrawn. The current zoom is taken into account. <br>Also, make sure nothing is moved over the image while capturing. </html>" |
public static final String |
KEY |
"CAPTURE_OVERLAY" |
public static final String |
NAME |
"Capture overlay" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>This action closes gaps in tracks by introducing new spots. The spots positions and size are calculated using linear interpolation.</html>" |
public static final String |
KEY |
"CLOSE_GAPS_BY_LINEAR_INPERPOLATION" |
public static final String |
NAME |
"Close gaps by introducing new spots" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Export the statistics of all spots to a table. The numerical features of all visible spots are exported, regardless of whether they are in a track or not.</html>" |
public static final String |
KEY |
"EXPORT_ALL_SPOTS_STATS" |
public static final String |
NAME |
"Export all spots statistics" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Compute and export all statistics to 3 tables. Statistics are separated in features computed for: <ol> \t<li> spots in visible tracks; \t<li> edges between those spots; \t<li> visible tracks. </ol> Note that spots and edges that are not in visible tracks won\'t be displayed in the tables.</html>" |
public static final String |
KEY |
"EXPORT_STATS" |
public static final String |
NAME |
"Export statistics to tables" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Export the tracks in the current model content to a XML file in a simple format. <p> The file will have one element per track, and each track contains several spot elements. These spots are sorted by frame number, and have 4 numerical attributes: the frame number this spot is in, and its X, Y, Z position in physical units as specified in the image properties. <p>As such, this format <u>cannot</u> handle track merging and splitting properly, and is suited only for non-branching tracks.</html>" |
public static final String |
KEY |
"EXPORT_TRACKS_TO_XML_SIMPLE" |
public static final String |
NAME |
"Export tracks to XML file" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html> Generate a stack of images taken from the track that joins two selected spots. <p> There must be exactly 1 or 2 spots selected for this action to work. If only one spot is selected, then the stack is extracted from the track it belongs to, from the first spot in time to the last in time. If there are two spots selected, they must belong to a track that connects them. A path is then found that joins them and the stack is extracted from this path.<p> A stack of images will be generated from the spots that join them. A GUI allows specifying the size of the extract, in units of the largest spot in the track, and whether to capture a 2D or 3D stack over time. All channels are captured. </html>" |
public static final String |
KEY |
"EXTRACT_TRACK_STACK" |
public static final String |
NAME |
"Extract track stack" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Export the current model content to a XML file following the ISBI 2012 particle tracking challenge format, as specified on <a href=\'http://bioimageanalysis.org/track/\'></a>. <p> Only tracks are exported. If there is no track, this action does nothing. </html>" |
public static final String |
KEY |
"EXPORT_TO_ISBI_CHALLENGE_FORMAT" |
public static final String |
NAME |
"Export to ISBI challenge format" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>This action creates a label image from the tracking results. <p> A new 16-bit image is generated, of same dimension and size that of the input image. The label image has one channel, with black baground (0 value) everywhere, except where there are spots. Each spot is painted with a uniform integer value equal to the trackID it belongs to. Spots that do not belong to tracks are painted with a unique integer larger than the last trackID in the dataset. <p> Only visible spots are painted. </html>" |
public static final String |
KEY |
"EXPORT_LABEL_IMG" |
public static final String |
NAME |
"Export label image" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Merge the current model with the data from another <br>file, specified by the user. This is useful <i>e.g.</i> <br>if two operators have been annotating the same datasets <br>and want to merge their work in a single file.<p>Only the spots belonging to visible tracks are imported <br>from the target file, which makes this action non-entirely <br>symmetrical. Numerical features are re-calculated using <br>the current settings. There is no check that the imported <br>data was generated on the raw source.</html>" |
public static final String |
KEY |
"MERGE_OTHER_FILE" |
public static final String |
NAME |
"Merge a TrackMate file" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Plot the number of spots in each frame as a function <br>of time. Only the filtered spots are taken into account. </html>" |
public static final String |
KEY |
"PLOT_NSPOTS_VS_TIME" |
public static final String |
NAME |
"Plot N spots vs time" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Calling this action causes the model to recompute all the features values for all spots, edges and tracks. All the feature analyzers discovered when running this action are added and computed. </html>" |
public static final String |
KEY |
"RECOMPUTE_FEATURES" |
public static final String |
NAME |
"Recompute all features" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Reset the time feature of all spots: it is set to the frame number times the frame interval. </html>" |
public static final String |
NAME |
"Reset spot time" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>This action performs sub-localization of spots using gaussian peak fitting. <p>The fit process will update the spot position and their radius, using the results from the gaussian fit. Of course it works best when the peaks in the image ressemble gaussian functions. The fitting process uses the spots information (position and radius) as initial values for the fit.<p>It works for both 2D and 3D images. In 3D it accounts for non-isotropic calibration (and possible PSF deformation in the Z direction) thanks to an elliptic gaussian function, with axes constrained to be along X, Y and Z. In 2D we use an isotropic gaussian.</html>" |
public static final String |
KEY |
"GAUSS_FIT" |
public static final String |
NAME |
"Refine spot position with gaussian fitting" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>This action trims the tracking data by removing anything that is not marked as visible. <p>The spots that do not belong to a visible track will be removed. The tracks that are not marked as visible will be removed as well. <p>This action is irreversible. It helps limiting the memory and disk space of tracking data that has been properly curated.</html>" |
public static final String |
KEY |
"TRIM_NOT_VISIBLE" |
public static final String |
NAME |
"Trim non-visible data" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEFAULT_DO_MEDIAN_FILTERING |
false |
public static final boolean |
DEFAULT_DO_SUBPIXEL_LOCALIZATION |
true |
public static final int |
DEFAULT_DOWNSAMPLE_FACTOR |
4 |
public static final double |
DEFAULT_RADIUS |
5.0 |
public static final int |
DEFAULT_TARGET_CHANNEL |
1 |
public static final double |
DEFAULT_THRESHOLD |
0.0 |
public static final String |
KEY_DO_MEDIAN_FILTERING |
"DO_MEDIAN_FILTERING" |
public static final String |
KEY_DO_SUBPIXEL_LOCALIZATION |
"DO_SUBPIXEL_LOCALIZATION" |
public static final String |
KEY_DOWNSAMPLE_FACTOR |
"DOWNSAMPLE_FACTOR" |
public static final String |
KEY_RADIUS |
"RADIUS" |
public static final String |
KEY_TARGET_CHANNEL |
"TARGET_CHANNEL" |
public static final String |
KEY_THRESHOLD |
"THRESHOLD" |
public static final String |
XML_ATTRIBUTE_DETECTOR_NAME |
"DETECTOR_NAME" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BASE_ERROR_MESSAGE |
"DogDetector: " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
THIS_DETECTOR_KEY |
"DOG_DETECTOR" |
public static final String |
THIS_INFO_TEXT |
"<html>This segmenter is based on an approximation of the LoG operator <br> by differences of gaussian (DoG). Computations are made in direct space. <br>It is the quickest for small spot sizes (< ~5 pixels). <p> Spots found too close are suppressed. This segmenter can do sub-pixel <br>localization of spots using a quadratic fitting scheme. It is based on <br>the scale-space framework made by Stephan Preibisch for ImgLib. </html>" |
public static final String |
THIS_NAME |
"DoG detector" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DETECTOR_KEY |
"LABEL_IMAGE_DETECTOR" |
public static final String |
INFO_TEXT |
"<html>This detector creates spots by importing regions from a label image.<p>A label image is an image where the pixel values are integers. Each object in a label image is represented by a single common pixel value (the label) that is unique to the object.<p>This detector reads such an image and create spots from each object. In 2D the contour of a label is imported. In 3D, spherical spots of the same volume that the label are created.</html>" |
public static final String |
NAME |
"Label image detector" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DETECTOR_KEY |
"LOG_DETECTOR" |
public static final String |
INFO_TEXT |
"<html>This detector applies a LoG (Laplacian of Gaussian) filter <br>to the image, with a sigma suited to the blob estimated size. <br>Calculations are made in the Fourier space. The maxima in the <br>filtered image are searched for, and maxima too close from each <br>other are suppressed. A quadratic fitting scheme allows to do <br>sub-pixel localization. </html>" |
public static final String |
NAME |
"LoG detector" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DETECTOR_KEY |
"MANUAL_DETECTOR" |
public static final String |
INFO_TEXT |
"<html>Selecting this will skip the automatic detection phase, and jump directly <br>to manual segmentation. A default spot size will be asked for. </html>" |
public static final String |
NAME |
"Manual annotation" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DETECTOR_KEY |
"MASK_DETECTOR" |
public static final String |
INFO_TEXT |
"<html>This detector creates spots from a black and white mask.<p>More precisely, all the pixels in the designated channel that have a value strictly larger than 0 are considered as part of the foreground, and used to build connected regions. In 2D, spots are created with the (possibly simplified) contour of the region. In 3D, a spherical spot is created for each region in its center, with a volume equal to the region volume.</html>" |
public static final String |
NAME |
"Mask detector" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DETECTOR_KEY |
"THRESHOLD_DETECTOR" |
public static final String |
INFO_TEXT |
"<html>This detector creates spots by thresholding a grayscale image.<p>Pixels in the designated channel that have a value larger than the threshold are considered as part of the foreground, and used to build connected regions. In 2D, spots are created with the (possibly simplified) contour of the region. In 3D, a spherical spot is created for each region in its center, with a volume equal to the region volume.</html>" |
public static final String |
KEY_INTENSITY_THRESHOLD |
"INTENSITY_THRESHOLD" |
public static final String |
KEY_SIMPLIFY_CONTOURS |
"SIMPLIFY_CONTOURS" |
public static final String |
NAME |
"Thresholding detector" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
BASE_ERROR_MESSAGE |
"[SemiAutoTracker] " |
protected static final double |
NEIGHBORHOOD_FACTOR |
2.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
USE_UNIFORM_COLOR_KEY |
"UNIFORM_COLOR" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DIRECTIONAL_CHANGE_RATE |
"DIRECTIONAL_CHANGE_RATE" |
public static final String |
KEY |
"Directional change" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DISPLACEMENT |
"DISPLACEMENT" |
public static final String |
KEY |
"Edge speed" |
public static final String |
SPEED |
"SPEED" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
EDGE_COST |
"LINK_COST" |
public static final String |
KEY |
"Edge target" |
public static final String |
SPOT_SOURCE_ID |
"SPOT_SOURCE_ID" |
public static final String |
SPOT_TARGET_ID |
"SPOT_TARGET_ID" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Edge location" |
public static final String |
TIME |
"EDGE_TIME" |
public static final String |
X_LOCATION |
"EDGE_X_LOCATION" |
public static final String |
Y_LOCATION |
"EDGE_Y_LOCATION" |
public static final String |
Z_LOCATION |
"EDGE_Z_LOCATION" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FEATURE |
"MANUAL_EGE_COLOR" |
public static final String |
KEY |
"Manual edge color" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FEATURE |
"MANUAL_SPOT_COLOR" |
public static final String |
KEY |
"Manual spot color" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final double |
RAD_PERCENTAGE |
1.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CONTRAST |
"CONTRAST_CH" |
public static final String |
KEY |
"Spot contrast and SNR" |
public static final String |
SNR |
"SNR_CH" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ASPECTRATIO |
"ELLIPSE_ASPECTRATIO" |
public static final String |
KEY |
"Spot fit 2D ellipse" |
public static final String |
MAJOR |
"ELLIPSE_MAJOR" |
public static final String |
MINOR |
"ELLIPSE_MINOR" |
public static final String |
THETA |
"ELLIPSE_THETA" |
public static final String |
X0 |
"ELLIPSE_X0" |
public static final String |
Y0 |
"ELLIPSE_Y0" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AREA |
"AREA" |
public static final String |
CIRCULARITY |
"CIRCULARITY" |
public static final String |
KEY |
"Spot 2D shape descriptors" |
public static final String |
PERIMETER |
"PERIMETER" |
public static final String |
SOLIDITY |
"SOLIDITY" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Branching analyzer" |
public static final String |
LONGEST_GAP |
"LONGEST_GAP" |
public static final String |
NUMBER_COMPLEX |
"NUMBER_COMPLEX" |
public static final String |
NUMBER_GAPS |
"NUMBER_GAPS" |
public static final String |
NUMBER_MERGES |
"NUMBER_MERGES" |
public static final String |
NUMBER_SPLITS |
"NUMBER_SPLITS" |
public static final String |
NUMBER_SPOTS |
"NUMBER_SPOTS" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Track duration" |
public static final String |
TRACK_DISPLACEMENT |
"TRACK_DISPLACEMENT" |
public static final String |
TRACK_DURATION |
"TRACK_DURATION" |
public static final String |
TRACK_START |
"TRACK_START" |
public static final String |
TRACK_STOP |
"TRACK_STOP" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Track index" |
public static final String |
TRACK_ID |
"TRACK_ID" |
public static final String |
TRACK_INDEX |
"TRACK_INDEX" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Track location" |
public static final String |
X_LOCATION |
"TRACK_X_LOCATION" |
public static final String |
Y_LOCATION |
"TRACK_Y_LOCATION" |
public static final String |
Z_LOCATION |
"TRACK_Z_LOCATION" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Track motility analysis" |
public static final String |
TRACK_CONFINMENT_RATIO |
"CONFINMENT_RATIO" |
public static final String |
TRACK_LINEARITY_OF_FORWARD_PROGRESSION |
"LINEARITY_OF_FORWARD_PROGRESSION" |
public static final String |
TRACK_MAX_DISTANCE_TRAVELED |
"MAX_DISTANCE_TRAVELED" |
public static final String |
TRACK_MEAN_DIRECTIONAL_CHANGE_RATE |
"MEAN_DIRECTIONAL_CHANGE_RATE" |
public static final String |
TRACK_MEAN_STRAIGHT_LINE_SPEED |
"MEAN_STRAIGHT_LINE_SPEED" |
public static final String |
TRACK_TOTAL_DISTANCE_TRAVELED |
"TOTAL_DISTANCE_TRAVELED" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Track speed" |
public static final String |
TRACK_MAX_SPEED |
"TRACK_MAX_SPEED" |
public static final String |
TRACK_MEAN_SPEED |
"TRACK_MEAN_SPEED" |
public static final String |
TRACK_MEDIAN_SPEED |
"TRACK_MEDIAN_SPEED" |
public static final String |
TRACK_MIN_SPEED |
"TRACK_MIN_SPEED" |
public static final String |
TRACK_STD_SPEED |
"TRACK_STD_SPEED" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"Track quality" |
public static final String |
TRACK_MEAN_QUALITY |
"TRACK_MEAN_QUALITY" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
INDENT |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DESCRIPTOR |
"LogPanel" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"ConfigureViews" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"ExecuteDetection" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"ExecuteTracking" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"InitialFiltering" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"LogPanel" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"ConfigureDetector" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"ConfigureTracker" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ANALYSER_ELEMENT_KEY |
"Analyzer" |
public static final String |
ANALYSER_KEY_ATTRIBUTE |
"key" |
public static final String |
ANALYZER_COLLECTION_ELEMENT_KEY |
"AnalyzerCollection" |
public static final String |
CROP_DETECTION_CHANNEL_ATTRIBUTE_NAME |
"detectionchannel" |
public static final String |
CROP_ELEMENT_KEY |
"BasicSettings" |
public static final String |
CROP_TEND_ATTRIBUTE_NAME |
"tend" |
public static final String |
CROP_TSTART_ATTRIBUTE_NAME |
"tstart" |
public static final String |
CROP_XEND_ATTRIBUTE_NAME |
"xend" |
public static final String |
CROP_XSTART_ATTRIBUTE_NAME |
"xstart" |
public static final String |
CROP_YEND_ATTRIBUTE_NAME |
"yend" |
public static final String |
CROP_YSTART_ATTRIBUTE_NAME |
"ystart" |
public static final String |
CROP_ZEND_ATTRIBUTE_NAME |
"zend" |
public static final String |
CROP_ZSTART_ATTRIBUTE_NAME |
"zstart" |
public static final String |
DETECTOR_SETTINGS_ELEMENT_KEY |
"DetectorSettings" |
public static final String |
DISPLAY_SETTINGS_ELEMENT_KEY |
"DisplaySettings" |
public static final String |
EDGE_ANALYSERS_ELEMENT_KEY |
"EdgeAnalyzers" |
public static final String |
EDGE_FEATURES_ELEMENT_KEY |
"EdgeFeatures" |
public static final String |
FEATURE_ATTRIBUTE |
"feature" |
public static final String |
FEATURE_DECLARATIONS_ELEMENT_KEY |
"FeatureDeclarations" |
public static final String |
FEATURE_DIMENSION_ATTRIBUTE |
"dimension" |
public static final String |
FEATURE_ELEMENT_KEY |
"Feature" |
public static final String |
FEATURE_ISINT_ATTRIBUTE |
"isint" |
public static final String |
FEATURE_NAME_ATTRIBUTE |
"name" |
public static final String |
FEATURE_SHORT_NAME_ATTRIBUTE |
"shortname" |
public static final String |
FILTER_ABOVE_ATTRIBUTE_NAME |
"isabove" |
public static final String |
FILTER_ELEMENT_KEY |
"Filter" |
public static final String |
FILTER_FEATURE_ATTRIBUTE_NAME |
"feature" |
public static final String |
FILTER_VALUE_ATTRIBUTE_NAME |
"value" |
public static final String |
FILTERED_TRACK_ELEMENT_KEY |
"FilteredTracks" |
public static final String |
FRAME_ATTRIBUTE_NAME |
"frame" |
public static final String |
GUI_STATE_ATTRIBUTE |
"state" |
public static final String |
GUI_STATE_ELEMENT_KEY |
"GUIState" |
public static final String |
GUI_VIEW_ATTRIBUTE |
"key" |
public static final String |
GUI_VIEW_ATTRIBUTE_POSITION_HEIGHT |
"height" |
public static final String |
GUI_VIEW_ATTRIBUTE_POSITION_WIDTH |
"width" |
public static final String |
GUI_VIEW_ATTRIBUTE_POSITION_X |
"x" |
public static final String |
GUI_VIEW_ATTRIBUTE_POSITION_Y |
"y" |
public static final String |
GUI_VIEW_ELEMENT_KEY |
"View" |
public static final String |
IMAGE_ELEMENT_KEY |
"ImageData" |
public static final String |
IMAGE_FILENAME_ATTRIBUTE_NAME |
"filename" |
public static final String |
IMAGE_FOLDER_ATTRIBUTE_NAME |
"folder" |
public static final String |
IMAGE_HEIGHT_ATTRIBUTE_NAME |
"height" |
public static final String |
IMAGE_NFRAMES_ATTRIBUTE_NAME |
"nframes" |
public static final String |
IMAGE_NSLICES_ATTRIBUTE_NAME |
"nslices" |
public static final String |
IMAGE_PIXEL_HEIGHT_ATTRIBUTE_NAME |
"pixelheight" |
public static final String |
IMAGE_PIXEL_WIDTH_ATTRIBUTE_NAME |
"pixelwidth" |
public static final String |
IMAGE_TIME_INTERVAL_ATTRIBUTE_NAME |
"timeinterval" |
public static final String |
IMAGE_VOXEL_DEPTH_ATTRIBUTE_NAME |
"voxeldepth" |
public static final String |
IMAGE_WIDTH_ATTRIBUTE_NAME |
"width" |
public static final String |
INITIAL_SPOT_FILTER_ELEMENT_KEY |
"InitialSpotFilter" |
public static final String |
LOG_ELEMENT_KEY |
"Log" |
public static final String |
MODEL_ELEMENT_KEY |
"Model" |
public static final String |
PLUGIN_VERSION_ATTRIBUTE_NAME |
"version" |
public static final String |
ROI_N_POINTS_ATTRIBUTE_NAME |
"ROI_N_POINTS" |
public static final String |
ROOT_ELEMENT_KEY |
"TrackMate" |
public static final String |
SETTINGS_ELEMENT_KEY |
"Settings" |
public static final String |
SPATIAL_UNITS_ATTRIBUTE_NAME |
"spatialunits" |
public static final String |
SPOT_ANALYSERS_ELEMENT_KEY |
"SpotAnalyzers" |
public static final String |
SPOT_COLLECTION_ELEMENT_KEY |
"AllSpots" |
public static final String |
SPOT_COLLECTION_NSPOTS_ATTRIBUTE_NAME |
"nspots" |
public static final String |
SPOT_ELEMENT_KEY |
"Spot" |
public static final String |
SPOT_FEATURES_ELEMENT_KEY |
"SpotFeatures" |
public static final String |
SPOT_FILTER_COLLECTION_ELEMENT_KEY |
"SpotFilterCollection" |
public static final String |
SPOT_FRAME_COLLECTION_ELEMENT_KEY |
"SpotsInFrame" |
public static final String |
SPOT_ID_ATTRIBUTE_NAME |
"ID" |
public static final String |
SPOT_NAME_ATTRIBUTE_NAME |
"name" |
public static final String |
TIME_UNITS_ATTRIBUTE_NAME |
"timeunits" |
public static final String |
TRACK_ANALYSERS_ELEMENT_KEY |
"TrackAnalyzers" |
public static final String |
TRACK_COLLECTION_ELEMENT_KEY |
"AllTracks" |
public static final String |
TRACK_EDGE_ELEMENT_KEY |
"Edge" |
public static final String |
TRACK_ELEMENT_KEY |
"Track" |
public static final String |
TRACK_FEATURES_ELEMENT_KEY |
"TrackFeatures" |
public static final String |
TRACK_FILTER_COLLECTION_ELEMENT_KEY |
"TrackFilterCollection" |
public static final String |
TRACK_ID_ELEMENT_KEY |
"TrackID" |
public static final String |
TRACK_NAME_ATTRIBUTE_NAME |
"name" |
public static final String |
TRACKER_ATTRIBUTE_NAME |
"trackername" |
public static final String |
TRACKER_SETTINGS_CLASS_ATTRIBUTE_NAME |
"trackersettingsclass" |
public static final String |
TRACKER_SETTINGS_ELEMENT_KEY |
"TrackerSettings" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final boolean |
DEBUG |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
XML_ELEMENT_NAME_FEATURE_PENALTIES |
"FeaturePenalties" |
public static final String |
XML_ELEMENT_NAME_GAP_CLOSING |
"GapClosing" |
public static final String |
XML_ELEMENT_NAME_LINKING |
"Linking" |
public static final String |
XML_ELEMENT_NAME_MERGING |
"TrackMerging" |
public static final String |
XML_ELEMENT_NAME_SPLITTING |
"TrackSplitting" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>Choosing this tracker skips the automated tracking step <br>and keeps the current annotation.</html>" |
public static final String |
NAME |
"Manual tracking" |
public static final String |
TRACKER_KEY |
"MANUAL_TRACKER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEFAULT_ALLOW_GAP_CLOSING |
true |
public static final boolean |
DEFAULT_ALLOW_TRACK_MERGING |
false |
public static final boolean |
DEFAULT_ALLOW_TRACK_SPLITTING |
false |
public static final double |
DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR |
1.05 |
public static final double |
DEFAULT_BLOCKING_VALUE |
1d/0d |
public static final double |
DEFAULT_CUTOFF_PERCENTILE |
0.9 |
public static final double |
DEFAULT_GAP_CLOSING_MAX_DISTANCE |
15.0 |
public static final int |
DEFAULT_GAP_CLOSING_MAX_FRAME_GAP |
2 |
public static final double |
DEFAULT_LINKING_MAX_DISTANCE |
15.0 |
public static final double |
DEFAULT_MERGING_MAX_DISTANCE |
15.0 |
public static final double |
DEFAULT_SPLITTING_MAX_DISTANCE |
15.0 |
public static final String |
KEY_ALLOW_GAP_CLOSING |
"ALLOW_GAP_CLOSING" |
public static final String |
KEY_ALLOW_TRACK_MERGING |
"ALLOW_TRACK_MERGING" |
public static final String |
KEY_ALLOW_TRACK_SPLITTING |
"ALLOW_TRACK_SPLITTING" |
public static final String |
KEY_ALTERNATIVE_LINKING_COST_FACTOR |
"ALTERNATIVE_LINKING_COST_FACTOR" |
public static final String |
KEY_BLOCKING_VALUE |
"BLOCKING_VALUE" |
public static final String |
KEY_CUTOFF_PERCENTILE |
"CUTOFF_PERCENTILE" |
public static final String |
KEY_GAP_CLOSING_FEATURE_PENALTIES |
"GAP_CLOSING_FEATURE_PENALTIES" |
public static final String |
KEY_GAP_CLOSING_MAX_DISTANCE |
"GAP_CLOSING_MAX_DISTANCE" |
public static final String |
KEY_GAP_CLOSING_MAX_FRAME_GAP |
"MAX_FRAME_GAP" |
public static final String |
KEY_LINKING_FEATURE_PENALTIES |
"LINKING_FEATURE_PENALTIES" |
public static final String |
KEY_LINKING_MAX_DISTANCE |
"LINKING_MAX_DISTANCE" |
public static final String |
KEY_MERGING_FEATURE_PENALTIES |
"MERGING_FEATURE_PENALTIES" |
public static final String |
KEY_MERGING_MAX_DISTANCE |
"MERGING_MAX_DISTANCE" |
public static final String |
KEY_SPLITTING_FEATURE_PENALTIES |
"SPLITTING_FEATURE_PENALTIES" |
public static final String |
KEY_SPLITTING_MAX_DISTANCE |
"SPLITTING_MAX_DISTANCE" |
public static final String |
TRACKER_SETTINGS_ALLOW_EVENT_ATTNAME |
"allowed" |
public static final String |
TRACKER_SETTINGS_ALTERNATE_COST_FACTOR_ATTNAME |
"alternatecostfactor" |
public static final String |
TRACKER_SETTINGS_BLOCKING_VALUE_ATTNAME |
"blockingvalue" |
public static final String |
TRACKER_SETTINGS_CUTOFF_PERCENTILE_ATTNAME |
"cutoffpercentile" |
public static final String |
TRACKER_SETTINGS_DISTANCE_CUTOFF_ATTNAME |
"value" |
public static final String |
TRACKER_SETTINGS_DISTANCE_CUTOFF_ELEMENT |
"DistanceCutoff" |
public static final String |
TRACKER_SETTINGS_FEATURE_ELEMENT |
"FeatureCondition" |
public static final String |
TRACKER_SETTINGS_GAP_CLOSING_ELEMENT |
"GapClosingCondition" |
public static final String |
TRACKER_SETTINGS_LINKING_ELEMENT |
"LinkingCondition" |
public static final String |
TRACKER_SETTINGS_MERGING_ELEMENT |
"MergingCondition" |
public static final String |
TRACKER_SETTINGS_SPLITTING_ELEMENT |
"SplittingCondition" |
public static final String |
TRACKER_SETTINGS_TIME_CUTOFF_ATTNAME |
"value" |
public static final String |
TRACKER_SETTINGS_TIME_CUTOFF_ELEMENT |
"TimeCutoff" |
public static final String |
XML_ATTRIBUTE_TRACKER_NAME |
"TRACKER_NAME" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY_KALMAN_SEARCH_RADIUS |
"KALMAN_SEARCH_RADIUS" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_TEXT |
"<html>This tracker is the most simple one, and is based on nearest neighbor <br>search. The spots in the target frame are searched for the nearest neighbor <br> of each spot in the source frame. If the spots found are closer than the <br>maximal allowed distance, a link between the two is created. <br><p>The nearest neighbor search relies upon the KD-tree technique implemented <br>in imglib by Johannes Schindelin and friends. This ensure a very efficient tracking and makes this tracker suitable for situation where a huge number <br>of particles are to be tracked over a very large number of frames. However, <br>because of the naiveness of its principles, it can result in pathological <br>tracks. It can only do frame-to-frame linking; there cannot be any track <br>merging or splitting, and gaps will not be closed. Also, the end results are non-deterministic. </html>" |
public static final String |
NAME |
"Nearest-neighbor tracker" |
public static final String |
TRACKER_KEY |
"NEAREST_NEIGHBOR_TRACKER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY_IOU_CALCULATION |
"IOU_CALCULATION" |
public static final String |
KEY_MIN_IOU |
"MIN_IOU" |
public static final String |
KEY_SCALE_FACTOR |
"SCALE_FACTOR" |
public static final String |
TRACKER_INFO_TEXT |
"<html> This tracker is a simple extension of the Intersection - over - Union (IoU) tracker. <p> <p> It generates links between spots whose shapes overlap between consecutive frames. When several spots are eligible as a source for a target, the one with the largest IoU is chosen.<p> <p> The minimal IoU parameter sets a threshold below which links won\'t be created. The scale factor allows for enlarging (>1) or shrinking (<1) the spot shapes before computing their IoU. Two methods can be used to compute IoU: The <it>Fast</it> one approximates the spot shapes by their rectangular bounding-box. The <it>Precise</it> one uses the actual spot polygon. <p> <p> Careful: this tracker is only suited to 2D images. It treats all the spots as 2D objects. The Z dimension is ignored. </html>" |
public static final String |
TRACKER_KEY |
"OVERLAP_TRACKER" |
public static final String |
TRACKER_NAME |
"Overlap tracker" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
THIS2_INFO_TEXT |
"<html>This tracker is identical to the sparse LAP tracker present in this trackmate, except that it <br>proposes fewer tuning options. Namely, only gap closing is allowed, based solely on <br>a distance and time condition. Track splitting and merging are not allowed, resulting <br>in having non-branching tracks. </html>" |
public static final String |
THIS2_NAME |
"Simple LAP tracker" |
public static final String |
THIS2_TRACKER_KEY |
"SIMPLE_SPARSE_LAP_TRACKER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
THIS_INFO_TEXT |
"<html>This tracker is based on the Linear Assignment Problem mathematical framework. <br>Its implementation is adapted from the following paper: <br><i>Robust single-particle tracking in live-cell time-lapse sequences</i> - <br>Jaqaman <i> et al.</i>, 2008, Nature Methods. <br><p>Tracking happens in 2 steps: First spots are linked from frame to frame to <br>build track segments. These track segments are investigated in a second step <br>for gap-closing (missing detection), splitting and merging events. <br> <p>Linking costs are proportional to the square distance between source and <br> target spots, which makes this tracker suitable for Brownian motion. <br> Penalties can be set to favor linking between spots that have similar <br> features. <p>Solving the LAP relies on the Jonker-Volgenant solver, and a sparse cost matrix formulation, allowing it to handle very large problems. </html>" |
public static final String |
THIS_NAME |
"LAP Tracker" |
public static final String |
THIS_TRACKER_KEY |
"SPARSE_LAP_TRACKER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BOTTOM_TO_TOP |
1 |
public static final int |
SIDE_BY_SIDE |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY |
"HYPERSTACKDISPLAYER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
SHAPE_NAME |
"scaledLabel" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DEFAULT_COLOR |
"#FF00FF" |
public static final String |
INFO_TEXT |
"<html>TrackScheme displays the tracking results as track lanes, <br>ignoring the spot actual position. <p>Tracks can be edited through link creation and removal.</html>" |
public static final String |
KEY |
"TRACKSCHEME" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PARSE_ACTION_COMMAND |
"Parse" |
public static final String |
QUIT_ACTION_COMMAND |
"Quit" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
PREFS_KEY |
"recent.command" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
EMAIL_KEY |
"fsalign.FSAlignListener.email" |
public static final String |
PASS_KEY |
"fsalign.FSAlignListener.password" |
public static final String |
PORT_KEY |
"fsalign.FSAlignListener.port" |
public static final String |
SMTP_KEY |
"fsalign.FSAlignListener.smtp" |
public static final String |
TOMAIL_KEY |
"fsalign.FSAlignListener.notifymail" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NONE |
-1 |
public static final int |
ORPHAN |
-3 |
public static final int |
TERMINAL |
-2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
numFolds |
10 |
public static final int |
numRuns |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BACK |
1 |
public static final int |
FRONT |
0 |
public static final int |
X_AXIS |
0 |
public static final int |
Y_AXIS |
1 |
public static final int |
Z_AXIS |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BB |
2 |
public static final int |
BS |
1 |
public static final int |
CO |
0 |
public static final int |
CS |
3 |
public static final int |
CUSTOM |
5 |
public static final int |
MULTIORTHO |
4 |
public static final int |
ORTHO |
1 |
public static final int |
PL |
4 |
public static final int |
SURFACE |
2 |
public static final int |
SURFACE_PLOT2D |
3 |
public static final int |
VOLUME |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ANIMATE_TG |
3 |
public static final int |
ATTRIBUTE_COORD_SYSTEM |
1 |
public static final int |
ATTRIBUTE_SCALEBAR |
0 |
public static final int |
CENTER_TG |
0 |
public static final int |
ROTATION_TG |
2 |
public static final int |
TRANSLATE_TG |
1 |
public static final int |
ZOOM_TG |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ADD |
"add" |
public static final String |
ADD_BOX |
"addBox" |
public static final String |
ADD_CONE |
"addCone" |
public static final String |
ADD_SPHERE |
"addSphere" |
public static final String |
ADD_TUBE_POINT |
"addTubePoint" |
public static final String |
APPLY_TRANSFORM |
"applyTransform" |
public static final String |
CLOSE |
"close" |
public static final String |
DELETE |
"delete" |
public static final String |
EXPORT |
"exportContent" |
public static final String |
EXPORT_TRANSFORMED |
"exportTransformed" |
public static final String |
FILL_SELECTION |
"fillSelection" |
public static final String |
FINISH_TUBE |
"finishTube" |
public static final String |
IMPORT |
"importContent" |
public static final String |
LOCK |
"lock" |
public static final String |
RECORD_360 |
"record360" |
public static final String |
RESET_TRANSFORM |
"resetTransform" |
public static final String |
RESET_VIEW |
"resetView" |
public static final String |
SAVE_TRANSFORM |
"saveTransform" |
public static final String |
SCALEBAR |
"scalebar" |
public static final String |
SET_CHANNELS |
"setChannels" |
public static final String |
SET_COLOR |
"setColor" |
public static final String |
SET_CS |
"setCoordinateSystem" |
public static final String |
SET_SLICES |
"setSlices" |
public static final String |
SET_THRESHOLD |
"setThreshold" |
public static final String |
SET_TRANSFORM |
"setTransform" |
public static final String |
SET_TRANSPARENCY |
"setTransparency" |
public static final String |
SHOW_CONTENT |
"showContent" |
public static final String |
SMOOTH |
"smooth" |
public static final String |
SNAPSHOT |
"snapshot" |
public static final String |
START_ANIMATE |
"startAnimate" |
public static final String |
START_FREEHAND_RECORDING |
"startFreehandRecording" |
public static final String |
STOP_ANIMATE |
"stopAnimate" |
public static final String |
STOP_FREEHAND_RECORDING |
"stopFreehandRecording" |
public static final String |
UNLOCK |
"unlock" |
public static final String |
WINDOW_SIZE |
"windowSize" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
PARALLEL |
0 |
public static final int |
PERSPECTIVE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ADJUST_BOTH |
2 |
public static final int |
ADJUST_HORIZONTAL |
0 |
public static final int |
ADJUST_VERTICAL |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BYTE_DATA |
1 |
public static final int |
INT_DATA |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ROTATE |
0 |
public static final int |
TRANSLATE |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
TWO_RAD |
0.03490658503988659 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
TRIGGER_ID |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
pi |
3.141592653589793 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AVG_PHYS_DIST |
2 |
public static final int |
COMBINED |
6 |
public static final int |
COMBINED_SCORE_INDICES |
10 |
public static final int |
CUM_PHYST_DIST |
4 |
public static final int |
DISSIMILARITY |
1 |
public static final int |
LEVENSHTEIN |
0 |
public static final int |
MEDIAN_PHYS_DIST |
3 |
public static final int |
PROXIMITY |
7 |
public static final int |
PROXIMITY_MUT |
8 |
public static final int |
STD_DEV |
5 |
public static final int |
STD_DEV_ALL |
9 |
public static final int |
TRANS_ROT |
0 |
public static final int |
TRANS_ROT_SCALE |
1 |
public static final int |
TRANS_ROT_SCALE_SHEAR |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
PAINT_ERODE |
2 |
public static final int |
PAINT_EXCLUDE |
1 |
public static final int |
PAINT_OVERLAP |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MIN_BUCKET_SIZE |
4096 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BLUE |
8 |
public static final int |
GREEN |
4 |
public static final int |
HEIGHT |
52 |
public static final int |
MONO |
1 |
public static final int |
RED |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CT_APPEND |
1 |
public static final int |
CT_PREAPPEND |
2 |
public static final int |
CT_REPLACE |
0 |
protected static final int |
REPAINT_MULTI_LAYER |
1 |
protected static final int |
REPAINT_RGB_LAYER |
2 |
protected static final int |
REPAINT_SINGLE_LAYER |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
COMPOSITE_ADD |
1 |
public static final byte |
COMPOSITE_COLOR_YCBCR |
5 |
public static final byte |
COMPOSITE_DIFFERENCE |
4 |
public static final byte |
COMPOSITE_MULTIPLY |
3 |
public static final byte |
COMPOSITE_NORMAL |
0 |
public static final byte |
COMPOSITE_SUBTRACT |
2 |
protected static final String |
TAG_ATTR1 |
"<!ATTLIST " |
protected static final String |
TAG_ATTR2 |
" NMTOKEN #REQUIRED>\n" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
HEIGHT |
52 |
public static final int |
LINK_STATE |
4 |
public static final int |
LOCK_STATE |
1 |
public static final int |
VISIBILITY_STATE |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ARROW |
1 |
public static final int |
DOT |
2 |
public static final int |
TEXT |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
REDO |
1 |
public static final int |
UNDO |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
IMAGE |
2 |
public static final int |
IMAGEPLUS |
3 |
public static final int |
IMAGEPROCESSOR |
0 |
public static final int |
PIXELARRAY |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BOTTOM |
16 |
public static final int |
CENTER |
8 |
public static final int |
DOWN |
15 |
public static final int |
EAST |
2 |
public static final int |
FLIP_HORIZONTAL |
11 |
public static final int |
FLIP_VERTICAL |
12 |
public static final int |
NORTH |
0 |
public static final int |
NORTHEAST |
1 |
public static final int |
NORTHWEST |
7 |
public static final int |
R270 |
10 |
public static final int |
R90 |
9 |
public static final int |
SOUTH |
4 |
public static final int |
SOUTHEAST |
3 |
public static final int |
SOUTHWEST |
5 |
public static final int |
TOP |
13 |
public static final int |
UP |
14 |
public static final int |
WEST |
6 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
MAX_EDGE_CONFIDENCE |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
SIDE |
50 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
DEFAULT_MIN_R |
0.4000000059604645f |
public static final int |
DONE |
0 |
public static final int |
ERROR |
1 |
public static final int |
INTERRUPTED |
2 |
public static final int |
LEFT_RIGHT |
5 |
public static final int |
SUCCESS |
3 |
public static final int |
TOP_BOTTOM |
4 |
public static final int |
WORKING |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
GREY |
1 |
public static final byte |
GREY_ALPHA |
2 |
public static final int |
HEADER_SIZE |
9 |
public static final byte |
RGB |
3 |
public static final byte |
RGBA |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
GREY |
1 |
public static final byte |
GREY_ALPHA |
2 |
public static final int |
HEADER_SIZE |
9 |
public static final byte |
RGB |
3 |
public static final byte |
RGBA |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BOTH |
2 |
public static final int |
DTD |
0 |
public static final int |
XML |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MIPMAP_JPEG |
0 |
public static final int |
MIPMAP_PNG |
1 |
public static final int |
MIPMAP_RAG |
4 |
public static final int |
MIPMAP_RAW |
3 |
public static final int |
MIPMAP_TIFF |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AREA_DOWNSAMPLING |
6 |
public static final int |
DEFAULT_MIPMAPS_MODE |
6 |
public static final int |
ERROR_PATH_NOT_FOUND |
2147483647 |
public static final int |
GAUSSIAN |
3 |
protected final int |
MAX_RETRIES |
3 |
public static final int |
PREPROCESSED |
-999999 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
always_interpolate_areas_with_distance_map |
"always_interpolate_areas_with_distance_map" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BRUSH |
17 |
public static final int |
PEN |
16 |
public static final int |
PENCIL |
15 |
public static final int |
SELECT |
10 |
public static final int |
WAND |
18 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
FL_ERROR |
1.0E-7 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DELETION |
1 |
public static final int |
INSERTION |
2 |
public static final int |
MUTATION |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
X_AXIS |
0 |
public static final int |
Y_AXIS |
1 |
public static final int |
Z_AXIS |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
CLOSED |
16 |
public static final byte |
MIRROR_X |
4 |
public static final byte |
MIRROR_Y |
2 |
public static final byte |
MIRROR_Z |
1 |
public static final byte |
REVERSED |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ASCII |
0 |
public static final int |
BINARY |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final double |
EPS |
1.0E-8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
LUT_BLACK |
57 |
public static final int |
LUT_BLUE |
56 |
public static final int |
LUT_FIRE |
53 |
public static final int |
LUT_GRADIENT |
58 |
public static final int |
LUT_GRADIENT2 |
59 |
public static final int |
LUT_GRAY |
51 |
public static final int |
LUT_ORANGE |
55 |
public static final int |
LUT_ORIGINAL |
50 |
public static final int |
LUT_SPECTRUM |
52 |
public static final int |
LUT_THERMAL |
54 |
public static final int |
POINT_CIRCLE |
1 |
public static final int |
POINT_DOT |
0 |
public static final int |
POINT_SPHERE |
2 |
public static final int |
SURFACEPLOT_DOTS |
11 |
public static final int |
SURFACEPLOT_DOTSNOLIGHT |
10 |
public static final int |
SURFACEPLOT_FILLED |
14 |
public static final int |
SURFACEPLOT_ISOLINES |
15 |
public static final int |
SURFACEPLOT_LINES |
12 |
public static final int |
SURFACEPLOT_MESH |
13 |
public static final int |
VOLUME_DOTS |
20 |
public static final int |
VOLUME_PROJECTION_TRILINEAR_FRONT |
25 |
public static final int |
VOLUME_SLICE_NEAREST_NEIGHBOR |
21 |
public static final int |
VOLUME_SLICE_TRILINEAR |
22 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CIRCLE |
1 |
public static final int |
DOT |
0 |
public static final int |
SPHERE |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
tryOptimizing |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CANCELLED |
2 |
public static final int |
COMPLETED |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CORRELATION |
3 |
public static final int |
MEAN_ABSOLUTE_DIFFERENCES |
1 |
public static final int |
MEAN_SQUARED_DIFFERENCES |
2 |
public static final int |
NORMALIZED_MUTUAL_INFORMATION |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
ALIVE |
2 |
public static final byte |
BAND |
1 |
public static final byte |
FAR |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected final double |
GREY_EPSILON |
1.0 |
protected final double |
GREY_T |
1.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
INSIDE |
-1 |
public static final int |
INSIDE_FAR |
-2147483648 |
public static final int |
OUTSIDE |
1 |
public static final int |
OUTSIDE_FAR |
2147483647 |
public static final int |
STATE_ZERO |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
URL_DATA_BROWSER |
"http://loci.wisc.edu/software/data-browser" |
public static final String |
URL_SOFTWARE |
"https://www.openmicroscopy.org/bio-formats" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MISSING_VERSION_CODE |
"!" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PROP_LUT |
"LUT-" |
public static final String |
PROP_SERIES |
"Series" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
COLOR_MODE_COLORIZED |
"Colorized" |
public static final String |
COLOR_MODE_COMPOSITE |
"Composite" |
public static final String |
COLOR_MODE_CUSTOM |
"Custom" |
public static final String |
COLOR_MODE_DEFAULT |
"Default" |
public static final String |
COLOR_MODE_GRAYSCALE |
"Grayscale" |
public static final String |
KEY_AUTOSCALE |
"autoscale" |
public static final String |
KEY_COLOR_MODE |
"colorMode" |
public static final String |
KEY_CONCATENATE |
"concatenate" |
public static final String |
KEY_CROP |
"crop" |
public static final String |
KEY_FIRST |
"firstTime" |
public static final String |
KEY_FORCE_THUMBS |
"forceThumbnails" |
public static final String |
KEY_GROUP_FILES |
"groupFiles" |
public static final String |
KEY_ID |
"id" |
public static final String |
KEY_LOCATION |
"location" |
public static final String |
KEY_MUST_GROUP |
"mustGroup" |
public static final String |
KEY_OPEN_ALL_SERIES |
"openAllSeries" |
public static final String |
KEY_QUIET |
"quiet" |
public static final String |
KEY_ROIS_MODE |
"roiMode" |
public static final String |
KEY_SHOW_METADATA |
"showMetadata" |
public static final String |
KEY_SHOW_OME_XML |
"showOMEXML" |
public static final String |
KEY_SHOW_ROIS |
"showROIs" |
public static final String |
KEY_SPECIFY_RANGES |
"specifyRanges" |
public static final String |
KEY_SPLIT_C |
"splitWindows" |
public static final String |
KEY_SPLIT_T |
"splitTimepoints" |
public static final String |
KEY_SPLIT_Z |
"splitFocalPlanes" |
public static final String |
KEY_STACK_FORMAT |
"stackFormat" |
public static final String |
KEY_STACK_ORDER |
"stackOrder" |
public static final String |
KEY_STITCH_TILES |
"stitchTiles" |
public static final String |
KEY_SWAP_DIMS |
"swapDimensions" |
public static final String |
KEY_UNGROUP_FILES |
"ungroupFiles" |
public static final String |
KEY_UPGRADE_CHECK |
"upgradeCheck" |
public static final String |
KEY_VIRTUAL |
"virtual" |
public static final String |
KEY_WINDOWLESS |
"windowless" |
public static final String |
LOCATION_HTTP |
"Internet" |
public static final String |
LOCATION_LOCAL |
"Local machine" |
public static final String |
LOCATION_OMERO |
"OMERO" |
public static final String |
ORDER_DEFAULT |
"Default" |
public static final String |
ORDER_XYCTZ |
"XYCTZ" |
public static final String |
ORDER_XYCZT |
"XYCZT" |
public static final String |
ORDER_XYTCZ |
"XYTCZ" |
public static final String |
ORDER_XYTZC |
"XYTZC" |
public static final String |
ORDER_XYZCT |
"XYZCT" |
public static final String |
ORDER_XYZTC |
"XYZTC" |
public static final String |
ROIS_MODE_MANAGER |
"ROI manager" |
public static final String |
ROIS_MODE_OVERLAY |
"Overlay" |
public static final String |
VIEW_BROWSER |
"Data Browser" |
public static final String |
VIEW_HYPERSTACK |
"Hyperstack" |
public static final String |
VIEW_IMAGE_5D |
"Image5D" |
public static final String |
VIEW_NONE |
"Metadata only" |
public static final String |
VIEW_STANDARD |
"Standard ImageJ" |
public static final String |
VIEW_VIEW_5D |
"View5D" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_DEFAULT |
"<i>Select an option for a detailed explanation. Documentation written by Glen MacDonald and Curtis Rueden.</i>" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_COMPONENTS |
256 |
public static final int |
MAX_SERIES_THUMBS |
200 |
public static final int |
MAX_SERIES_TOGGLES |
200 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INI_DEFAULT |
"default" |
public static final String |
INI_INFO |
"info" |
public static final String |
INI_KEY |
"header" |
public static final String |
INI_LABEL |
"label" |
public static final String |
INI_SAVE |
"save" |
public static final String |
KEY_PREFIX |
"bioformats." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
STATUS_CANCELED |
1 |
public static final int |
STATUS_FINISHED |
2 |
public static final int |
STATUS_OK |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INI_TYPE |
"type" |
public static final String |
TYPE_BOOLEAN |
"boolean" |
public static final String |
TYPE_STRING |
"string" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INI_POSSIBLE |
"values" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
BORDER |
10 |
protected static final String |
HELP_MENU |
"Help>About Plugins" |
protected static final String |
NORMAL_MENU |
"Plugins>Bio-Formats" |
protected static final String |
OPENER_PLUGIN |
"Bio-Formats Importer" |
protected static final String |
SHORTCUT_PLUGIN |
"Bio-Formats Plugins Shortcut Window" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_BROWSER_WIDTH |
400 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
IMAGEJ_MSG |
"Sorry, the Bio-Formats plugins require ImageJ v1.43 or later." |
public static final String |
IMAGEJ_VERSION |
"1.43" |
public static final String |
URL_BF_SOFTWARE |
"https://www.openmicroscopy.org/bio-formats" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PREF_CELLSENS_FAIL |
"bioformats.cellsens.fail_on_missing_ets" |
public static final String |
PREF_CZI_ATTACHMENT |
"bioformats.zeissczi.include.attachments" |
public static final String |
PREF_CZI_AUTOSTITCH |
"bioformats.zeissczi.allow.autostitch" |
public static final String |
PREF_LEICA_LIF_PHYSICAL_SIZE |
"bioformats.leicalif.physicalsize.compatibility" |
public static final String |
PREF_ND2_CHUNKMAP |
"bioformats.nativend2.chunkmap" |
public static final String |
PREF_ND2_NIKON |
"bioformats.nd2.nikon" |
public static final String |
PREF_PICT_QTJAVA |
"bioformats.pict.qtjava" |
public static final String |
PREF_QT_QTJAVA |
"bioformats.qt.qtjava" |
public static final String |
PREF_READER_ENABLED |
"bioformats.enabled" |
public static final String |
PREF_READER_WINDOWLESS |
"bioformats.windowless" |
public static final String |
PREF_SDT_INTENSITY |
"bioformats.sdt.intensity" |
public static final String |
PREF_SLICE_LABEL_BASE_INDEX |
"bioformats.sliceLabelBaseIndex" |
public static final String |
PREF_SLICE_LABEL_PATTERN |
"bioformats.sliceLabelPattern" |
public static final String |
PREF_TIFF_IMAGEIO |
"bioformats.tiff.imageio" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_TRIES |
5 |
public static final String |
TOO_MANY_TRIES |
"Too many LuraWave license code attempts; giving up." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
matCols |
4 |
public static final int |
matRows |
4 |
public static final int |
matSize |
16 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CIRCLE |
0 |
public static final int |
CLINE |
5 |
public static final int |
DIAMOND |
1 |
public static final int |
DILATE |
64 |
public static final int |
ERODE |
32 |
public static final int |
FREE |
-1 |
public static final int |
FULLAREA |
-32 |
public static final int |
HLINE |
4 |
public static final int |
HMINUS |
-1 |
public static final int |
HPLUS |
1 |
public static final int |
HPOINTS |
6 |
public static final int |
LINE |
2 |
public static final int |
MAXSIZE |
151 |
public static final int |
PERIM |
-16 |
public static final int |
RING |
8 |
public static final int |
SQARE |
7 |
public static final int |
VLINE |
3 |
public static final int |
VPOINTS |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BINF |
-256 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
M_2PI |
6.283185307179586 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
flags |
29 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
flags |
29 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_THETA |
180 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
COLOR_RGB |
4 |
public static final int |
GRAY32 |
2 |
public static final int |
GRAY8 |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final float |
piSquare |
9.869604110717773f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CHANNEL |
"Channel" |
public static final String |
TIME |
"Time" |
public static final String |
X |
"X" |
public static final String |
Y |
"Y" |
public static final String |
Z |
"Z" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_NUM_MATCHES |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ANGLE_ROTATIONAXIS_TAG |
"axis" |
public static final String |
ANGLE_ROTATIONDEGREES_TAG |
"degrees" |
public static final String |
ANGLE_TAG |
"Angle" |
public static final String |
ANGLES_TAG |
"Angles" |
public static final String |
ATTRIBUTES_NAME_ATTRIBUTE_NAME |
"name" |
public static final String |
ATTRIBUTES_SPECIALIZED_ATTRIBUTE_NAME |
"specialized" |
public static final String |
ATTRIBUTES_TAG |
"Attributes" |
public static final String |
BASEPATH_TAG |
"BasePath" |
public static final String |
CHANNEL_TAG |
"Channel" |
public static final String |
CHANNELS_TAG1 |
"Channels" |
public static final String |
ID_TAG |
"id" |
public static final String |
ILLUMINATION_TAG |
"Illumination" |
public static final String |
ILLUMINATIONS_TAG |
"Illuminations" |
public static final String |
IMGLOADER_FORMAT_ATTRIBUTE_NAME |
"format" |
public static final String |
IMGLOADER_TAG |
"ImageLoader" |
public static final String |
MISSINGVIEW_SETUP_ATTRIBUTE_NAME |
"setup" |
public static final String |
MISSINGVIEW_TAG |
"MissingView" |
public static final String |
MISSINGVIEW_TIMEPOINT_ATTRIBUTE_NAME |
"timepoint" |
public static final String |
MISSINGVIEWS_TAG |
"MissingViews" |
public static final String |
NAME_TAG |
"name" |
public static final String |
SEQUENCEDESCRIPTION_TAG |
"SequenceDescription" |
public static final String |
SPIMDATA_TAG |
"SpimData" |
public static final String |
SPIMDATA_VERSION_ATTRIBUTE_CURRENT |
"0.2" |
public static final String |
SPIMDATA_VERSION_ATTRIBUTE_NAME |
"version" |
public static final String |
TILE_LOCATION_TAG |
"location" |
public static final String |
TILE_TAG |
"Tile" |
public static final String |
TILES_TAG |
"Tiles" |
public static final String |
TIMEPOINTS_LIST_TYPE |
"list" |
public static final String |
TIMEPOINTS_PATTERN_TAG |
"integerpattern" |
public static final String |
TIMEPOINTS_PATTERN_TYPE |
"pattern" |
public static final String |
TIMEPOINTS_RANGE_FIRST |
"first" |
public static final String |
TIMEPOINTS_RANGE_LAST |
"last" |
public static final String |
TIMEPOINTS_RANGE_TYPE |
"range" |
public static final String |
TIMEPOINTS_TAG |
"Timepoints" |
public static final String |
TIMEPOINTS_TIMEPOINT_TAG |
"Timepoint" |
public static final String |
TIMEPOINTS_TYPE_ATTRIBUTE_NAME |
"type" |
public static final String |
VIEWREGISTRATION_SETUP_ATTRIBUTE_NAME |
"setup" |
public static final String |
VIEWREGISTRATION_TAG |
"ViewRegistration" |
public static final String |
VIEWREGISTRATION_TIMEPOINT_ATTRIBUTE_NAME |
"timepoint" |
public static final String |
VIEWREGISTRATIONS_TAG |
"ViewRegistrations" |
public static final String |
VIEWSETUP_ANGLE_ID_TAG |
"angle" |
public static final String |
VIEWSETUP_ATTRIBUTES_TAG |
"attributes" |
public static final String |
VIEWSETUP_CHANNEL_ID_TAG |
"channel" |
public static final String |
VIEWSETUP_ILLUMINATION_ID_TAG |
"illumination" |
public static final String |
VIEWSETUP_SIZE_TAG |
"size" |
public static final String |
VIEWSETUP_TAG |
"ViewSetup" |
public static final String |
VIEWSETUP_VOXELSIZE_TAG |
"voxelSize" |
public static final String |
VIEWSETUPS_TAG |
"ViewSetups" |
public static final String |
VIEWTRANSFORM_AFFINE_TAG |
"affine" |
public static final String |
VIEWTRANSFORM_CLASS_ATTRIBUTE_NAME |
"class" |
public static final String |
VIEWTRANSFORM_NAME_TAG |
"Name" |
public static final String |
VIEWTRANSFORM_TAG |
"ViewTransform" |
public static final String |
VIEWTRANSFORM_TYPE_ATTRIBUTE_NAME |
"type" |
public static final String |
VIEWTRANSFORM_TYPE_VALUE_AFFINE |
"affine" |
public static final String |
VIEWTRANSFORM_TYPE_VALUE_GENERIC |
"generic" |
public static final String |
VOXELDIMENSIONS_SIZE_TAG |
"size" |
public static final String |
VOXELDIMENSIONS_UNIT_TAG |
"unit" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
minValue |
9.999999747378752E-5f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEBUG_ALL |
0 |
public static final int |
DEBUG_ERRORONLY |
2 |
public static final int |
DEBUG_MAIN |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
debugBeads |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
storeBeadPosition |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
beadSize |
3.0f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ELASTIC_BLOCK_CORRESPONDENCES |
2 |
public static final int |
LINEAR_PHASE_CORRELATION |
0 |
public static final int |
LINEAR_SIFT_CORRESPONDENCES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BASE_JAVADOC_URL |
"http://javadoc.imagej.net/ImageJ/" |
public static final int |
COLUMN_MARGIN |
5 |
public static final int |
DETAILS_WINDOW_WIDTH |
400 |
public static final int |
HIDE_COOLDOWN |
1500 |
public static final String |
IMG_REGEX |
"ArrayImg|PlanarImg|RandomAccessibleInterval|IterableInterval|Img|Histogram1d" |
public static final String |
IMGPLUS_REGEX |
"ImgPlus|Dataset" |
public static final int |
MAIN_WINDOW_HEIGHT |
700 |
public static final String |
NO_NAMESPACE |
"(global)" |
public static final String |
NUMBER_REGEX |
"int|short|long|double|float|byte|RealType" |
public static final String |
SIMPLE_KEY |
"net.imagej.ui.swing.ops.opfinder.simple" |
public static final String |
WINDOW_HEIGHT |
"op.viewer.height" |
public static final String |
WINDOW_WIDTH |
"op.viewer.width" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NRRD_BIG_ENDIAN |
4321 |
public static final int |
NRRD_DIM_MAX |
16 |
public static final int |
NRRD_FALSE |
0 |
public static final int |
NRRD_LITTLE_ENDIAN |
1234 |
public static final int |
NRRD_SPACE_DIM_MAX |
8 |
public static final int |
NRRD_TRUE |
1 |
public static final int |
NRRD_UNKNOWN |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
OUTSIDE_CANVAS |
2 |
public static final double |
RES_THRESHOLD |
512.0 |
public static final int |
RESOLUTION_SUFFICIENT |
0 |
public static final int |
RESOLUTION_UNSUFFICIENT |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
SIZE |
128 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MACRO_CMD |
"var brushWidth = 10;\nvar leftClick=16, altOrShift=9;\nvar pollDelay = 10;\nmacro \"Show Current Label [l]\" { label=call(\'LabelBrush_.getLabelMessage\')\n showStatus(label);\n}\nmacro \'Label Brush Tool - C111O11ffC100T6c0aL\' {\n while (true) {\n getCursorLoc(x, y, z, flags);\n if (flags&leftClick==0) exit();\n if (flags&altOrShift==0){\n call(\'LabelBrush_.label\', x,y,z,flags,brushWidth);\n }else{\n call(\'LabelBrush_.unlabel\', x,y,z,flags,brushWidth);\n }\n wait(pollDelay);\n }\n}\n\nmacro \'Label Brush Tool Options...\' {\n brushWidth = getNumber(\'Label Brush Width (pixels):\', brushWidth);\n}" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CURRENT_MATERIAL |
"SegmentatorModel.currentMaterial" |
public static final String |
LABEL_CANVAS |
"SegmentatorModel.labels.canvas" |
public static final String |
LABEL_IMAGE_PLUS |
"SegmentatorModel.labels" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CANCEL_OPTION |
2 |
public static final int |
OK_OPTION |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected final int |
iterations |
1000 |
protected final float |
maxEpsilon |
0.10000000149011612f |
protected final float |
maxTrust |
3.0f |
protected final float |
minInlierRatio |
0.10000000149011612f |
protected final int |
minNumInliers |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected final int |
iterations |
1000 |
protected final double |
maxEpsilon |
0.1 |
protected final double |
maxTrust |
3.0 |
protected final double |
minInlierRatio |
0.1 |
protected final int |
minNumInliers |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
INFO_PROPERTY |
"Info" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
POOL_TIMEOUT_IN_SECONDS |
1200 |
public static final int |
STD_THREAD_POOL_SIZE |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ADD_EDGE |
"add" |
public static final float |
BACKGROUND_CONFIDENCE |
0.10000000149011612f |
public static final float |
CERTAIN_BACKGROUND_CONFIDENCE |
0.0f |
public static final float |
CERTAIN_FOREGROUND_CONFIDENCE |
1.0f |
public static final float |
FOREGROUND_CONFIDENCE |
0.800000011920929f |
public static final String |
SUB_EDGE |
"subtract" |
public static final float |
UNKNOWN_REGION_CONFIDENCE |
0.5f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ELLIPSE_SELECTION |
"Ellipse" |
public static final String |
LASSO_SELECTION |
"Lasso" |
public static final String |
RECTANGLE_SELECTION |
"Rectangle" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
INCH_UNITS |
2 |
public static final int |
METRIC_UNITS |
1 |
public static final int |
NO_UNITS |
0 |
public static final int |
PIXEL_UNITS |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FRAME_TITLE |
"SIOX Api Demo" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
EMPTY_RULER |
0 |
public static final int |
INCH_RULER |
2 |
public static final int |
METRIC_RULER |
1 |
public static final int |
NO_RULER |
-1 |
public static final int |
PIXEL_RULER |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BEALE_SORENSON_HESTENES_STIEFEL_UPDATE |
2 |
public static final int |
FLETCHER_REEVES_UPDATE |
0 |
public static final int |
POLAK_RIBIERE_UPDATE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
myURL |
"http://preibischlab.mdc-berlin.de" |
protected static final String |
paperURL |
"http://www.nature.com/nmeth/journal/v7/n6/full/nmeth0610-418.html" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BLOW |
0 |
public static final int |
LASSO |
1 |
public static final int |
MAX_TOOL |
2 |
public static final int |
MIN_LASSO |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
version |
"1.2" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
MACRO_CMD |
"var leftClick=16, alt=9;\nmacro \'Flood Fill Tool - C111O11ffC100T6c0aF\' {\n while (true) {\n getCursorLoc(x, y, z, flags);\n if (flags&leftClick==0) exit();\n call(\'process3d.Flood_Fill.fill\', x,y,z);\n exit(); }\n}\n\n" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
HARRIS_THRESHOLD |
20.0f |
public static final float |
K |
0.14000000059604645f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAXIMUM |
1 |
public static final int |
MEDIAN |
2 |
public static final int |
MINIMUM |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CTRL_HEIGHT |
100 |
public static final int |
INDENT |
40 |
public static final int |
size |
300 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AFFINE |
3 |
public static final int |
ELASTIC |
4 |
public static final String |
exts |
".tif.jpg.png.gif.tiff.jpeg.bmp.pgm.ima.dm3.dm4" |
public static final int |
MAX_ITER |
300 |
public static final int |
MOVING_LEAST_SQUARES |
5 |
public static final int |
RIGID |
1 |
public static final int |
SIMILARITY |
2 |
public static final float |
STOP_THRESHOLD |
0.009999999776482582f |
public static final int |
TRANSLATION |
0 |
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 |
NONE |
0 |
public static final int |
SHORTEST_BRANCH |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BACK |
1 |
public static final int |
TREE |
0 |
public static final int |
UNDEFINED |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
OPEN |
0 |
public static final int |
SAVE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CURRENT_TYPE |
1 |
public static final int |
IMAGE_FILE_PATH |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
PREF_KEY |
"Coloc_2." |
Modifier and Type | Constant Field | Value |
---|---|---|
protected final int |
maxErrorRetries |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected final double |
maxSaturatedRatio |
0.10000000149011612 |
protected final double |
maxZeroZeroRatio |
0.10000000149011612 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
WIN_HEIGHT |
600 |
protected static final int |
WIN_WIDTH |
350 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
VERSION |
"1.2.6-DEV" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BUTTON_ACTIVATE_COLOR_CHOOSER |
"Color" |
public static final String |
BUTTON_DEACTIVATE_COLOR_CHOOSER |
"Color" |
public static final int |
DEFAULT_DISPLAY_MODE |
1 |
public static final String |
DISPLAY_MODE_PREF |
"image5d.displayMode" |
public static final int |
ONE_CHANNEL_COLOR |
1 |
public static final int |
ONE_CHANNEL_GRAY |
0 |
public static final int |
OVERLAY |
2 |
public static final int |
TILED |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CANVAS |
"main" |
public static final String |
CHANNEL_SELECTOR |
"channel" |
public static final String |
FRAME_SELECTOR |
"frame" |
public static final String |
SLICE_SELECTOR |
"slice" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
tagCAL |
4407628 |
public static final int |
tagCB |
4400706 |
public static final int |
tagGRA |
4674113 |
public static final int |
tagLBL |
4997708 |
public static final int |
tagLUT |
5002580 |
public static final int |
tagOVL |
5199436 |
public static final int |
tagTHR |
5523538 |
Modifier and Type | Constant Field | Value |
---|---|---|
public final String |
int16Types |
"short, short int, signed short, signed short int, int16, int16_t" |
public final String |
int32Types |
"int, signed int, int32, int32_t" |
public final String |
uint16Types |
"ushort, unsigned short, unsigned short int, uint16, uint16_t" |
public final String |
uint32Types |
"uint, unsigned int, uint32, uint32_t" |
public final String |
uint8Types |
"uchar, unsigned char, uint8, uint8_t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NRRD_VERSION |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEFAULT_INVERSE |
false |
public static final int |
DEFAULT_THRESHOLD |
128 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PLUGIN_NAME |
"OMEVisual" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
FILLING_URI |
"https://imagej.net/SNT:_Step-By-Step_Instructions#Filling" |
Modifier and Type | Constant Field | Value |
---|---|---|
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 |
7 |
public static final String |
SWC_CUSTOM_LABEL |
"custom" |
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 String |
SWC_END_POINT_LABEL |
"end point" |
public static final int |
SWC_FORK_POINT |
5 |
public static final String |
SWC_FORK_POINT_LABEL |
"fork point" |
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" |
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_SWC |
3 |
protected static final int |
TRACES_FILE_TYPE_UNCOMPRESSED_XML |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MIDPOINTS |
2 |
public static final int |
RADII |
1 |
public static final int |
RADII_AND_MIDPOINTS |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
TABLE_TITLE |
"SNT Measurements" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
NO_IMAGE_ASSOCIATED_DATA |
"noImgData" |
public static final String |
RESIZE_REQUIRED |
"resizeNeeded" |
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 |
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 |
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 |
"?" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ASSIGNED_VALUE |
"Assigned value" |
public static final String |
HIGHEST_PATH_ORDER |
"Highest path order" |
public static final String |
ID |
"Cell/id" |
public static final String |
LENGTH |
"Cable length" |
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_TIPS |
"No. of tips" |
public static final String |
STRAHLER_NUMBER |
"Horton-Strahler number" |
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 |
AVG_SPINE_DENSITY |
"Average spine/varicosity density" |
public static final String |
DEPTH |
"Depth" |
public static final String |
HEIGHT |
"Height" |
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 |
LENGTH |
"Cable length" |
public static final String |
MEAN_RADIUS |
"Mean radius" |
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_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 |
PRIMARY_LENGTH |
"Length of primary branches (sum)" |
public static final String |
STRAHLER_NUMBER |
"Horton-Strahler number" |
public static final String |
STRAHLER_RATIO |
"Horton-Strahler bifurcation ratio" |
public static final String |
TERMINAL_LENGTH |
"Length of terminal branches (sum)" |
public static final String |
WIDTH |
"Width" |
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 |
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" |
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 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CENTERLINE |
"None. Path coordinates only." |
public static final String |
CIRCLE |
"Circle (Hollow)" |
public static final String |
DISK |
"Disk (Solid)" |
public static final String |
SPHERE |
"Sphere" |
public static final String |
X_VALUES |
"x-values" |
public static final String |
Y_VALUES |
"y-values" |
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 |
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 |
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 |
SUM |
"Sum" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AVG_SPINE_DENSITY |
"Average spine/varicosity density" |
public static final String |
LENGTH |
"Path length" |
public static final String |
MEAN_RADIUS |
"Path mean radius" |
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_DISTANCE |
"Path distance to soma" |
public static final String |
PATH_FRAME |
"Path frame" |
public static final String |
PATH_ORDER |
"Path order" |
public static final String |
SHOLL_COUNTS |
"Sholl inters. (root centered)" |
public static final String |
STRAHLER_NUMBER |
"Horton-Strahler number" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AVG_SPINE_DENSITY |
"Average spine/varicosity density" |
public static final String |
BRANCH_LENGTH |
"Branch length" |
public static final String |
CONTRACTION |
"Contraction" |
public static final String |
FRACTAL_DIMENSION |
"Fractal dimension" |
public static final String |
INNER_LENGTH |
"Length of inner branches" |
public static final String |
INTER_NODE_DISTANCE |
"Inter-node distance" |
public static final String |
INTER_NODE_DISTANCE_SQUARED |
"Inter-node distance (squared)" |
public static final String |
MEAN_RADIUS |
"Path mean radius" |
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 |
PARTITION_ASYMMETRY |
"Partition asymmetry" |
public static final String |
PATH_CHANNEL |
"Path channel" |
public static final String |
PATH_FRAME |
"Path frame" |
public static final String |
PATH_LENGTH |
"Path length" |
public static final String |
PATH_ORDER |
"Path order" |
public static final String |
PRIMARY_LENGTH |
"Length of primary branches" |
public static final String |
REMOTE_BIF_ANGLES |
"Remote bif. angles" |
public static final String |
TERMINAL_LENGTH |
"Length of terminal branches" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BRANCH_POINTS |
"branch points" |
public static final String |
EDGES |
"edges" |
public static final String |
LENGTH |
"length" |
public static final String |
TIPS |
"tips" |
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 |
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_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 |
"?" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
URL |
"https://imagej.net/Sholl_Analysis" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
THICK_LINE |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final double |
UNASSIGNED_VALUE |
4.9E-324 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final double |
UNASSIGNED_VALUE |
4.9E-324 |
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 |
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 |
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_UNDEFINED |
6 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
BRAIN_ROOT_ID |
997 |
public static final String |
VERSION |
"2.5 (ML legacy)" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
ANY_HEMISPHERE |
0 |
public static final char |
LEFT_HEMISPHERE |
108 |
public static final char |
RIGHT_HEMISPHERE |
114 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_MENU_WEIGHT |
1d/0d |
public static final String |
LAF_DARCULA |
"FlatLaf Darcula" |
public static final String |
LAF_DARK |
"FlatLaf Dark" |
public static final String |
LAF_DEFAULT |
"System default" |
public static final String |
LAF_LIGHT |
"FlatLaf Light" |
public static final String |
LAF_LIGHT_INTJ |
"FlatLaf IntelliJ" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AXES_NORMAL |
1 |
public static final int |
NORMALIZED_FOR_SPHERE_VOLUME |
2 |
public static final int |
NOT_NORMALIZED |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
SHOW_SEARCH_OPTIONS |
128 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
EMPTY_LABEL |
"<html> " |
protected static final String |
HEADER_HTML |
"<html><body><div style=\'font-weight:bold;\'>" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FITCHOICE_KEY |
"choice" |
public static final String |
FITINPLACE_KEY |
"inplace" |
public static final String |
MAXRADIUS_KEY |
"maxrad" |
public static final String |
SECLAYER_KEY |
"secondary" |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AXON |
"axon" |
public static final String |
DENDRITE |
"dendrite" |
public static final String |
SOMA |
"soma" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
TAG_REGEX_PATTERN |
"\\{Group \\d+\\}" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
EMPTY_LABEL |
"<html> " |
protected static final String |
HEADER_HTML |
"<html><body><div style=\'font-weight:bold;\'>" |
protected static final String |
HEADER_TOOLTIP |
"<HTML><div WIDTH=650>" |
Modifier and Type | Constant Field | Value |
---|---|---|
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 |
20 |
public static final int |
DEF_MIN_DEGREE |
2 |
public static final double |
DEF_RSQUARED |
0.8 |
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:400px\'>" |
protected static final String |
HEADER_HTML |
"<html><body><div style=\'font-weight:bold;\'>" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BIN_AVERAGE |
0 |
public static final int |
BIN_MEDIAN |
1 |
public static final int |
BIN_MODE |
2 |
public static final int |
MAX_N_SPANS |
10 |
public static final String |
URL |
"https://imagej.net/Sholl_Analysis" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ALL_PLOTS |
0 |
public static final int |
CENTER |
8 |
public static final int |
CENTROID |
32768 |
public static final String |
COMMAND_LABEL |
"Metrics & Options..." |
public static final int |
CURVE_FITTING |
4 |
public static final int |
DIRECTORY |
1 |
public static final int |
ENCLOSING_RADIUS |
256 |
protected static final String |
ENCLOSING_RADIUS_KEY |
"F" |
protected static final String |
END_RADIUS_KEY |
"B" |
public static final int |
ENDING_RADIUS |
32 |
protected static final int |
FITTED_MASK |
1 |
public static final int |
GUESS_LOG_METHOD |
256 |
public static final int |
HIDE_SAVED_FILES |
4096 |
public static final int |
INFER_PRIMARY |
2 |
protected static final String |
INTEGRATION_KEY |
"E" |
public static final int |
INTERSECTING_RADII |
512 |
public static final int |
KURTOSIS |
16384 |
public static final int |
MEAN_INTERS |
2048 |
public static final int |
MEDIAN_INTERS |
4096 |
public static final int |
NO_PLOTS |
2 |
public static final int |
NO_TABLE |
262144 |
protected static final String |
NORMALIZER_INDEX_KEY |
"I" |
protected static final String |
NSAMPLES_KEY |
"D" |
public static final int |
ONLY_LINEAR_PLOT |
1 |
public static final int |
OVERLAY_SHELLS |
1024 |
public static final int |
P1090_REGRESSION |
65536 |
protected static final String |
POLYNOMIAL_INDEX_KEY |
"H" |
protected static final String |
PRIMARY_BRANCHES_KEY |
"G" |
protected static final String |
QUAD_CHOICE_KEY |
"K" |
public static final int |
RADIUS_STEP |
64 |
public static final int |
SAMPLES_PER_RADIUS |
128 |
protected static final String |
SAVE_DIR_KEY |
"J" |
public static final int |
SAVE_FILES |
2048 |
public static final int |
SHOLL_LOG |
128 |
public static final int |
SHOLL_N |
16 |
public static final int |
SHOLL_NS |
32 |
public static final int |
SHOLL_SLOG |
64 |
public static final int |
SHOW_MASK |
512 |
public static final int |
SKEWNESS |
8192 |
public static final String |
SKIP_BITMAP_OPTIONS_LABEL |
"skip-bitmap" |
public static final int |
SKIP_SINGLE_VOXELS |
8192 |
protected static final String |
START_RADIUS_KEY |
"A" |
public static final int |
STARTING_RADIUS |
16 |
protected static final String |
STEP_SIZE_KEY |
"C" |
public static final int |
SUM_INTERS |
1024 |
public static final int |
THRESHOLD |
4 |
public static final int |
TRIM_BOUNDS |
1 |
public static final int |
UNIT |
2 |
public static final int |
VERBOSE |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final String |
URL |
"https://imagej.net/Strahler_Analysis" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CANCELLED |
1 |
public static final byte |
CLOSED_FROM_GOAL |
4 |
public static final byte |
CLOSED_FROM_START |
2 |
public static final byte |
FREE |
5 |
public static final byte |
OPEN_FROM_GOAL |
3 |
public static final byte |
OPEN_FROM_START |
1 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MIN_COST_PER_UNIT_DISTANCE |
1.0 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DELETE |
-4 |
public static final int |
KEEP |
-8 |
public static final int |
NONE |
-1 |
public static final int |
VISITED |
-2 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
SWC_TYPE_IGNORED |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MERGE |
4 |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final float |
DEF_NODE_RADIUS |
3.0f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
ANGLE_PATTERN |
97 |
public static final char |
CHANNEL_PATTERN |
99 |
public static final char |
ILLUMINATION_PATTERN |
105 |
public static final char |
TIMEPOINT_PATTERN |
116 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
warningLabel |
" (WARNING: Only available for " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
messagePaper |
"Please note that the SPIM Registration is based on a publication.\nIf you use it successfully for your research please be so kind to cite our work:\nPreibisch et al., Nature Methods (2010), 7(6):418-419\n" |
public static final String |
messageWebsite |
"This plugin is written and maintained by Stephan Preibisch (click for webpage)\n" |
public static final String |
myURL |
"http://www.preibisch.net/" |
public static final String |
paperURL |
"http://www.nature.com/nmeth/journal/v7/n6/full/nmeth0610-418.html" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BOUNDINGBOX_TAG |
"BoundingBoxDefinition" |
public static final String |
BOUNDINGBOX_TAG_MAX |
"max" |
public static final String |
BOUNDINGBOX_TAG_MIN |
"min" |
public static final String |
BOUNDINGBOX_TAG_NAME |
"name" |
public static final String |
BOUNDINGBOXES_TAG |
"BoundingBoxes" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
askWhenMoreThan |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
askWhenMoreThan |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
askWhenMoreThan |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
BITS_PER_SAMPLE |
258 |
public static final int |
COMMENTS_HEADER |
84720485 |
public static final int |
COMMENTS_OFFSET_HEADER |
99384722 |
public static final int |
DISPLAY_SETTINGS_HEADER |
347834724 |
public static final int |
DISPLAY_SETTINGS_OFFSET_HEADER |
483765892 |
public static final char |
IMAGE_DESCRIPTION |
270 |
public static final int |
INDEX_MAP_HEADER |
3453623 |
public static final int |
INDEX_MAP_OFFSET_HEADER |
54773648 |
public static final char |
MM_METADATA |
51123 |
public static final char |
SAMPLES_PER_PIXEL |
277 |
public static final char |
STRIP_BYTE_COUNTS |
279 |
public static final char |
STRIP_OFFSETS |
273 |
public static final int |
SUMMARY_MD_HEADER |
2355492 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AMPLITUDE_DIR_TAG |
"amplitudeDir" |
public static final String |
AMPLITUDE_ID_TAG |
"amplitudeId" |
public static final String |
EXTENSION_TAG |
"ext" |
public static final String |
PHASE_DIR_TAG |
"phaseDir" |
public static final String |
PHASE_ID_TAG |
"phaseId" |
public static final String |
STACK_DIR_TAG |
"stackDir" |
public static final String |
TIMEPOINTS_TAG |
"timepoints" |
public static final String |
ZPLANES_TAG |
"zplanes" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DIRECTORY_TAG |
"imagedirectory" |
public static final String |
IMGLIB2CONTAINER_PATTERN_TAG |
"imglib2container" |
public static final String |
MASTER_FILE_TAG |
"masterfile" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DIRECTORY_TAG |
"imagedirectory" |
public static final String |
IMGLIB2CONTAINER_PATTERN_TAG |
"imglib2container" |
public static final String |
MASTER_FILE_TAG |
"masterfile" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DIRECTORY_TAG |
"imagedirectory" |
public static final String |
IMGLIB2CONTAINER_PATTERN_TAG |
"imglib2container" |
public static final String |
MASTER_FILE_TAG |
"masterfile" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DIRECTORY_TAG |
"imagedirectory" |
public static final String |
FILE_PATTERN_TAG |
"filePattern" |
public static final String |
IMGLIB2CONTAINER_PATTERN_TAG |
"imglib2container" |
public static final String |
LAYOUT_ANGLE_TAG |
"layoutAngles" |
public static final String |
LAYOUT_CHANNEL_TAG |
"layoutChannels" |
public static final String |
LAYOUT_ILLUMINATION_TAG |
"layoutIlluminations" |
public static final String |
LAYOUT_TP_TAG |
"layoutTimepoints" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
VIEWINTERESTPOINTS_LABEL_ATTRIBUTE_NAME |
"label" |
public static final String |
VIEWINTERESTPOINTS_PARAMETERS_ATTRIBUTE_NAME |
"params" |
public static final String |
VIEWINTERESTPOINTS_SETUP_ATTRIBUTE_NAME |
"setup" |
public static final String |
VIEWINTERESTPOINTS_TAG |
"ViewInterestPoints" |
public static final String |
VIEWINTERESTPOINTS_TIMEPOINT_ATTRIBUTE_NAME |
"timepoint" |
public static final String |
VIEWINTERESTPOINTSFILE_TAG |
"ViewInterestPointsFile" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
minValue |
9.999999747378752E-5f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AFFINE |
128 |
public static final int |
CONGRUENT |
64 |
public static final int |
IDENTITY |
2 |
public static final int |
NEGATIVE_DETERMINANT |
256 |
public static final int |
ORTHOGONAL |
16 |
public static final int |
RIGID |
32 |
public static final int |
SCALE |
4 |
public static final int |
TRANSLATION |
8 |
public static final int |
ZERO |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
F |
2 |
public static final int |
GAUSSIAN_STACK_FOCUSER |
3 |
public static final int |
MAX_PROJECTION |
1 |
public static final int |
MIN_PROJECTION |
2 |
public static final int |
NO_PROJECTION |
0 |
public static final int |
T |
4 |
public static final int |
X |
0 |
public static final int |
Y |
1 |
public static final int |
Z |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
MODE_2D_GEL |
4 |
public static final byte |
MODE_BARREL |
3 |
public static final byte |
MODE_ELASTIC |
0 |
public static final byte |
MODE_FISHEYE |
1 |
public static final byte |
MODE_PERSPECTIVE |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PLUGIN_VERSION |
"1.2" |
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 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
AVG |
0 |
public static final int |
LIN_BLEND |
1 |
public static final int |
MAX |
2 |
public static final int |
MIN |
3 |
public static final int |
NONE |
5 |
public static final int |
RED_CYAN |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_SET_SIZE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MIN_SET_SIZE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ANISOTROPIC_DIFFUSION |
10 |
public static final int |
BILATERAL |
11 |
public static final int |
DERIVATIVES |
15 |
public static final int |
DOG |
3 |
public static final int |
ENTROPY |
18 |
public static final int |
GABOR |
14 |
public static final int |
GAUSSIAN |
0 |
public static final int |
HESSIAN |
2 |
public static final int |
KUWAHARA |
13 |
public static final int |
LAPLACIAN |
16 |
public static final int |
LIPSCHITZ |
12 |
public static final int |
MAXIMUM |
8 |
public static final int |
MEAN |
6 |
public static final int |
MEDIAN |
9 |
public static final int |
MEMBRANE |
4 |
public static final int |
MINIMUM |
7 |
public static final int |
NEIGHBORS |
19 |
public static final int |
SOBEL |
1 |
public static final int |
STRUCTURE |
17 |
public static final int |
VARIANCE |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DERIVATIVES |
2 |
public static final int |
DOG |
6 |
public static final int |
EDGES |
5 |
public static final int |
GAUSSIAN |
0 |
public static final int |
HESSIAN |
1 |
public static final int |
LAPLACIAN |
3 |
public static final int |
MAXIMUM |
8 |
public static final int |
MEAN |
9 |
public static final int |
MEDIAN |
10 |
public static final int |
MINIMUM |
7 |
public static final int |
STRUCTURE |
4 |
public static final int |
VARIANCE |
11 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ADD_TRACE |
"addTrace" |
public static final String |
APPLY_CLASSIFIER |
"applyClassifier" |
public static final String |
CHANGE_CLASS_NAME |
"changeClassName" |
public static final String |
CREATE_CLASS |
"createNewClass" |
public static final String |
DELETE_TRACE |
"deleteTrace" |
public static final String |
GET_PROBABILITY |
"getProbability" |
public static final String |
GET_RESULT |
"getResult" |
public static final String |
LAUNCH_WEKA |
"launchWeka" |
public static final String |
LOAD_CLASSIFIER |
"loadClassifier" |
public static final String |
LOAD_DATA |
"loadData" |
public static final String |
PLOT_RESULT |
"plotResultGraphs" |
public static final String |
PLUGIN_NAME |
"Trainable Weka Segmentation" |
public static final String |
SAVE_CLASSIFIER |
"saveClassifier" |
public static final String |
SAVE_DATA |
"saveData" |
public static final String |
SAVE_FEATURE_STACK |
"saveFeatureStack" |
public static final String |
SET_BALANCE |
"setClassBalance" |
public static final String |
SET_CLASSIFIER |
"setClassifier" |
public static final String |
SET_FEATURE |
"setFeature" |
public static final String |
SET_HOMOGENIZATION |
"setClassHomogenization" |
public static final String |
SET_MAXIMUM_SIGMA |
"setMaximumSigma" |
public static final String |
SET_MEMBRANE_PATCH |
"setMembranePatchSize" |
public static final String |
SET_MEMBRANE_THICKNESS |
"setMembraneThickness" |
public static final String |
SET_MINIMUM_SIGMA |
"setMinimumSigma" |
public static final String |
SET_OPACITY |
"setOpacity" |
public static final String |
TOGGLE_OVERLAY |
"toggleOverlay" |
public static final String |
TRAIN_CLASSIFIER |
"trainClassifier" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_NUM_CLASSES |
100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
VARIANCE |
0 |
public static final int |
VARIANCE_DIV_MEAN |
1 |
public static final int |
VARIANCE_DIV_MEAN_SQUARE |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_FLAGS |
63 |
public static final int |
HOLE_ADDITION |
4 |
public static final int |
HOLE_DELETION |
32 |
public static final int |
MERGE |
1 |
public static final int |
OBJECT_ADDITION |
16 |
public static final int |
OBJECT_DELETION |
8 |
public static final double |
SIMPLE_POINT_THRESHOLD |
0.0 |
public static final int |
SPLIT |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PLUGIN_VERSION |
"1.3" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CHANNELS |
2 |
public static final int |
FRAMES |
4 |
public static final int |
HEIGHT |
1 |
public static final int |
LOG_PROBABILITIES |
1 |
public static final int |
PROBABILITIES |
0 |
public static final int |
SELF_INFORMATION |
2 |
public static final int |
SLICES |
3 |
public static final int |
WIDTH |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PLUGIN_VERSION |
"1.1" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
CHECKBOX |
2 |
protected static final int |
LABEL |
1 |
protected static final int |
RADIO |
3 |
protected static final int |
TEXTFIELD |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PLUGIN_VERSION |
"1.2" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
DEFAULT_QUOTE_CHARACTER |
34 |
public static final char |
DEFAULT_SEPARATOR |
44 |
public static final int |
DEFAULT_SKIP_LINES |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
DEFAULT_ESCAPE_CHARACTER |
34 |
public static final String |
DEFAULT_LINE_END |
"\n" |
public static final char |
DEFAULT_QUOTE_CHARACTER |
34 |
public static final char |
DEFAULT_SEPARATOR |
44 |
public static final char |
NO_ESCAPE_CHARACTER |
0 |
public static final char |
NO_QUOTE_CHARACTER |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CENTER |
2 |
public static final String |
CONFIG_FILE |
"options.config" |
public static final int |
GREY |
0 |
public static final int |
LABEL_DIFFUSION |
3 |
public static final int |
LABEL_SURFACE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
EMBOSSED_OUT |
5 |
public static final int |
ETCHED_IN |
4 |
public static final int |
LINE |
1 |
public static final int |
NONE |
0 |
public static final int |
ROUND_RECT |
6 |
public static final int |
THREED_IN |
2 |
public static final int |
THREED_OUT |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ARMED |
1 |
public static final int |
DISABLED |
3 |
public static final int |
OVER |
2 |
public static final int |
UNARMED |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BOOKSTEIN |
0 |
public static final int |
FASTMATRIX |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_NUM_SLICES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_NUM_SLICES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_PIX_PER_SLICE |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_NUM_SLICES |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_NUM_SLICES |
20 |
public static final int |
DEF_TRANSITION |
0 |
public static final int |
FADE |
0 |
public static final int |
H_STRIPES |
1 |
public static final int |
V_STRIPES |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
COPY |
0 |
public static final int |
CUT |
1 |
public static final int |
DEF_MODE |
0 |
public static final int |
DEF_PIX_PER_SLICE |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_HEIGHT |
512 |
public static final int |
DEF_WIDTH |
512 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialSubSubVersionUID |
5L |
public static final long |
serialSubVersionUID |
3L |
public static final long |
serialVersionUID |
2L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
TRANSPARENCY |
0.4000000059604645f |
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