Index

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) (TracX.@ImageProcessing.ImageProcessing method)

assignDaughterImmediate() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) assignMammalianTrackparent() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) 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_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) (TracX.@Utils.Utils method) clearMarkerTracking() (TracX.@LineageData.LineageData method) computeAssignmentCostMatrix() (in module TracX.@LAP) (TracX.@LAP.LAP method) computeAssignmentFingerprintDistanceArray() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeCLAHE() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) computeDeltaDistance() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFFPCostMatrix() (in module TracX.@LAP) (TracX.@LAP.LAP method) computeFingerprint() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFingerprint3D() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFingerprintAsgmtFrac() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFingerprintDistance() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFingerprintForFrame() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFingerprintForFrame3D() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeFPDistThreshold() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeNeighbourhoodMotionCostMatrix() (in module TracX.@LAP) (TracX.@LAP.LAP method) computeNeighbourProbFPBelowAss() (in module TracX.@Fingerprint) (TracX.@Fingerprint.Fingerprint method) computeNewFrameAssignment() (in module TracX.@LAP) (TracX.@LAP.LAP method) computeOrientationDifference() (in module TracX.@LAP) (TracX.@LAP.LAP method) computeOrientationDifferenceMatrix() (in module TracX.@LAP) (TracX.@LAP.LAP method) 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) (TracX.@IO.IO method) convertedImageFileNameArray (TracX.@IO.IO attribute) convertImageFileNames() (in module TracX.@IO) (TracX.@IO.IO method) convertXLSToCSV() (in module TracX.@IO) (TracX.@IO.IO method) copyResultsToTrackerData() (TracX.@LineageData.LineageData method) (TracX.@Tracker.Tracker method) correctMDMisassignment() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) correctTrackMisassignment() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) 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) (TracX.@TrackerData.TrackerData method) delByFeature() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) delByROI() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) deleteByFeature() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) deleteByROI() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) deleteData() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) deleteEntry() (TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method) deleteRow() (TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method) deleteSegArtefacts() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) deleteSegObjAtBorder() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) delSegArtefacts() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) destackTimepoints() (in module TracX.@IO) (TracX.@IO.IO method)

detectBudNeckMarkerPixelArray() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) 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) (TracX.@Utils.Utils method)

E

ensureResultsDirExists() (TracX.@ProjectConfiguration.ProjectConfiguration method) evaluateNewMammalianRoots() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) evaluateObjSigAroundTrustedFrames() (TracX.@LineageData.LineageData method) evaluateTrackAge() (TracX.@NonAssignedTracks.NonAssignedTracks method) evaluation (TracX.@Tracker.Tracker attribute)

exportCellCycleResults() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) exportFinalTrackingMasks() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) exportTrackerConfiguration() (TracX.@TrackerConfiguration.TrackerConfiguration method) exportTrackingResults() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method)

F

filenameSorterForCellXinput() (in module TracX.@IO) (TracX.@IO.IO method) fillTrackHoles() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) filterVectorField() (in module TracX.@Motion) (TracX.@Motion.Motion method) findParentCandidatesTolerant() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) Fingerprint (class in TracX.@Fingerprint) fingerprint (TracX.@Lineage.Lineage attribute) (TracX.@Tracker.Tracker attribute) 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) (TracX.@LAP.LAP method) 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_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) (TracX.@ImageProcessing.ImageProcessing method) generate4DImageStackMarker() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateAnnotatedControlImageFrame() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateFingerprintControlImageFrame() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateLineageFrame() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateLineageMovie() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateLineageTreeObject() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) generateMarkerControlImageFrame() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateMarkerTimeSeriesImage() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateMaskForMatrixCorners() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateMergedMask() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateMergedMaskForReSegmentation() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateMultiTrackControlMovie() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generatePoleAgeControlImageFrame() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateScriptFromTracker() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) generateSingleTrackControlMovie() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateTimeSeriesImageMatrix() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateTrackControlImageFramePadded() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) generateTrackerControlMaskImageFrame() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) getBkgCorrSig() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getBWLabelColor() (in module TracX.@Utils) (TracX.@Utils.Utils method) getCellCyclePhaseTable() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getCellStruct() (TracX.@NonAssignedTracks.NonAssignedTracks method) getCloseCellNeighbourIdx() (in module TracX.@LineageData) (in module TracX.@TrackerData) (TracX.@LineageData.LineageData method) (TracX.@TrackerData.TrackerData method) getColorMap() (in module TracX.@Utils) (TracX.@Utils.Utils method) getCommonLogical() (in module TracX.@Utils) (TracX.@Utils.Utils method) getCommonTrackDataSubset() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getConditionalFieldArray() (TracX.@LineageData.LineageData method) (TracX.@TrackerData.TrackerData method) getConsecutiveCloseCellNeighbourIdx() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getControlImageFormat() (TracX.@ProjectConfiguration.ProjectConfiguration method) getDivisionFrames() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method)

getFieldArray() (TracX.@TrackerData.TrackerData method) getFieldArray_withGhosts() (TracX.@TrackerData.TrackerData method) getFieldArrayColorMap() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getFieldArrayForFrame() (TracX.@LineageData.LineageData method) (TracX.@TrackerData.TrackerData method) getFieldArrayForSubsetOnFrame() (TracX.@TrackerData.TrackerData method) getFieldArrayForTrackIndex() (TracX.@TrackerData.TrackerData method) getFieldArrayForTrackIndexForFrame() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getFieldCMap() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) getFluoID() (TracX.@ProjectConfiguration.ProjectConfiguration method) getFluoImage() (TracX.@ProjectConfiguration.ProjectConfiguration method) getInvalidVectors() (in module TracX.@Motion) (TracX.@Motion.Motion method) getLeadingZeros() (in module TracX.@Utils) (TracX.@Utils.Utils method) getLineageSummary() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getLineProfileVerification() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getMaskBasedDPairs() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getMaxNumCompThreads() (in module TracX.@Utils) (TracX.@Utils.Utils method) getMotionCorrNeighbours() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getNewickFormat() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getNumberOfFluoImages() (TracX.@ProjectConfiguration.ProjectConfiguration method) getNumberOfRowsFromFrame() (TracX.@LineageData.LineageData method) (TracX.@TrackerData.TrackerData method) getPotSegArtefacts() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getRecursiveTrackParentColoring() (in module TracX.@Utils) (TracX.@Utils.Utils method) getRootTrackRelatedDaughterArray() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getRootTrackTreeObject() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getSegAreaBoundingBox() (in module TracX.@Utils) (TracX.@Utils.Utils method) getSortIdxForTrackIndices() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getStartEndFrameOfTrack() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getTemporaryDataStruct() (TracX.@TrackerData.TrackerData method) getTextOnJavaImage() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) getTrackAssignmentReconsiderationArray() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) getTrackIndexStorageIndicies() (TracX.@LineageData.LineageData method) (TracX.@Tracker.Tracker method) getTracks2Merge() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getTreeNodeDurations() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) getUUIDOutsideROI() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) 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) (TracX.@IO.IO method) 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 (class in TracX.@ImageProcessing) imageProcessing (TracX.@ImageVisualization.ImageVisualization attribute) (TracX.@Tracker.Tracker attribute) ImageProcessing() (TracX.@ImageProcessing.ImageProcessing method) ImageVisualization (class in TracX.@ImageVisualization) imageVisualization (TracX.@Tracker.Tracker attribute) ImageVisualization() (TracX.@ImageVisualization.ImageVisualization method) imageWidth (TracX.@ProjectConfiguration.ProjectConfiguration attribute) imcrop3C() (in module TracX.@Utils) (TracX.@Utils.Utils method) imcropC() (in module TracX.@Utils) (TracX.@Utils.Utils method) importAlphaShapes() (in module TracX.@TrackerData) (TracX.@Tracker.Tracker method) (TracX.@TrackerData.TrackerData method) importAlphaShapesForFrame() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) 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) (TracX.@TrackerData.TrackerData method) insertNewData() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) insertValueAtIdx() (in module TracX.@Utils) (TracX.@Utils.Utils method) interpolateVectorComponents() (in module TracX.@Motion) (TracX.@Motion.Motion method) IO (class in TracX.@IO) 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() (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) (TracX.@Utils.Utils method) isReady (TracX.@Tracker.Tracker attribute)

J

joinedTrackerData (TracX.@TrackerData.TrackerData attribute) joinedTrackerDataTable (TracX.@TrackerData.TrackerData attribute)

joinTrackerDataAsTable() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method)

L

labelImageTrackMasks() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) LAP (class in TracX.@LAP) lap (TracX.@Lineage.Lineage attribute) (TracX.@Tracker.Tracker attribute) LAP() (TracX.@LAP.LAP method) lapjv() (in module TracX.@LAP) (TracX.@LAP.LAP method) Lineage (class in TracX.@Lineage)

lineage (TracX.@ImageProcessing.ImageProcessing attribute) (TracX.@ImageVisualization.ImageVisualization attribute) (TracX.@Tracker.Tracker attribute) Lineage() (TracX.@Lineage.Lineage method) LineageData (class in TracX.@LineageData) lineageData (TracX.@Lineage.Lineage attribute) 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) (TracX.@LAP.LAP method) mammalianLineageReconstruction() (TracX.@Lineage.Lineage method) mapCrop2RawCoordinates() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) 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) (TracX.@IO.IO method) 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) (TracX.@ImageProcessing.ImageProcessing method) 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 (class in TracX.@Motion) motion (TracX.@Lineage.Lineage attribute) (TracX.@Tracker.Tracker attribute) Motion() (TracX.@Motion.Motion method) moveToVeryOld() (in module TracX.@LineageData) (TracX.@LineageData.LineageData method) (TracX.@Tracker.Tracker method)

N

natSortNames() (in module TracX.@Utils) (TracX.@Utils.Utils method) 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) (TracX.@ImageProcessing.ImageProcessing method) 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.@TrackerData.TrackerData attribute) OldFrameEval (TracX.@TrackerData.TrackerData attribute) orientationCompressor() (in module TracX.@IO) (TracX.@IO.IO method) orientationDecompressor() (in module TracX.@LAP) (TracX.@LAP.LAP method) overlayMaskOnImage() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method)

P

padImageCrop() (in module TracX.@Utils) (TracX.@Utils.Utils method) ParameterConfiguration (class in TracX.@ParameterConfiguration) (TracX.@TrackerConfiguration.TrackerConfiguration attribute) patch (TracX.@ParameterConfiguration.ParameterConfiguration attribute) pixelsPerZPlaneInterval (TracX.@ParameterConfiguration.ParameterConfiguration attribute) plotAnnotatedControlImageFrame() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotDifferenceAlphaShapeVsReducedAlphaShape() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotFingerprintControlImageFrame() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotFingerprintEvalSummary() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotFPVsDeltaDistPlot() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotLineageTree() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotPoleAgeControlImageFrame() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) plotSummaryTracksAboveFPThreshold() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method)

plotTrackControlImageFrame() (in module TracX.@ImageVisualization) (TracX.@ImageVisualization.ImageVisualization method) prepareDataFromSegmentationMask() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) printTimeLeft() (in module TracX.@Utils) (TracX.@Utils.Utils method) printToConsole() (in module TracX.@Utils) (TracX.@Utils.Utils method) progressBar() (in module TracX.@Utils) (TracX.@Utils.Utils method) progressUpdateParallel() (in module TracX.@Utils) (TracX.@Utils.Utils method) ProjectConfiguration (class in TracX.@ProjectConfiguration) (TracX.@TrackerConfiguration.TrackerConfiguration attribute) ProjectConfiguration() (TracX.@ProjectConfiguration.ProjectConfiguration method) projectName (TracX.@ProjectConfiguration.ProjectConfiguration attribute) propagatePendingDaughters() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) propagatePendingDaughtersFinalFrame() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method)

Q

QuantificationData (class in TracX.@QuantificationData) (TracX.@TrackerData.TrackerData attribute)

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) (TracX.@IO.IO method) readFromXML() (in module TracX.@IO) (TracX.@IO.IO method) readImageToGrayScale() (in module TracX.@IO) (TracX.@IO.IO method) readImageToRGB() (in module TracX.@IO) (TracX.@IO.IO method) readSegmentationData() (in module TracX.@IO) (TracX.@IO.IO method) readSegmentationMask() (in module TracX.@IO) (TracX.@IO.IO method) recalculateMotionCorrNeighbourhood() (TracX.@TemporaryTrackingData.TemporaryTrackingData method) reconstructionIsFinished (TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment attribute) recursiveTrackParentColoring() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) registerGhostParent() (TracX.@TrackerData.TrackerData method)

relabelMaskIndices() (in module TracX.@ImageProcessing) (TracX.@ImageProcessing.ImageProcessing method) removeCell() (TracX.@NonAssignedTracks.NonAssignedTracks method) replaceOrAddNew() (TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment method) reshapeDataToTrackerTableFormat() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) resolveCircAssignment() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) revertSegmentationImageCrop() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) rgb2java() (in module TracX.@Utils) (TracX.@Utils.Utils method) run() (TracX.@TrackerCommandLineParser.TrackerCommandLineParser method) runLineageReconstruction() (in module TracX.@Tracker) (TracX.@Lineage.Lineage method) (TracX.@Tracker.Tracker method) runMarkerTracking() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) runReQuantification() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) runTracker() (TracX.@Tracker.Tracker method)

S

saveCurrentTrackerState() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerCellCycleResultsAsTable() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerControlImageFrame() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerControlMaskImageFrame() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerMarkerControlImages() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerMaskFrame() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerProjectControlImages() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackerResultsAsTable() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) saveTrackingAssignmentsToTrackerData() (TracX.@LineageData.LineageData method) saveTrackingProject() (TracX.@Tracker.Tracker method) segmentationControlFileArray (TracX.@ProjectConfiguration.ProjectConfiguration attribute) SegmentationData (class in TracX.@SegmentationData) (TracX.@TrackerData.TrackerData attribute) 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) (TracX.@Lineage.Lineage method) setCellDivisionType() (TracX.@ProjectConfiguration.ProjectConfiguration method) setCellPoleCoordinates() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) 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) (TracX.@Lineage.Lineage method) setParentMamDivCells() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) setParentSymDivCells() (in module TracX.@TrackerData) (TracX.@TrackerData.TrackerData method) 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) (TracX.@Lineage.Lineage method) setTrackAge() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) 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) (TracX.@Lineage.Lineage method) setupDependencies() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) setUsedFunctionsForCostMatrix() (TracX.@ParameterConfiguration.ParameterConfiguration method) setUUID() (TracX.@LineageData.LineageData method) (TracX.@QuantificationData.QuantificationData method) (TracX.@SegmentationData.SegmentationData method) solveLAP() (in module TracX.@LAP) (TracX.@LAP.LAP method) splitSurvivingParentTracks() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) stackZPlanes() (in module TracX.@IO) (TracX.@IO.IO method) 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) (TracX.@Tracker.Tracker method) testFeatureDataRemoval() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) testImageBorderDataRemoval() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) testMarkerTrackingParameters() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) testROIDataRemoval() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) testSegmentationArtefactRemoval() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) testTrackingParameters() (in module TracX.@Tracker) (TracX.@Tracker.Tracker method) 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) 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) TrackerCommandLineParser (class in TracX.@TrackerCommandLineParser) 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) 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.@TrackerCommandLineParser (module) TracX.@TrackerConfiguration (module) TracX.@TrackerData (module) TracX.@Utils (module)

U

unresolvedTempLinAss (TracX.@Lineage.Lineage attribute) updateTemporaryTrackingDataForNextFrameEvaluation() (TracX.@LineageData.LineageData method) usedFunctionsForCostMatrix (TracX.@ParameterConfiguration.ParameterConfiguration attribute) Utils (class in TracX.@Utils) 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() (TracX.@Utils.Utils method) uuid (TracX.@LineageData.LineageData attribute) (TracX.@QuantificationData.QuantificationData attribute) (TracX.@SegmentationData.SegmentationData attribute)

V

validateTmpLinAss() (in module TracX.@Lineage) (TracX.@Lineage.Lineage method) 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) (TracX.@ImageVisualization.ImageVisualization method)

W

writeBudNeckCellSegmentationMaskImage() (in module TracX.@IO) (TracX.@IO.IO method) writeToCSV() (in module TracX.@IO) (TracX.@IO.IO method) writeToMAT() (in module TracX.@IO) (TracX.@IO.IO method) writeToPNG() (in module TracX.@IO) (TracX.@IO.IO method) writeToTIF() (in module TracX.@IO) (TracX.@IO.IO method)

writeToTXT() (in module TracX.@IO) (TracX.@IO.IO method) writeToXLS() (in module TracX.@IO) (TracX.@IO.IO method) writeToXML() (in module TracX.@IO) (TracX.@IO.IO method) writeTrackerDataToDisk() (in module TracX.@IO) (TracX.@IO.IO method)