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A
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C
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D
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E
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F
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G
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H
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I
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J
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Symbols
+TracX (module)
+TracX.@Fingerprint (module)
+TracX.@ImageProcessing (module)
+TracX.@ImageVisualization (module)
+TracX.@IO (module)
+TracX.@LAP (module)
+TracX.@Lineage (module)
+TracX.@LineageData (module)
+TracX.@Motion (module)
+TracX.@NonAssignedTracks (module)
+TracX.@ParameterConfiguration (module)
+TracX.@ProjectConfiguration (module)
+TracX.@QuantificationData (module)
+TracX.@SegmentationData (module)
+TracX.@TemporaryData (module)
+TracX.@TemporaryLineageAssignment (module)
+TracX.@TemporaryTrackingData (module)
+TracX.@Tracker (module)
+TracX.@TrackerConfiguration (module)
+TracX.@TrackerData (module)
+TracX.@Utils (module)
A
active3DFingerprint (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
addCell() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
addData() (+TracX.@TemporaryTrackingData.TemporaryTrackingData method)
addFluoImage() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
addFluoImageTag() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
addTimestampScalebar() (in module +TracX.@ImageProcessing)
assignMammalianTrackparent() (in module +TracX.@TrackerData)
asymmetricalLineageReconstruction() (+TracX.@Lineage.Lineage method)
averageCellSizeGrowth (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
C
cell_area (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_center_x (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_center_y (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_center_z (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_close_neighbour (+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_del (+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_dif_x (+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_dif_y (+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_dif_z (+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_eccentricity (+TracX.@SegmentationData.SegmentationData attribute)
cell_filtered_dif_x (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_filtered_dif_y (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_filtered_dif_z (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_fractionOfGoodMembranePixels (+TracX.@SegmentationData.SegmentationData attribute)
cell_frame (+TracX.@SegmentationData.SegmentationData attribute)
cell_index (+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_majoraxis (+TracX.@SegmentationData.SegmentationData attribute)
cell_mask_boundary_points (+TracX.@SegmentationData.SegmentationData attribute)
cell_mem_area (+TracX.@SegmentationData.SegmentationData attribute)
cell_mem_volume (+TracX.@SegmentationData.SegmentationData attribute)
cell_minoraxis (+TracX.@SegmentationData.SegmentationData attribute)
cell_nuc_area (+TracX.@SegmentationData.SegmentationData attribute)
cell_nuc_radius (+TracX.@SegmentationData.SegmentationData attribute)
cell_orientation (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
cell_perimeter (+TracX.@SegmentationData.SegmentationData attribute)
cell_pole1_age (+TracX.@SegmentationData.SegmentationData attribute)
cell_pole1_x (+TracX.@SegmentationData.SegmentationData attribute)
cell_pole1_y (+TracX.@SegmentationData.SegmentationData attribute)
cell_pole2_age (+TracX.@SegmentationData.SegmentationData attribute)
cell_pole2_x (+TracX.@SegmentationData.SegmentationData attribute)
cell_pole2_y (+TracX.@SegmentationData.SegmentationData attribute)
cell_timepoint (+TracX.@SegmentationData.SegmentationData attribute)
cell_volume (+TracX.@SegmentationData.SegmentationData attribute)
cell_zplane (+TracX.@SegmentationData.SegmentationData attribute)
cellCyclePhaseTable (+TracX.@Lineage.Lineage attribute)
cellDivisionMarkerData (+TracX.@TrackerData.TrackerData attribute)
cellDivisionType (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
cellThumbSideLength (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
checkParameterConfiguration() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
checkProjectConfiguration() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
checkToolboxStatus() (in module +TracX.@Utils)
clearMarkerTracking() (+TracX.@LineageData.LineageData method)
computeAssignmentCostMatrix() (in module +TracX.@LAP)
computeAssignmentFingerprintDistanceArray() (in module +TracX.@Fingerprint)
computeCLAHE() (in module +TracX.@ImageProcessing)
computeDeltaDistance() (in module +TracX.@Fingerprint)
computeFFPCostMatrix() (in module +TracX.@LAP)
computeFingerprint() (in module +TracX.@Fingerprint)
computeFingerprint3D() (in module +TracX.@Fingerprint)
computeFingerprintAsgmtFrac() (in module +TracX.@Fingerprint)
computeFingerprintDistance() (in module +TracX.@Fingerprint)
computeFingerprintForFrame() (in module +TracX.@Fingerprint)
computeFingerprintForFrame3D() (in module +TracX.@Fingerprint)
computeFPDistThreshold() (in module +TracX.@Fingerprint)
computeNeighbourhoodMotionCostMatrix() (in module +TracX.@LAP)
computeNeighbourProbFPBelowAss() (in module +TracX.@Fingerprint)
computeNewFrameAssignment() (in module +TracX.@LAP)
computeOrientationDifference() (in module +TracX.@LAP)
computeOrientationDifferenceMatrix() (in module +TracX.@LAP)
configuration (+TracX.@ImageProcessing.ImageProcessing attribute)
(+TracX.@ImageVisualization.ImageVisualization attribute)
(+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
controlPrefix (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
convertChallengeFilesToParseable() (in module +TracX.@IO)
convertedImageFileNameArray (+TracX.@IO.IO attribute)
convertImageFileNames() (in module +TracX.@IO)
convertXLSToCSV() (in module +TracX.@IO)
copyResultsToTrackerData() (+TracX.@LineageData.LineageData method)
(+TracX.@Tracker.Tracker method)
correctMDMisassignment() (in module +TracX.@Tracker)
correctTrackMisassignment() (in module +TracX.@Tracker)
createNewTrackingProject() (+TracX.@Tracker.Tracker method)
createProjectConfiguration() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
D
data (+TracX.@ImageProcessing.ImageProcessing attribute)
(+TracX.@ImageVisualization.ImageVisualization attribute)
(+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
data3D (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
daughterCell (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
daughterCellStartFrame (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
debugLevel (+TracX.@Fingerprint.Fingerprint attribute)
(+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
decompressOrientationData() (in module +TracX.@TrackerData)
delByFeature() (in module +TracX.@TrackerData)
delByROI() (in module +TracX.@TrackerData)
deleteByFeature() (in module +TracX.@Tracker)
deleteByROI() (in module +TracX.@Tracker)
deleteData() (in module +TracX.@TrackerData)
deleteEntry() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
deleteRow() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
deleteSegArtefacts() (in module +TracX.@Tracker)
deleteSegObjAtBorder() (in module +TracX.@Tracker)
delSegArtefacts() (in module +TracX.@TrackerData)
destackTimepoints() (in module +TracX.@IO)
detectBudNeckMarkerPixelArray() (in module +TracX.@Lineage)
determineMotherCell() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
divisionMarkerAverageObjSizeGrowth (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerConvexAreaLowerThresh (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerConvexAreaUpperThresh (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerDenoising (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerEdgeSensitivityThresh (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerFingerprintHalfWindowSideLength (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerFingerprintMaxConsideredFrequencies (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerFingerprintResizeFactor (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerIndividualFunctionPenalty (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerLineProfileLength (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerLineProfilePeakLowerBound (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerLineProfilePeakUpperBound (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMaxExpectedMovement (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMaxMajorAxisRotation (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMaxObjCenterDisplacement (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMaxObjSizeDecrease (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMaxObjSizeIncrease (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMaxTrackFrameSkipping (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMeanObjDiameter (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerMeanObjDiameterScalingFactor (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerNeighbourhoodSearchRadius (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerRadiusVectorFilterX (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerRadiusVectorFilterY (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerRadiusVectorFilterZ (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
divisionMarkerUsedFunctionsForCostMatrix (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
downloadFile() (in module +TracX.@Utils)
E
ensureResultsDirExists() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
evaluateNewMammalianRoots() (in module +TracX.@Lineage)
evaluateObjSigAroundTrustedFrames() (+TracX.@LineageData.LineageData method)
evaluateTrackAge() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
evaluation (+TracX.@Tracker.Tracker attribute)
exportCellCycleResults() (in module +TracX.@Tracker)
exportFinalTrackingMasks() (in module +TracX.@Tracker)
exportTrackerConfiguration() (+TracX.@TrackerConfiguration.TrackerConfiguration method)
exportTrackingResults() (in module +TracX.@Tracker)
F
filenameSorterForCellXinput() (in module +TracX.@IO)
fillTrackHoles() (in module +TracX.@TrackerData)
filterVectorField() (in module +TracX.@Motion)
fingerprint (+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
Fingerprint (class in +TracX.@Fingerprint)
Fingerprint() (+TracX.@Fingerprint.Fingerprint method)
fingerprintDistThreshold (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
fingerprintHalfWindowSideLength (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
fingerprintMaxConsideredFrequencies (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
fingerprintResizeFactor (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
fingperprintCostMatrixRefinement() (in module +TracX.@LAP)
fluo_background_mean (+TracX.@QuantificationData.QuantificationData attribute)
fluo_background_std (+TracX.@QuantificationData.QuantificationData attribute)
fluo_bright_euler (+TracX.@QuantificationData.QuantificationData attribute)
fluo_bright_q25 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_bright_q50 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_bright_q75 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_bright_total (+TracX.@QuantificationData.QuantificationData attribute)
fluo_cell_q25 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_cell_q50 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_cell_q75 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_cell_total (+TracX.@QuantificationData.QuantificationData attribute)
fluo_id (+TracX.@QuantificationData.QuantificationData attribute)
fluo_mem_q25 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_mem_q50 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_mem_q75 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_mem_total (+TracX.@QuantificationData.QuantificationData attribute)
fluo_name (+TracX.@QuantificationData.QuantificationData attribute)
fluo_nuc_q25 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_nuc_q50 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_nuc_q75 (+TracX.@QuantificationData.QuantificationData attribute)
fluo_nuc_total (+TracX.@QuantificationData.QuantificationData attribute)
fluoFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
fluoImageIdentifier (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
fluoLineageFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
fontSize (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
frameOfMDPair (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
G
generate4DImageStack() (in module +TracX.@ImageProcessing)
generate4DImageStackMarker() (in module +TracX.@ImageProcessing)
generateAnnotatedControlImageFrame() (in module +TracX.@ImageProcessing)
generateFingerprintControlImageFrame() (in module +TracX.@ImageProcessing)
generateLineageFrame() (in module +TracX.@ImageProcessing)
generateLineageMovie() (in module +TracX.@ImageProcessing)
generateLineageTreeObject() (in module +TracX.@Lineage)
generateMarkerControlImageFrame() (in module +TracX.@ImageProcessing)
generateMarkerTimeSeriesImage() (in module +TracX.@ImageProcessing)
generateMaskForMatrixCorners() (in module +TracX.@ImageProcessing)
generateMergedMask() (in module +TracX.@ImageProcessing)
generateMergedMaskForReSegmentation() (in module +TracX.@ImageProcessing)
generateMultiTrackControlMovie() (in module +TracX.@ImageProcessing)
generatePoleAgeControlImageFrame() (in module +TracX.@ImageProcessing)
generateScriptFromTracker() (in module +TracX.@Tracker)
generateSingleTrackControlMovie() (in module +TracX.@ImageProcessing)
generateTimeSeriesImageMatrix() (in module +TracX.@ImageProcessing)
generateTrackControlImageFramePadded() (in module +TracX.@ImageProcessing)
generateTrackerControlMaskImageFrame() (in module +TracX.@ImageProcessing)
getBkgCorrSig() (in module +TracX.@Lineage)
getBWLabelColor() (in module +TracX.@Utils)
getCellCyclePhaseTable() (in module +TracX.@Lineage)
getCellStruct() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
getCloseCellNeighbourIdx() (in module +TracX.@LineageData)
(in module +TracX.@TrackerData)
getColorMap() (in module +TracX.@Utils)
getCommonLogical() (in module +TracX.@Utils)
getCommonTrackDataSubset() (in module +TracX.@TrackerData)
getConditionalFieldArray() (+TracX.@LineageData.LineageData method)
(+TracX.@TrackerData.TrackerData method)
getConsecutiveCloseCellNeighbourIdx() (in module +TracX.@TrackerData)
getControlImageFormat() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
getDivisionFrames() (in module +TracX.@Lineage)
getFieldArray() (+TracX.@TrackerData.TrackerData method)
getFieldArrayColorMap() (in module +TracX.@TrackerData)
getFieldArrayForFrame() (+TracX.@LineageData.LineageData method)
(+TracX.@TrackerData.TrackerData method)
getFieldArrayForSubsetOnFrame() (+TracX.@TrackerData.TrackerData method)
getFieldArrayForTrackIndex() (+TracX.@TrackerData.TrackerData method)
getFieldArrayForTrackIndexForFrame() (in module +TracX.@TrackerData)
getFieldCMap() (in module +TracX.@ImageProcessing)
getFluoID() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
getFluoImage() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
getInvalidVectors() (in module +TracX.@Motion)
getLineageSummary() (in module +TracX.@Lineage)
getLineProfileVerification() (in module +TracX.@Lineage)
getMaskBasedDPairs() (in module +TracX.@TrackerData)
getMaxNumCompThreads() (in module +TracX.@Utils)
getMotionCorrNeighbours() (in module +TracX.@TrackerData)
getNewickFormat() (in module +TracX.@Lineage)
getNumberOfFluoImages() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
getNumberOfRowsFromFrame() (+TracX.@LineageData.LineageData method)
(+TracX.@TrackerData.TrackerData method)
getPotSegArtefacts() (in module +TracX.@TrackerData)
getRecursiveTrackParentColoring() (in module +TracX.@Utils)
getRootTrackRelatedDaughterArray() (in module +TracX.@Lineage)
getRootTrackTreeObject() (in module +TracX.@Lineage)
getSegAreaBoundingBox() (in module +TracX.@Utils)
getSortIdxForTrackIndices() (in module +TracX.@TrackerData)
getStartEndFrameOfTrack() (in module +TracX.@TrackerData)
getTemporaryDataStruct() (+TracX.@TrackerData.TrackerData method)
getTextOnJavaImage() (in module +TracX.@ImageProcessing)
getTrackAssignmentReconsiderationArray() (in module +TracX.@TrackerData)
getTrackIndexStorageIndicies() (+TracX.@LineageData.LineageData method)
(+TracX.@Tracker.Tracker method)
getTracks2Merge() (in module +TracX.@Lineage)
getTreeNodeDurations() (in module +TracX.@Lineage)
getUUIDOutsideROI() (in module +TracX.@TrackerData)
getWeightedScore() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
H
hasBudNeckSignal (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
I
imageBitDepth (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageCropCoordinateArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageCropCoordinatePriorReversionArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageDepth (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageDir (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageFileFormat (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageFileNameParser() (in module +TracX.@IO)
imageFingerprintFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageFrameNumberArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageHeight (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageMaxSampleValue (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageMinSampleValue (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imagePositionArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imagePrefixArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imageProcessing (+TracX.@ImageVisualization.ImageVisualization attribute)
(+TracX.@Tracker.Tracker attribute)
ImageProcessing (class in +TracX.@ImageProcessing)
ImageProcessing() (+TracX.@ImageProcessing.ImageProcessing method)
imageVisualization (+TracX.@Tracker.Tracker attribute)
ImageVisualization (class in +TracX.@ImageVisualization)
ImageVisualization() (+TracX.@ImageVisualization.ImageVisualization method)
imageWidth (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
imcrop3C() (in module +TracX.@Utils)
imcropC() (in module +TracX.@Utils)
importAlphaShapes() (+TracX.@Tracker.Tracker method)
(in module +TracX.@TrackerData)
importAlphaShapesForFrame() (in module +TracX.@TrackerData)
importData() (+TracX.@Tracker.Tracker method)
(+TracX.@TrackerData.TrackerData method)
importTrackerConfiguration() (+TracX.@TrackerConfiguration.TrackerConfiguration method)
improveInitialTracking() (+TracX.@Tracker.Tracker method)
increaseTrackAge() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
individualFunctionPenalty (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
initializeCellCloseNeighbours() (+TracX.@LineageData.LineageData method)
initializeNewFrame() (+TracX.@LineageData.LineageData method)
initializeOldFrame() (+TracX.@LineageData.LineageData method)
(+TracX.@TemporaryData.TemporaryData method)
initializeTrackerCore() (+TracX.@Tracker.Tracker method)
InitializeVeryOld() (+TracX.@LineageData.LineageData method)
initNewEntry() (+TracX.@SegmentationData.SegmentationData method)
insertMergedData() (in module +TracX.@TrackerData)
insertNewData() (in module +TracX.@TrackerData)
insertValueAtIdx() (in module +TracX.@Utils)
interpolateVectorComponents() (in module +TracX.@Motion)
io (+TracX.@Fingerprint.Fingerprint attribute)
(+TracX.@ImageProcessing.ImageProcessing attribute)
(+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
(+TracX.@TrackerConfiguration.TrackerConfiguration attribute)
(+TracX.@TrackerData.TrackerData attribute)
IO (class in +TracX.@IO)
IO() (+TracX.@IO.IO method)
isAllInstalled (+TracX.@Tracker.Tracker attribute)
isCorrectMotion (+TracX.@Tracker.Tracker attribute)
isFFPEval (+TracX.@Tracker.Tracker attribute)
isFullCosts (+TracX.@Tracker.Tracker attribute)
isManualCorr (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
isPointInsideEllipse() (in module +TracX.@Utils)
isReady (+TracX.@Tracker.Tracker attribute)
J
joinedTrackerData (+TracX.@TrackerData.TrackerData attribute)
joinedTrackerDataTable (+TracX.@TrackerData.TrackerData attribute)
joinTrackerDataAsTable() (in module +TracX.@TrackerData)
L
labelImageTrackMasks() (in module +TracX.@ImageProcessing)
lap (+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
LAP (class in +TracX.@LAP)
LAP() (+TracX.@LAP.LAP method)
lapjv() (in module +TracX.@LAP)
lineage (+TracX.@ImageProcessing.ImageProcessing attribute)
(+TracX.@ImageVisualization.ImageVisualization attribute)
(+TracX.@Tracker.Tracker attribute)
Lineage (class in +TracX.@Lineage)
Lineage() (+TracX.@Lineage.Lineage method)
lineageData (+TracX.@Lineage.Lineage attribute)
LineageData (class in +TracX.@LineageData)
lineageTable (+TracX.@Lineage.Lineage attribute)
lineProfile (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
loadTrackingProject() (+TracX.@Tracker.Tracker method)
M
major (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
mammalianLineageCost() (in module +TracX.@LAP)
mammalianLineageReconstruction() (+TracX.@Lineage.Lineage method)
mapCrop2RawCoordinates() (in module +TracX.@TrackerData)
markerChannelID (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
markerID (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
markerTrack (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
markerTrackEndFrame (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
markerTrackStartFrame (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
maskInterface3D() (in module +TracX.@IO)
maskOverlayAlpha (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
maskPrefix (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
maxCellCenterDisplacement (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
maxCellSizeDecrease (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
maxCellSizeIncrease (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
maxExpectedMovement (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
maxFrameEvalAfterBirth (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
maxMajorAxisRotation (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
maxTrackFrameSkipping (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
meanCellDiameter (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
meanCellDiameterScalingFactor (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
merge() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
mergeBudPriorDivision() (in module +TracX.@ImageProcessing)
minor (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
motherAssignmentProb (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
motherAssignmentScore (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
motherCell (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
motherCellCandidates (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
motherCellCandidatesStartFrame (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
motherSigInNucCandidates (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
motion (+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
Motion (class in +TracX.@Motion)
Motion() (+TracX.@Motion.Motion method)
moveToVeryOld() (+TracX.@Tracker.Tracker method)
(in module +TracX.@LineageData)
N
natSortNames() (in module +TracX.@Utils)
neighbourhoodSearchRadius (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
NewFrame (+TracX.@LineageData.LineageData attribute)
(+TracX.@TemporaryData.TemporaryData attribute)
(+TracX.@TrackerData.TrackerData attribute)
NewFrameEval (+TracX.@TrackerData.TrackerData attribute)
nFramesToImport (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
NonAssignedTracks (class in +TracX.@NonAssignedTracks)
NonAssignedTracks() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
normalizeImage() (in module +TracX.@ImageProcessing)
numberOfTracks (+TracX.@LineageData.LineageData attribute)
(+TracX.@TrackerData.TrackerData attribute)
O
obj_area (+TracX.@LineageData.LineageData attribute)
obj_center_x (+TracX.@LineageData.LineageData attribute)
obj_center_y (+TracX.@LineageData.LineageData attribute)
obj_center_z (+TracX.@LineageData.LineageData attribute)
obj_channel_id (+TracX.@LineageData.LineageData attribute)
obj_close_neighbour (+TracX.@LineageData.LineageData attribute)
obj_dif_x (+TracX.@LineageData.LineageData attribute)
obj_dif_y (+TracX.@LineageData.LineageData attribute)
obj_dif_z (+TracX.@LineageData.LineageData attribute)
obj_filtered_dif_x (+TracX.@LineageData.LineageData attribute)
obj_filtered_dif_y (+TracX.@LineageData.LineageData attribute)
obj_filtered_dif_z (+TracX.@LineageData.LineageData attribute)
obj_fluo_mean (+TracX.@LineageData.LineageData attribute)
obj_fluo_total (+TracX.@LineageData.LineageData attribute)
obj_fluoImgDenoised (+TracX.@LineageData.LineageData attribute)
obj_frame (+TracX.@LineageData.LineageData attribute)
obj_index (+TracX.@LineageData.LineageData attribute)
obj_major_axis (+TracX.@LineageData.LineageData attribute)
obj_minor_axis (+TracX.@LineageData.LineageData attribute)
obj_orientation (+TracX.@LineageData.LineageData attribute)
obj_parent_fluo_mean (+TracX.@LineageData.LineageData attribute)
obj_parent_fluo_total (+TracX.@LineageData.LineageData attribute)
obj_parent_seg_mask_id (+TracX.@LineageData.LineageData attribute)
obj_parent_track_index (+TracX.@LineageData.LineageData attribute)
obj_parent_uuid (+TracX.@LineageData.LineageData attribute)
obj_perimeter (+TracX.@LineageData.LineageData attribute)
obj_pixelIdxList (+TracX.@LineageData.LineageData attribute)
obj_track_age (+TracX.@LineageData.LineageData attribute)
obj_track_fingerprint_real (+TracX.@LineageData.LineageData attribute)
obj_track_index (+TracX.@LineageData.LineageData attribute)
OldFrame (+TracX.@LineageData.LineageData attribute)
(+TracX.@TemporaryData.TemporaryData attribute)
(+TracX.@TrackerData.TrackerData attribute)
OldFrameEval (+TracX.@TrackerData.TrackerData attribute)
orientationCompressor() (in module +TracX.@IO)
orientationDecompressor() (in module +TracX.@LAP)
overlayMaskOnImage() (in module +TracX.@ImageProcessing)
P
padImageCrop() (in module +TracX.@Utils)
ParameterConfiguration (+TracX.@TrackerConfiguration.TrackerConfiguration attribute)
(class in +TracX.@ParameterConfiguration)
patch (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
pixelsPerZPlaneInterval (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
plotAnnotatedControlImageFrame() (in module +TracX.@ImageVisualization)
plotDifferenceAlphaShapeVsReducedAlphaShape() (in module +TracX.@ImageVisualization)
plotFingerprintControlImageFrame() (in module +TracX.@ImageVisualization)
plotFingerprintEvalSummary() (in module +TracX.@ImageVisualization)
plotFPVsDeltaDistPlot() (in module +TracX.@ImageVisualization)
plotLineageTree() (in module +TracX.@ImageVisualization)
plotPoleAgeControlImageFrame() (in module +TracX.@ImageVisualization)
plotSummaryTracksAboveFPThreshold() (in module +TracX.@ImageVisualization)
plotTrackControlImageFrame() (in module +TracX.@ImageVisualization)
prepareDataFromSegmentationMask() (in module +TracX.@Tracker)
printTimeLeft() (in module +TracX.@Utils)
printToConsole() (in module +TracX.@Utils)
progressBar() (in module +TracX.@Utils)
progressUpdateParallel() (in module +TracX.@Utils)
ProjectConfiguration (+TracX.@TrackerConfiguration.TrackerConfiguration attribute)
(class in +TracX.@ProjectConfiguration)
ProjectConfiguration() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
projectName (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
Q
QuantificationData (+TracX.@TrackerData.TrackerData attribute)
(class in +TracX.@QuantificationData)
QuantificationData() (+TracX.@QuantificationData.QuantificationData method)
R
radiusVectorFilterX (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
radiusVectorFilterY (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
radiusVectorFilterZ (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
rawImageFileNameArray (+TracX.@IO.IO attribute)
readCellXParameters() (in module +TracX.@IO)
readFromXML() (in module +TracX.@IO)
readImageToGrayScale() (in module +TracX.@IO)
readImageToRGB() (in module +TracX.@IO)
readSegmentationData() (in module +TracX.@IO)
readSegmentationMask() (in module +TracX.@IO)
recalculateMotionCorrNeighbourhood() (+TracX.@TemporaryTrackingData.TemporaryTrackingData method)
reconstructionIsFinished (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute)
recursiveTrackParentColoring() (in module +TracX.@Lineage)
relabelMaskIndices() (in module +TracX.@ImageProcessing)
removeCell() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
replaceOrAddNew() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
reshapeDataToTrackerTableFormat() (in module +TracX.@TrackerData)
resolveCircAssignment() (in module +TracX.@Lineage)
revertSegmentationImageCrop() (in module +TracX.@Tracker)
rgb2java() (in module +TracX.@Utils)
runLineageReconstruction() (+TracX.@Lineage.Lineage method)
(in module +TracX.@Tracker)
runMarkerTracking() (in module +TracX.@Lineage)
runReQuantification() (in module +TracX.@Tracker)
runTracker() (+TracX.@Tracker.Tracker method)
S
saveCurrentTrackerState() (in module +TracX.@Tracker)
saveTrackerCellCycleResultsAsTable() (in module +TracX.@Tracker)
saveTrackerControlImageFrame() (in module +TracX.@Tracker)
saveTrackerControlMaskImageFrame() (in module +TracX.@Tracker)
saveTrackerMarkerControlImages() (in module +TracX.@Tracker)
saveTrackerMaskFrame() (in module +TracX.@Tracker)
saveTrackerProjectControlImages() (in module +TracX.@Tracker)
saveTrackerResultsAsTable() (in module +TracX.@Tracker)
saveTrackingAssignmentsToTrackerData() (+TracX.@LineageData.LineageData method)
saveTrackingProject() (+TracX.@Tracker.Tracker method)
segmentationControlFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
SegmentationData (+TracX.@TrackerData.TrackerData attribute)
(class in +TracX.@SegmentationData)
SegmentationData() (+TracX.@SegmentationData.SegmentationData method)
segmentationResultDir (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
segmentationResultFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
segmentationResultMaskFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
segmentationResultMatFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
setActive3DFingerprint() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setAverageCellSizeGrowth() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setBirthToDivPhase() (in module +TracX.@Lineage)
setCellDivisionType() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setCellPoleCoordinates() (in module +TracX.@TrackerData)
setCellThumbSideLength() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setControlPrefix() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setData3D() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDebugLevel() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerAverageObjSizeGrowth() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerConvexAreaLowerThresh() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerConvexAreaUpperThresh() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerDenoising() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerEdgeSensitivityThresh() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerFingerprintHalfWindowSideLength() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerFingerprintMaxConsideredFrequencies() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerFingerprintResizeFactor() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerIndividualFunctionPenalty() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerLineProfileLength() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerLineProfilePeakLowerBound() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerLineProfilePeakUpperBound() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMaxExpectedMovement() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMaxMajorAxisRotation() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMaxObjCenterDisplacement() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMaxObjSizeDecrease() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMaxObjSizeIncrease() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMaxTrackFrameSkipping() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMeanObjDiameter() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerMeanObjDiameterScalingFactor() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerNeighbourhoodSearchRadius() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerRadiusVectorFilterX() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerRadiusVectorFilterY() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerRadiusVectorFilterZ() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setDivisionMarkerUsedFunctionsForCostMatrix() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setFieldArray() (+TracX.@TrackerData.TrackerData method)
setFieldArrayForFrame() (+TracX.@LineageData.LineageData method)
(+TracX.@TrackerData.TrackerData method)
setFieldnameValueForTrack() (+TracX.@TrackerData.TrackerData method)
setFieldnameValueForTrackSubset() (+TracX.@TrackerData.TrackerData method)
setFieldnameValuesForTracksOnFrame() (+TracX.@TrackerData.TrackerData method)
setFingerprintDistThreshold() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setFingerprintHalfWindowSideLength() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setFingerprintImageNames() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setFingerprintMaxConsideredFrequencies() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setFingerprintResizeFactor() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setFluoFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setFluoImageIdentifier() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setFluoLineageFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setFontSize() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageBitDepth() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageCropCoordinateArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageCropCoordinatePriorReversionArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageDepth() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageDir() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageFileFormat() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageFingerprintFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageFrameNumberArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageHeight() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageIdentifiers() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageMaxSampleValue() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageMinSampleValue() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImagePositionArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImagePrefixArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageProperties() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setImageWidth() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setIndividualFunctionPenalty() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setLineageTable() (+TracX.@Lineage.Lineage method)
setMarker() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
setMarkerTracks() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
setMaskOverlayAlpha() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMaskPrefix() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setMatFileNames() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setMaxCellCenterDisplacement() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMaxCellSizeDecrease() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMaxCellSizeIncrease() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMaxExpectedMovement() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMaxMajorAxisRotation() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMaxTrackFrameSkipping() (+TracX.@NonAssignedTracks.NonAssignedTracks method)
(+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMeanCellDiameter() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMeanCellDiameterScalingFactor() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setMotherDaughterPair() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
setNeighbourhoodSearchRadius() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setNFramesToImport() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setObjParent() (+TracX.@LineageData.LineageData method)
setParentAndHasBud() (in module +TracX.@Lineage)
setParentMamDivCells() (in module +TracX.@Lineage)
setParentSymDivCells() (in module +TracX.@TrackerData)
setPixelsPerZPlaneInterval() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setProjectName() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setRadiusVectorFilterX() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setRadiusVectorFilterY() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setRadiusVectorFilterZ() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setSegmentationControlFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setSegmentationFiles() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setSegmentationResultDir() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setSegmentationResultFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setSegmentationResultMaskFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setSegmentationResultMatFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setSigInNuc() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
setSignalInNucleus() (in module +TracX.@Lineage)
setTrackAge() (in module +TracX.@Lineage)
setTrackerEndFrame() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setTrackerPrefix() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setTrackerResultMaskFileArray() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setTrackerResultsDirectory() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setTrackerStartFrame() (+TracX.@ProjectConfiguration.ProjectConfiguration method)
setTrackGeneration() (in module +TracX.@Lineage)
setupDependencies() (in module +TracX.@Tracker)
setUsedFunctionsForCostMatrix() (+TracX.@ParameterConfiguration.ParameterConfiguration method)
setUUID() (+TracX.@LineageData.LineageData method)
(+TracX.@QuantificationData.QuantificationData method)
(+TracX.@SegmentationData.SegmentationData method)
solveLAP() (in module +TracX.@LAP)
splitSurvivingParentTracks() (in module +TracX.@Lineage)
stackZPlanes() (in module +TracX.@IO)
symmetricalLineageReconstruction() (+TracX.@Lineage.Lineage method)
T
TemporaryData (class in +TracX.@TemporaryData)
TemporaryData() (+TracX.@TemporaryData.TemporaryData method)
TemporaryLineageAssignment (class in +TracX.@TemporaryLineageAssignment)
TemporaryLineageAssignment() (+TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method)
TemporaryTrackingData (class in +TracX.@TemporaryTrackingData)
TemporaryTrackingData() (+TracX.@TemporaryTrackingData.TemporaryTrackingData method)
testBudNeckSegmentation() (in module +TracX.@Tracker)
testFeatureDataRemoval() (in module +TracX.@Tracker)
testImageBorderDataRemoval() (in module +TracX.@Tracker)
testMarkerTrackingParameters() (in module +TracX.@Tracker)
testROIDataRemoval() (in module +TracX.@Tracker)
testSegmentationArtefactRemoval() (in module +TracX.@Tracker)
testTrackingParameters() (in module +TracX.@Tracker)
TmpLinAss (+TracX.@TrackerData.TrackerData attribute)
track_age (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_area_assignment_cost (+TracX.@SegmentationData.SegmentationData attribute)
track_assignment_fraction (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_budneck_total (+TracX.@SegmentationData.SegmentationData attribute)
track_cell_cycle_phase (+TracX.@SegmentationData.SegmentationData attribute)
track_contained_in_track (+TracX.@SegmentationData.SegmentationData attribute)
track_end_frame (+TracX.@SegmentationData.SegmentationData attribute)
track_fingerprint_age (+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_fingerprint_real (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_fingerprint_real_distance (+TracX.@LineageData.LineageData attribute)
(+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_frame_skipping_cost (+TracX.@SegmentationData.SegmentationData attribute)
track_generation (+TracX.@SegmentationData.SegmentationData attribute)
track_has_bud (+TracX.@SegmentationData.SegmentationData attribute)
track_index (+TracX.@NonAssignedTracks.NonAssignedTracks attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_index_corrected (+TracX.@SegmentationData.SegmentationData attribute)
track_index_qc (+TracX.@SegmentationData.SegmentationData attribute)
(+TracX.@TemporaryTrackingData.TemporaryTrackingData attribute)
track_lineage_tree (+TracX.@SegmentationData.SegmentationData attribute)
track_parent (+TracX.@SegmentationData.SegmentationData attribute)
track_parent_frame (+TracX.@SegmentationData.SegmentationData attribute)
track_parent_prob (+TracX.@SegmentationData.SegmentationData attribute)
track_parent_score (+TracX.@SegmentationData.SegmentationData attribute)
track_position_assignment_cost (+TracX.@SegmentationData.SegmentationData attribute)
track_rotation_assignment_cost (+TracX.@SegmentationData.SegmentationData attribute)
track_start_frame (+TracX.@SegmentationData.SegmentationData attribute)
track_total_assignment_cost (+TracX.@SegmentationData.SegmentationData attribute)
Tracker (class in +TracX.@Tracker)
Tracker() (+TracX.@Tracker.Tracker method)
TrackerConfiguration (class in +TracX.@TrackerConfiguration)
TrackerConfiguration() (+TracX.@TrackerConfiguration.TrackerConfiguration method)
TrackerData (class in +TracX.@TrackerData)
TrackerData() (+TracX.@TrackerData.TrackerData method)
trackerEndFrame (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
trackerPrefix (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
trackerResultMaskFileArray (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
trackerResultsDir (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
trackerStartFrame (+TracX.@ProjectConfiguration.ProjectConfiguration attribute)
tracks2Merge (+TracX.@Lineage.Lineage attribute)
U
unresolvedTempLinAss (+TracX.@Lineage.Lineage attribute)
updateTemporaryTrackingDataForNextFrameEvaluation() (+TracX.@LineageData.LineageData method)
usedFunctionsForCostMatrix (+TracX.@ParameterConfiguration.ParameterConfiguration attribute)
utils (+TracX.@Fingerprint.Fingerprint attribute)
(+TracX.@ImageProcessing.ImageProcessing attribute)
(+TracX.@IO.IO attribute)
(+TracX.@Lineage.Lineage attribute)
(+TracX.@Tracker.Tracker attribute)
(+TracX.@TrackerData.TrackerData attribute)
Utils (class in +TracX.@Utils)
Utils() (+TracX.@Utils.Utils method)
uuid (+TracX.@LineageData.LineageData attribute)
(+TracX.@QuantificationData.QuantificationData attribute)
(+TracX.@SegmentationData.SegmentationData attribute)
V
validateTmpLinAss() (in module +TracX.@Lineage)
version (+TracX.@Tracker.Tracker attribute)
VeryOld (+TracX.@LineageData.LineageData attribute)
(+TracX.@TemporaryData.TemporaryData attribute)
(+TracX.@TrackerData.TrackerData attribute)
VeryOldEval (+TracX.@TrackerData.TrackerData attribute)
visualise3DCells() (in module +TracX.@ImageVisualization)
W
writeBudNeckCellSegmentationMaskImage() (in module +TracX.@IO)
writeToCSV() (in module +TracX.@IO)
writeToMAT() (in module +TracX.@IO)
writeToPNG() (in module +TracX.@IO)
writeToTIF() (in module +TracX.@IO)
writeToTXT() (in module +TracX.@IO)
writeToXLS() (in module +TracX.@IO)
writeToXML() (in module +TracX.@IO)
writeTrackerDataToDisk() (in module +TracX.@IO)