Core Classes ¶

TrackerCommandLineParser ¶

class TracX.@TrackerCommandLineParser.TrackerCommandLineParser¶

Bases: handle

TrackerCommandLineParser Command-line interface for TracX batch processing.

Lives under the TracX package folder so it is called as:: parser = TracX.TrackerCommandLineParser(args);
Logging is delegated to the Tracker’s own utility:: Tracker.utils.printToConsole(msg)

which produces timestamped output identical to the interactive session. Before the Tracker instance exists the parser formats its own timestamps.

USAGE (compiled executable)

TracXRunner <projectConfig.xml> [options] TracXRunner <trackerState.mat> [options] TracXRunner –create-project [–create-* options] TracXRunner <source> –call <method.path> [–call-arg <v>]… [–call-out <file>]

USAGE (MATLAB source)

parser = TracX.TrackerCommandLineParser({‘project.xml’,’–verbose’}); parser.run();

REQUIRED (normal run)

<projectConfig.xml> OR <trackerState.mat>: Either an existing TracX project XML (created by GUI or CLI), or a .mat state file saved by Tracker.saveCurrentTrackerState(). The .mat file contains a fully configured Tracker instance which may already have tracking results — useful for post-processing, debugging, or continuing interrupted work without re-running.

GLOBAL OPTIONS

--workflow: <file|keyword> Workflow XML or .m script (see keywords below)
--state: <file.mat> Load Tracker from a .mat state file (alternative to passing it as first argument)
--output: <dir> Override tracker results directory
--image-dir <dir>: Override image directory in project XML
--seg-dir: <dir> Override segmentation results directory
--log: <file> Append all console output to a log file
--dryrun: Validate inputs only; do not run
--verbose: Extra diagnostic output

–help | -h Print this help and exit

INLINE CALL MODE (–call)

Calls any single method reachable from the Tracker instance without needing a workflow file. Useful for interactive debugging, one-off queries, and wrapper scripts.

--call

<method.path> Dotted method path relative to Tracker, e.g. imageProcessing.overlayMaskOnImage

io.readFromXML configuration.ParameterConfiguration.setMaxCellCenterDisplacement runTracker

--call-arg

<value> Typed argument passed to the method. Repeat for each argument. Type inference:

true / false -> logical 3.14 / [1 2 3] -> double (eval’d) anything else -> char string

Quote strings to protect them:: –call-arg “‘BFdivide’”

--call-out

<file> Write any return value as CSV to this file (stdout is always used regardless).

EXAMPLES

TracXRunner state.mat –call imageProcessing.overlayMaskOnImage: –call-arg image.tif –call-arg mask.tif
TracXRunner state.mat –call data.getFieldArray: –call-arg “‘track_index’” –call-arg 1 –call-out tracks.csv
TracXRunner state.mat –call configuration.ParameterConfiguration.setMaxCellCenterDisplacement: –call-arg 25

CALLMETHOD WORKFLOW STEP

The same capability is available as a workflow step named CallMethod, enabling arbitrary method calls within an XML workflow sequence. Params:

Method (required) dotted method path Args pipe-delimited typed arg list: “25|false|some/path” Delimiter CSV delimiter for output (default ,) OutFile optional output CSV file

BUILT-IN WORKFLOW KEYWORDS

default LoadProject -> OverridePaths -> ClearData -> ImportData: -> RunTracker -> SaveState -> SaveProject -> SaveTable -> SaveControlImages

yeast default + RevertCrop + RunLineage + SaveCellCycleTable tuning Test steps only; saves project XML at end generic-masks PrepareGenericMasks -> LoadCustomProject -> default pipeline

PROJECT CREATION FLAG

--create-project: Enter the interactive project-creation wizard (create_project.m). All –create-* options below are forwarded to it; they may also be supplied without –create-project to run non-interactively.

PROJECT CREATION OPTIONS

--create-name: <str> Project name
--create-image-dir: <dir> Path to raw images
--create-seg-dir: <dir> Path to segmentation results
--create-fp-channel: <str> Fingerprint channel identifier (e.g. BFdivide)
--create-lineage-ch: <str> Lineage marker channel (e.g. mKate)
--create-well-id: <str> Well-position identifier (empty = none)
--create-crop: <x,y,h,w> CellX crop coordinates (empty = none)
--create-movie-length: <int> Number of frames to track
--create-division-type <str>: asym | sym
--create-from-generic-segmentation: <bool> true/false. creates

minimal project file for tracking from generic segmentation masks. –create-run-tuning Also run tuning workflow after creation

WORKFLOW STEP NAMES

Project / data lifecycle

LoadProject Tracker.loadTrackingProject(dir, file) LoadCustomProject Creates a full TracX project file from a

minimal generic masks project.

OverridePaths Apply –image-dir / –seg-dir / –output ClearData Tracker.data.clearAllData() ImportData Tracker.importData() RevertCrop Tracker.revertSegmentationImageCrop()

Image / filename utilities

ParseFileNames Tracker.io.imageFileNameParser(…) ConvertFileNames Tracker.io.convertImageFileNames(…) DestackTif Tracker.io.destackTimepoints(…)

Segmentation preparation

PrepareGenericMasks Tracker.prepareDataFromSegmentationMask(…)

Segmentation filtering / constraint

RemoveArtefacts Tracker.deleteSegArtefacts(‘channel’,ch,’stdFactor’,f) RemoveByFeature Tracker.deleteByFeature(feature, threshold) RemoveAtBorder Tracker.deleteSegObjAtBorder(borderOffset) RemoveByROI Tracker.deleteByROI(roi)

Test / diagnostic steps (write control images; do not alter state)

TestParameters Tracker.testTrackingParameters([start,end]) TestBudNeck Tracker.testBudNeckSegmentation(frame,…) TestMarkerTracking Tracker.testMarkerTrackingParameters([start,end]) TestArtefactRemoval Tracker.testSegmentationArtefactRemoval(frame,ch,std) TestFeatureRemoval Tracker.testFeatureDataRemoval(frame,feature,thresh) TestBorderRemoval Tracker.testImageBorderDataRemoval(frame,offset) TestROIRemoval Tracker.testROIDataRemoval(frame)

Tracking

RunTracker Tracker.runTracker() RunLineage Tracker.runLineageReconstruction(…)

Manual corrections

CorrectLineage Tracker.correctMDMisassignment(daughters, mothers) CorrectTracks Tracker.correctTrackMisassignment(frames, old, new)

Save / export

SaveState Tracker.saveCurrentTrackerState(…) SaveProject Tracker.saveTrackingProject(filePath, fileName) SaveTable Tracker.saveTrackerResultsAsTable(…) SaveCellCycleTable Tracker.saveTrackerCellCycleResultsAsTable(…) SaveControlImages Tracker.saveTrackerProjectControlImages(…)

Visualisation

PlotAnnotated Tracker.imageVisualization.plotAnnotatedControlImageFrame(…) PlotFingerprint Tracker.imageVisualization.plotFingerprintControlImageFrame(…) PlotTracking Tracker.imageVisualization.plotTrackControlImageFrame(…) PlotPoleAge Tracker.imageVisualization.plotPoleAgeControlImageFrame(…) PlotLineageTree Tracker.imageVisualization.plotLineageTree(…) GenerateMovie Tracker.imageProcessing.generateLineageMovie(…) GenerateMarkerSeries Tracker.imageProcessing.generateMarkerTimeSeriesImage(…)

Data retrieval (CSV to stdout + optional file; no timestamp in output)

ExportFieldArray Tracker.data.getFieldArray(property, channelId) ExportFieldFrame Tracker.data.getFieldArrayForFrame(property,frame,ch) ExportFieldTrack Tracker.data.getFieldArrayForTrackIndex(property,track,ch)

Arbitrary method call (any TracX API, including sub-objects)

CallMethod any Tracker method via dotted path + typed args

See also: TracX.TrackerWorkflow, tracx_main, create_project% :Authors:

Andreas P. Cuny - initial implementation

Method Summary

run()¶

Main entry point: parse -> validate -> execute.

Three top-level modes, selected by the first positional argument or by flags:

Normal workflow TracXRunner project.xml [–workflow …] State-file mode TracXRunner state.mat [–workflow …] Inline call mode TracXRunner project.xml –call method [args…]

TracXRunner state.mat –call method [args…]

Project creation TracXRunner –create-project [–create-* …]

Fingerprint ¶

TracX.@Fingerprint.computeFingerprintAsgmtFrac(this, crfO, crfN, dCRFAsgmt, nhbrhdM)¶

COMPUTEFINGERPRINTASGMTFRAC Computes the faction for each assigned cell that a neighbouring cells has lower fingerprint distance (dCRF) as the difference of dCRF(assignment) - dCRF(neighbour). So there is a more similar cell according to the fingerprint (CRF) measure.

Parameters:

this (object) – Fingerprint instance
crfO (array) – Fingerprint (CRF) array for oldFrame.
crfN (array) – Fingerprint (CRF) array fpr newFrame.
dCRFAsgmt (array) – Fingerprint distance (dCRF) of all assignments between old and newFrame
nhbrhdM (array) – Neighbourhood indices locial matrix

Returns:

FFPa (array) – Fraction of neighbouring cells with lower dCRF for each assigned cell
FFP (array) – Fraction of neighbouring cells with lower dCRF (size of # neighbour)
NNFPa (array) – Sum of dCRFDiff > 0 for each assigned cell
NNFP (array) – Sum of dCRFDiff > 0 (size of # neighbour)
nNhbra (array) – Total number of neighbouring cells for each assigned cell
nNhbr (array) – Total number of neighbouring cells (size of # neighbour)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Fingerprint.computeFingerprint3D(~, img, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies)¶

COMPUTEFINGERPRINT3D Computes a unique cell quality control featured based on an image using the DCT transform. Here the fingerprint is computed for the image using DCT and binarization of the frequencies containing the structural information of the cell resulting in a unique string.

Parameters:

ignoredArg (object) – Fingerprint instance
img (uint8 NxNx3 uint8, 16, 32, 64) – Image matrix
fingerprintResizeFactor (int) – +TracX.ParameterConfiguration.fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – +TracX.ParameterConfiguration.fingerprintMaxConsideredFrequencies

Returns:

retFq – [1x64] Real frequency fingerprint array.

Return type:

float 1xM

Authors:

Tomas Kuendig - initial implementation

TracX.@Fingerprint.computeFingerprintForFrame3D(this, fromFrame, toFrame, fingerprintHalfWindowSideLength, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies, imageDir, imageFingerprintFileArray, imageCropCoordinateArray, cellFrameArray, cellCenterXArray, cellCenterYArray, cellCenterZArray, pixelPerZplane, active3DFingerprint)¶

COMPUTEFINGERPRINTFORFRAME3D Computes a unique cell quality control feature based on an out-of-focus Brightfield 3D image using the DCT transform. Here the fingerprints are computed for each frame using DCT and the frequencies containing the structural information of the cell resulting in a unique string. It is possible to only calculate the fingerprint for a number of specified image frames.

Parameters:

this (object) – Fingerprint instance
fromFrame (int) – Starting frame for calculation
toFrame (int) – End frame for calculation
fingerprintHalfWindowSideLength (int) – +TracX.ParameterConfiguration.fingerprintHalfWindowSideLength
fingerprintResizeFactor (int) – +TracX.ParameterConfiguration.fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – +TracX.ParameterConfiguration.fingerprintMaxConsideredFrequencies
imageDir (str) – +TracX.ProjectConfiguration.imageDir
imageFingerprintFileArray (cell array 1xK) – +TracX.ProjectConfiguration.imageFingerprintFileArray
imageCropCoordinateArray (double 1x4) – +TracX.ProjectConfiguration.imageCropCoordinateArray
cellFrameArray (int) – Array with all image frame numbers.
cellCenterXArray (int) – Array with centroid x coordinates of segmented objects.
cellCenterYArray (int) – Array with centroid y coordinates of segmented objects.
cellCenterZArray (int) – Array with centroid z coordinates of segmented objects.
pixelPerZplane (int) – Number of pixel per Zplane
active3DFingerprint (bool) – Switch for active 3D fingerprint.

Returns:

retFq – fingerprints for each segmented object.

Return type:

double Array with the real

Authors:

Tomas Kuendig - initial implementation

TracX.@Fingerprint.computeDeltaDistance(this, data, startFrame, endFrame)¶

COMPUTEDELTADISTANCE Computes the delta distance for non or tracked data. The delta distance is defined as the difference in fingerprint distance among two image frames of the lowest to the second lowest value. In case the data was tracked. it is the difference between the fingerprint distance of the assignment and the lowest one from either all other cells, the neighbourhood of the assigned one or the lowest one thereof.

Parameters:

this (object) – Fingerprint instance
data (object) – TrackerData instance
startFrame (int) – trackerStartFrame
endFrame (int) – trackerEndFrame

Returns:

deltaDistance (double) – Array of the delta distance for each assignment on all frames concatenated.
deltaDistanceNeighbours (double) – Array of the delta distance of the neighbourhood of each assignment on all frames concatenated.
fingerprintDistance (double) – Array of the fingerprint distance for each assignment on all frames concatenated.
fingerprintDistanceNeighboursSize (double) – Array of the fingerprint distance of theneighbourhood of each assignment on all frames concatenated.
deltaDistanceLowestNeighbour (double) – Array of the lowest delta distance of the neighbourhood of each assignment on all frames concatenated.
deltaDistance2ndLowest (double) – Array of the second lowest delta distance for each assignment on all frames concatenated.
deltaDistance2ndLowestNeighbour (double) – Array of the second lowest delta distance of the neighbourhood for each assignment on all frames concatenated.
assignedFPdistAllFrames (cell) – Cell array of the fingerprint distance for each assignment on all frames.
neighbourDeltaDistTotalMovie (cell) – Cell array of the delta distances of the neighbourhood for each assignment on all frames.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Fingerprint.computeFPDistThreshold(~, xFPDistAssigned, xFPDistAssignedToCompare, yDeltaDistAssigned, yDeltaDistToCompare, lowerQuantile)¶

COMPUTEFPDISTTHRESHOLD Computes the fingerprint distance threshold based on the lower quantile of negative delta distances.

Parameters:

ignoredArg (object) – Fingerprint instance
xFPDistAssigned (array 1xN) – Fingerprint distance of all assignments
xFPDistAssignedToCompare (array 1xM) – Fingerprint distances of neighbouring cells for each assigned cell.
yDeltaDistAssigned (array 1xN) – Delta distance of all assignments to the minimal FPdist of all possible assignments for each cell.
yDeltaDistToCompare (array 1xM) – Delta distance of all assignments to their comparator (i.e. its direct neighbours or all other cells)
lowerQuantile (float 1x1) – Lower quantile in the range [0,1];

Returns:

fpDistThreshold (float 1x1:) – Fingerprint distance threshold.
fpDistThresholdMadCorr (float 1x1:) – Fingerprint distance threshold outlier corrected.
fpDistanceSubset (float 1x1:) – Data used for fingerprint threshold determination.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Fingerprint.computeFingerprintDistance(~, realTrackFingerprintOldFrame, realTrackFingerprintNewFrame)¶

COMPUTEFINGERPRINTDISTANCE Computes the fingerprint distance between two typically subsequent image frames (oldFrame and newFrame) based on real fingerprints. For real fingerprints the least square distance is computed. The DC component (0,0) of the real fingerprints are removed.

Parameters:

ignoredArg (object) – Fingerprint instance
realTrackFingerprintOldFrame (cell array) – Real fingerprint array for all cells in the oldFrame
realTrackFingerprintNewFrame (cell array) – Real fingerprint array for all cells in the subsequent image frame (newFrame).

Returns:

realTrackFingerprintDistance – Fingerprint distances between all cells from the oldFrame and all its assigned cells in the newFrame based on the real fingerprints.

Return type:

double

Authors:

Andreas P. Cuny - initial implementation

Authors:

Joerg Stelling - speed optimization

TracX.@Fingerprint.computeAssignmentFingerprintDistanceArray(this, oldFrame, newFrame)¶

COMPUTEASSIGNMENTFINGERPRINTDISTANCEARRAY Computes the fingerprint distance for real fingerprints for all assigned cells between oldFrame and newFrame.

Parameters:

this (object) – Fingerprint instance
oldFrame (object) – oldFrame
newFrame (object) – mewFrame

Returns:

realFingerprintTrackDistance – Array with fingerprint distances from real fingerprints.

Return type:

double

Authors:

Andreas P. Cuny - initial implementation

TracX.@Fingerprint.computeFingerprintForFrame(this, fromFrame, toFrame, fingerprintHalfWindowSideLength, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies, imageDir, imageFingerprintFileArray, imageCropCoordinateArray, cellFrameArray, cellCenterXArray, cellCenterYArray)¶

COMPUTEFINGERPRINTFORFRAME Computes a unique cell quality control feature based on an out-of-focus Brightfield image using the DCT transform. Here the fingerprints are computed for each frame using DCT and the frequencies containing the structural information of the cell resulting in a unique string. It is possible to only calculate the fingerprint for a number of specified image frames.

Parameters:

this (object) – Fingerprint instance
fromFrame (int) – Starting frame for calculation
toFrame (int) – End frame for calculation
fingerprintHalfWindowSideLength (int) – +TracX.ParameterConfiguration.fingerprintHalfWindowSideLength
fingerprintResizeFactor (int) – +TracX.ParameterConfiguration.fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – +TracX.ParameterConfiguration.fingerprintMaxConsideredFrequencies
imageDir (str) – +TracX.ProjectConfiguration.imageDir
imageFingerprintFileArray (cell array 1xK) – +TracX.ProjectConfiguration.imageFingerprintFileArray
imageCropCoordinateArray (double 1x4) – +TracX.ProjectConfiguration.imageCropCoordinateArray
cellFrameArray (int) – Array with all image frame numbers.
cellCenterXArray (int) – Array with centroid x coordinates of segmented objects.
cellCenterYArray (int) – Array with centroid x coordinates of segmented objects.

Returns:

retFq – fingerprints for each segmented object.

Return type:

double Array with the real

Authors:

Andreas P. Cuny - initial implementation

TracX.@Fingerprint.computeNeighbourProbFPBelowAss(~, assignedFPdistTotalMovie, neighbourDeltaDistTotalMovie, FPByFraction, startIdx, nData)¶

COMPUTENEIGHBOURPROBFPBELOWASS Computes the cumultative probability for each assigned cell that a neighbouring cells has lower fingerprint distance (negative delta distance) and would a more similar cell according to the fingerprint measure alone.

Parameters:

ignoredArg (object) – Fingerprint instance
assignedFPdistTotalMovie (cell array) – Array of fingerprint distances of the assigned cells for each tracked frame.
neighbourDeltaDistTotalMovie (cell array) – Array of delta distances from the neighbours of the assigned cells for each tracked frame.
FPByFraction (bool) – True (default): calculate faction of neighbours with lower FP distance. False: calculate if any neighbour has lower FP distance
startIdx (int) – Start index for the first frame tracking started.
nData (int) – Total length of the data columns.

Returns:

pLowerFPArray – Cumultative probability for each assignment that a neighbour has a lower fingerprint distance.

Return type:

float:

Authors:

Joerg Stelling - initial implementation of the idea

Authors:

Andreas P. Cuny - implementation for TracX evaluation

TracX.@Fingerprint.computeFingerprint(~, img, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies)¶

COMPUTEFINGERPRINT Computes a unique cell quality control featured based on an image using the DCT transform. Here the fingerprint is computed for the image using DCT and the frequencies containing the structural information of the cell resulting in a unique string.

Parameters:

img (uint8 NxNx1 uint8, 16, 32, 64) – Image matrix
fingerprintResizeFactor (int) – fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – fingerprintMaxConsideredFrequencies

Returns:

retFq – [1x64] Real frequency fingerprint array.

Return type:

float 1xM

Authors:

Andreas P. Cuny - initial implementation

class TracX.@Fingerprint.Fingerprint¶

Fingerprint class constructs a Fingerprint object to compute the cell region fingerprint. Additionally it implements all the methods to compute the fingerprint and delta distance.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

Fingerprint(utils, io)¶

Fingerprint constructs an empty object of type Fingerprint. This class implements the fingerprint and related functionalities.

Parameters:

utils (object) – Utils instance.
io (object) – IO instance.
configuration (object) – ImageProcessing instance.

Returns:

obj – Returns a Fingerprint instance

Return type:

object

Authors:

Andreas P. Cuny - initial implementation

Property Summary

debugLevel¶: Debug level

io¶: TracX.@IO instance implementing read/write methods

utils¶: TracX.@Utils instance implementing utility methods

Method Summary

computeAssignmentFingerprintDistanceArray(this, oldFrame, newFrame)¶

COMPUTEASSIGNMENTFINGERPRINTDISTANCEARRAY Computes the fingerprint distance for real fingerprints for all assigned cells between oldFrame and newFrame.

Parameters:

this (object) – Fingerprint instance
oldFrame (object) – oldFrame
newFrame (object) – mewFrame

Returns:

realFingerprintTrackDistance – Array with fingerprint distances from real fingerprints.

Return type:

double

Authors:

Andreas P. Cuny - initial implementation

computeDeltaDistance(this, data, startFrame, endFrame)¶

Parameters:

this (object) – Fingerprint instance
data (object) – TrackerData instance
startFrame (int) – trackerStartFrame
endFrame (int) – trackerEndFrame

Returns:

deltaDistance (double) – Array of the delta distance for each assignment on all frames concatenated.
deltaDistanceNeighbours (double) – Array of the delta distance of the neighbourhood of each assignment on all frames concatenated.
fingerprintDistance (double) – Array of the fingerprint distance for each assignment on all frames concatenated.
fingerprintDistanceNeighboursSize (double) – Array of the fingerprint distance of theneighbourhood of each assignment on all frames concatenated.
deltaDistanceLowestNeighbour (double) – Array of the lowest delta distance of the neighbourhood of each assignment on all frames concatenated.
deltaDistance2ndLowest (double) – Array of the second lowest delta distance for each assignment on all frames concatenated.
deltaDistance2ndLowestNeighbour (double) – Array of the second lowest delta distance of the neighbourhood for each assignment on all frames concatenated.
assignedFPdistAllFrames (cell) – Cell array of the fingerprint distance for each assignment on all frames.
neighbourDeltaDistTotalMovie (cell) – Cell array of the delta distances of the neighbourhood for each assignment on all frames.

Authors:

Andreas P. Cuny - initial implementation

computeFPDistThreshold(~, xFPDistAssigned, xFPDistAssignedToCompare, yDeltaDistAssigned, yDeltaDistToCompare, lowerQuantile)¶

COMPUTEFPDISTTHRESHOLD Computes the fingerprint distance threshold based on the lower quantile of negative delta distances.

Parameters:

ignoredArg (object) – Fingerprint instance
xFPDistAssigned (array 1xN) – Fingerprint distance of all assignments
xFPDistAssignedToCompare (array 1xM) – Fingerprint distances of neighbouring cells for each assigned cell.
yDeltaDistAssigned (array 1xN) – Delta distance of all assignments to the minimal FPdist of all possible assignments for each cell.
yDeltaDistToCompare (array 1xM) – Delta distance of all assignments to their comparator (i.e. its direct neighbours or all other cells)
lowerQuantile (float 1x1) – Lower quantile in the range [0,1];

Returns:

fpDistThreshold (float 1x1:) – Fingerprint distance threshold.
fpDistThresholdMadCorr (float 1x1:) – Fingerprint distance threshold outlier corrected.
fpDistanceSubset (float 1x1:) – Data used for fingerprint threshold determination.

Authors:

Andreas P. Cuny - initial implementation

computeFingerprint(~, img, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies)¶

Parameters:

img (uint8 NxNx1 uint8, 16, 32, 64) – Image matrix
fingerprintResizeFactor (int) – fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – fingerprintMaxConsideredFrequencies

Returns:

retFq – [1x64] Real frequency fingerprint array.

Return type:

float 1xM

Authors:

Andreas P. Cuny - initial implementation

computeFingerprint3D(~, img, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies)¶

Parameters:

ignoredArg (object) – Fingerprint instance
img (uint8 NxNx3 uint8, 16, 32, 64) – Image matrix
fingerprintResizeFactor (int) – +TracX.ParameterConfiguration.fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – +TracX.ParameterConfiguration.fingerprintMaxConsideredFrequencies

Returns:

retFq – [1x64] Real frequency fingerprint array.

Return type:

float 1xM

Authors:

Tomas Kuendig - initial implementation

computeFingerprintAsgmtFrac(this, crfO, crfN, dCRFAsgmt, nhbrhdM)¶

Parameters:

this (object) – Fingerprint instance
crfO (array) – Fingerprint (CRF) array for oldFrame.
crfN (array) – Fingerprint (CRF) array fpr newFrame.
dCRFAsgmt (array) – Fingerprint distance (dCRF) of all assignments between old and newFrame
nhbrhdM (array) – Neighbourhood indices locial matrix

Returns:

FFPa (array) – Fraction of neighbouring cells with lower dCRF for each assigned cell
FFP (array) – Fraction of neighbouring cells with lower dCRF (size of # neighbour)
NNFPa (array) – Sum of dCRFDiff > 0 for each assigned cell
NNFP (array) – Sum of dCRFDiff > 0 (size of # neighbour)
nNhbra (array) – Total number of neighbouring cells for each assigned cell
nNhbr (array) – Total number of neighbouring cells (size of # neighbour)

Authors:

Andreas P. Cuny - initial implementation

computeFingerprintDistance(~, realTrackFingerprintOldFrame, realTrackFingerprintNewFrame)¶

Parameters:

ignoredArg (object) – Fingerprint instance
realTrackFingerprintOldFrame (cell array) – Real fingerprint array for all cells in the oldFrame
realTrackFingerprintNewFrame (cell array) – Real fingerprint array for all cells in the subsequent image frame (newFrame).

Returns:

realTrackFingerprintDistance – Fingerprint distances between all cells from the oldFrame and all its assigned cells in the newFrame based on the real fingerprints.

Return type:

double

Authors:

Andreas P. Cuny - initial implementation

Authors:

Joerg Stelling - speed optimization

computeFingerprintForFrame(this, fromFrame, toFrame, fingerprintHalfWindowSideLength, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies, imageDir, imageFingerprintFileArray, imageCropCoordinateArray, cellFrameArray, cellCenterXArray, cellCenterYArray)¶

Parameters:

this (object) – Fingerprint instance
fromFrame (int) – Starting frame for calculation
toFrame (int) – End frame for calculation
fingerprintHalfWindowSideLength (int) – +TracX.ParameterConfiguration.fingerprintHalfWindowSideLength
fingerprintResizeFactor (int) – +TracX.ParameterConfiguration.fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – +TracX.ParameterConfiguration.fingerprintMaxConsideredFrequencies
imageDir (str) – +TracX.ProjectConfiguration.imageDir
imageFingerprintFileArray (cell array 1xK) – +TracX.ProjectConfiguration.imageFingerprintFileArray
imageCropCoordinateArray (double 1x4) – +TracX.ProjectConfiguration.imageCropCoordinateArray
cellFrameArray (int) – Array with all image frame numbers.
cellCenterXArray (int) – Array with centroid x coordinates of segmented objects.
cellCenterYArray (int) – Array with centroid x coordinates of segmented objects.

Returns:

retFq – fingerprints for each segmented object.

Return type:

double Array with the real

Authors:

Andreas P. Cuny - initial implementation

computeFingerprintForFrame3D(this, fromFrame, toFrame, fingerprintHalfWindowSideLength, fingerprintResizeFactor, fingerprintMaxConsideredFrequencies, imageDir, imageFingerprintFileArray, imageCropCoordinateArray, cellFrameArray, cellCenterXArray, cellCenterYArray, cellCenterZArray, pixelPerZplane, active3DFingerprint)¶

Parameters:

this (object) – Fingerprint instance
fromFrame (int) – Starting frame for calculation
toFrame (int) – End frame for calculation
fingerprintHalfWindowSideLength (int) – +TracX.ParameterConfiguration.fingerprintHalfWindowSideLength
fingerprintResizeFactor (int) – +TracX.ParameterConfiguration.fingerprintResizeFactor
fingerprintMaxConsideredFrequencies (int) – +TracX.ParameterConfiguration.fingerprintMaxConsideredFrequencies
imageDir (str) – +TracX.ProjectConfiguration.imageDir
imageFingerprintFileArray (cell array 1xK) – +TracX.ProjectConfiguration.imageFingerprintFileArray
imageCropCoordinateArray (double 1x4) – +TracX.ProjectConfiguration.imageCropCoordinateArray
cellFrameArray (int) – Array with all image frame numbers.
cellCenterXArray (int) – Array with centroid x coordinates of segmented objects.
cellCenterYArray (int) – Array with centroid y coordinates of segmented objects.
cellCenterZArray (int) – Array with centroid z coordinates of segmented objects.
pixelPerZplane (int) – Number of pixel per Zplane
active3DFingerprint (bool) – Switch for active 3D fingerprint.

Returns:

retFq – fingerprints for each segmented object.

Return type:

double Array with the real

Authors:

Tomas Kuendig - initial implementation

computeNeighbourProbFPBelowAss(~, assignedFPdistTotalMovie, neighbourDeltaDistTotalMovie, FPByFraction, startIdx, nData)¶

Parameters:

ignoredArg (object) – Fingerprint instance
assignedFPdistTotalMovie (cell array) – Array of fingerprint distances of the assigned cells for each tracked frame.
neighbourDeltaDistTotalMovie (cell array) – Array of delta distances from the neighbours of the assigned cells for each tracked frame.
FPByFraction (bool) – True (default): calculate faction of neighbours with lower FP distance. False: calculate if any neighbour has lower FP distance
startIdx (int) – Start index for the first frame tracking started.
nData (int) – Total length of the data columns.

Returns:

pLowerFPArray – Cumultative probability for each assignment that a neighbour has a lower fingerprint distance.

Return type:

float:

Authors:

Joerg Stelling - initial implementation of the idea

Authors:

Andreas P. Cuny - implementation for TracX evaluation

ImageProcessing ¶

TracX.@ImageProcessing.generateMarkerControlImageFrame(this, frameNumber)¶

GENERATEMARKERCONTROLIMAGEFRAME Generates a marker tracking control image to visualize i.e budneck marker tracking.

Parameters:

this (object) – ImageProcessing instance
frameNumber (int) – Image frame number

Returns:

Image matrix including segmentation mask of cell cycle marker.

Return type:

labeledMask array NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateMergedMaskForReSegmentation(this, tracks2Merge)¶

GENERATEMERGEDMASKFORRESEGMENTATION Generates masks for resegmentation and quantification by deleteing all unaffected cells from the mask and copying them into the segmentationResultDir/tmp subfolder.

Parameters:

this (object) – ImageProcessing instance
tracks2Merge (array kx1) – Image matrix

Returns:

Writes new massks to disk directly into a tmp folder. segmentationResultDir

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.addTimestampScalebar(this, img, imageFrequency, frame, varargin)¶

ADDTIMESTAMPSCALEBAR Adds a timestamp (frame number or time in units time as well as a scale bar to an image.

Parameters:

this (object) – ImageProcessing instance
img (uint8 NxNx1 uint8, 16, 32, 64) – Image matrix
imageFrequency (float) – Image frequency in hours
frame (int) – Image frame number
varargin (str varchar) –
- scaleBarLength (float): Length of scalebar in terms of unit.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Options are pixel, px, pixels.

Returns:

Image matrix including timestamp and scalebar.

Return type:

img unit8 NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateMarkerTimeSeriesImage(this, varargin)¶

GENERATEMARKERTIMESERIESIMAGE Generates and saves an image series for each track and image frame of the experimet. Each track is labeled with its segmentation mask and centered.

Parameters:

this (object) – ImageProcessing instance
img (uint8 NxNx1 uint8, 16, 32, 64) – Image matrix
imageFrequency (float) – Image frequency in hours
frame (int) – Image frame number
varargin (str varchar) –
- fontSize (float): Fontsize of labeles. Defaults to 12.
- halfWindowLength (int): Half window side length around cell center to be used for each image frame. Defaults to 50.
- cycleMarker (array): Cell array with flourescence channel identifiers depicting cell cycle markers i.e {‘mKO’, ‘mKate’}.
- isPlotMarkerSignal (bool): Flag to plot cell cycle marker ‘raw’ signal as additional overlay; Defaults to false.

Returns:

Resulting images are written to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateMultiTrackControlMovie(this, fromImageFrame, toImageFrame, movieFileName, varargin)¶

GENERATEMULTITRACKCONTROLMOVIE Exports a movie for all detected and tracked cells in the indicated image frame range. The movie helps the user to visually inspect the tracking accuracy.

Parameters:

this (object) – ImageProcessing instance
fromImageFrame (int) – Frame (image) number to start movie from.
toImageFrame (int) – Frame (image) number to end movie.
movieFileName (str) – Name for the resulting movie to save.
varargin (str varchar) –
- fieldname (str): Field name for which to create color map. Defaults to ‘track_index’; Any SegmentationData property
- videoQuality (int 0-100): Quality (0:100) of exported movie; Defaults to 100.
- videoFrameRate (int ): Frame per second in exported movie; Defaults to 5.
- videoProfile (str ): Compression format that should be used for the exported move; Defautls to ‘MPEG-4’; help VideoWriter in cmd for more help.
- scaleBarLength (float): Length of scalebar in terms of unit. Defaults to 10.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Options are pixel, px, pixels.
- imageFrequency (int): Images aquired per hour.
- roi (array, 1x4): Region of interest to export defined as crop array [x, y, h, w]. Default is empty.
- tracksOfInterest (array,): Array of track indices to be labeled.

Returns:

A movie with all cells in a track labeled is written to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.overlayMaskOnImage(this, image, mask, varargin)¶

OVERLAYMASKONIMAGE Overlays a mask file on an image where as the transparency of the overlay is set trough the optional maskOverlayAlpha argument.

Parameters:

this (object) – ImageProcessing instance
image (array NxM) – Image matrix
mask (array) – the specified channel with the in alpha specified transparency.
varargin (str varchar) –
- maskOverlayAlpha (float 0-1): Sets the transparency of the mask in the range[0,1].
- imageBrightness (float 0-1): Sets the brightness of the image in the range [0,1].
- customColorMap (array, Kx3): Applies a custom colormap of the size [K,3], with K = max(track_index) number

Returns:

Image with mask overlayed onto image with user defined transparency.

Return type:

labeledImg double NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateLineageMovie(this, rootTrack, imageFrequency, movieName, varargin)¶

GENERATELINEAGEMOVIE Generates a video displaying the cell lineage, labeled image and quantified signals over time.

Parameters:

this (object) – ImageProcessing instance
rootTrack (int) – Track index of the lineage root to be visualized.
imageFrequency (float) – Image frequency in hours
movieName (str) – Name of the movie
varargin (str varchar) –
- figurePosition (float): Figure position and size (x,y, width, height) array for the movie generation. Default is: [10 10 1350 600]
- videoQuality (int 0-100): Quality (0:100) of exported movie; Defaults to 100.
- videoFrameRate (int ): Frame per second in exported movie; Defaults to 5.
- videoProfile (str ): Compression format that should be used for the exported move; Defautls to ‘MPEG-4’; help VideoWriter in cmd for more help.
- scaleBarLength (float): Length of scalebar in terms of unit.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Opthons are pixel, px, pixels.

Returns:

Writes movie to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateTrackerControlMaskImageFrame(this, frameNumber, varargin)¶

GENERATETRACKERCONTROLMASKIMAGEFRAME Generates a tracker control image where the labeled tracker mask are overlayed onto the raw image. Optionaly the label color can be set using a cmap.

Parameters:

this (object) – ImageProcessing instance
frameNumber (int) – Image frame number
varargin (str varchar) –
- useTrackIndices (bool): If track indices should be used. Defaults to true. Othewise cell indices are used.
- customCMap (array kx3): Use custom colormat to color the cell segmentation masks. Otherwise auto generates one.

Returns:

Image matrix with tracked cell segmentation masks.

Return type:

labeledMask array NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.relabelMaskIndices(~, mask, newLabelArray, oldLabelArray)¶

RELABELMASKINDICES Relabels indices on a 2D mask [NxM].

Parameters:

ignoredArg (object) – ImageProcessing instance
mask (uint16 NxM) – Matrix with numerical labels
newLabelArray (int 1xN) – Array containing the new numerical labels to replace the old ones with.
oldLabelArray (int 1xN) – Array containing all the numerical labels of mask.

Returns:

Matrix with labels replaced.

Return type:

maskRelabeled double NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateLineageFrame(this, rootTrack, imageFrequency, frame, varargin)¶

GENERATELINEAGEFRAME Generates a figure for a specific image frame for the lineage movie generation. The figure consists of a labeled image, the lineage tree and a plotting area to plot quantified signals over time.

Parameters:

this (object) – ImageProcessing instance
rootTrack (int) – Track index of the lineage root to be visualized.
imageFrequency (float) – Image frequency in hours
frame (int) – Image frame number
varargin (str varchar) –
- figurePosition (float): Figure position and size (x,y, width, height) array for the movie generation. Default is: [10 10 1350 600]
- scaleBarLength (float): Length of scalebar in terms of unit.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Opthons are pixel, px, pixels.

Returns:

Figure handle.

Return type:

fh object

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.labelImageTrackMasks(this, trackToLabelArray, frameNumber, varargin)¶

LABELIMAGETRACKMASKS Generates a color image where all cell tracks found on that frame are labeled with the segmentation mask. The mask are overlayed onto the raw (Brightfield) image. The transparency of the mask (maskOverlayAlpha) and the brightness of the image (imageTransparency) can be optionally controlled. Also a the labels can be colored with custom colors from a color map of the appropriate size.

Parameters:

this (object) – ImageProcessing instance
trackToLabelArray (array 1xK) – Array of track numbers which should be labeled with their segmentation mask on an image.
frameNumber (int 1x1) – Image frame number
varargin (str varchar) –
- maskOverlayAlpha (float 0-1): Sets the transparency of the mask in the range[0,1].
- imageBrightness (float 0-1): Sets the brightness of the image in the range [0,1].
- customColorMap (array, Kx3): Applies a custom colormap of the size [K,3], with K = max(track_index) number

Returns:

labeledImg – RGB image with all tracks of interest are labeled with their masks..

Return type:

array NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.computeCLAHE(image, claheBlockSize, claheClipLimit)¶

COMPUTECLAHE Computes the Contrast Limited Adaptive Histogram Equalization (CLAHE) to enhance the local contrast of an image.

Parameters:

image (str) – Path to image file.
claheBlockSize (int [M, N]) – The size of the local region around a pixel for which the histogram is equalized. This size should be larger than the size of features to be preserved.
claheClipLimit (float [0-1]) – Real scalar that specifies a contrast enhancement limit. Higher numbers result in more contrast.

Returns:

Image matrix with enhanced contrast.

Return type:

claheImage ddouble NxM

Authors:

Sotiris Dimopoulos - initial implementation in CellX

Authors:

Andreas P. Cuny - adaptation for TracX

TracX.@ImageProcessing.generate4DImageStackMarker(this, imageFilePath, segmentationResultDir, imageFileNameArray, trackerResultMaskArray, cycleMarker, halfWindowLength, trackOI, fontSize, isPlotMarkerSignal)¶

GENERATE4DIMAGESTACKMARKER Generates 2D images with single precision in either greyscale or RGB into 4D stack 4th dimension here is time. To save memory, images are converted with im2uint8 from >8bit to 8bit images for cell cycle markers.

Parameters:

this (object) – ImageProcessing instance
imageFilePath (str) – Path to image location
segmentationResultDir (str) – Path to segmentation result files.
imageFileNameArray (str 1xN) – Cell array with image file names
trackerResultMaskArray (str 1xN) – Cell array with tracker mask file names.
cycleMarker (array 1x2) – Cell array with marker file identifiers i.e {‘mKate’, ‘mKO’}
halfWindowLength (int) – Half window length of a square around cell center to cut out from the total image matrix.
trackOI – selected Track (current track of interest)
fontSize (int 1x1) – Fontsize for labels.
isPlotMarkerSignal (bool) – Flag if cell cycle marker signal shold be plotted as additional layer. Default to false.

Returns:

ImgStack – 4D Stack containing the image of cell of interest windowed around its cell center.

Return type:

array WxHx3xN

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateMergedMask(this)¶

GENERATEMERGEDMASK Merges the bud mask with the mother mask prior cell division if exists (i.e. with CellX segmentation it does).

Parameters:: this (object) – ImageProcessing instance
Returns:: void – Corrected masks are saved directly to disk.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateAnnotatedControlImageFrame(this, frameNumber, varargin)¶

GENERATEANNOTATEDCONTROLIMAGEFRAME Generates a control image where all data found on an image frame for a given property are overlayed onto a (Brightfield) image. The default property is ‘track_index’ but it can be any of ‘SegmentationData’.

Parameters:

this (obj) – ImageProcessing object
frameNumber (int) – Image frame number.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- highlightFieldNameVal (int): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- fontSize (str): Font size of property to be displayed. Defaults to 14.
  - fontName (str): Font name of property to be displayed. Defaults to Arial.
  - fontEmphasis (int): Font emphasis of property to be displayed. Defaults to 0 (regular). Options 1 (bold), 2 (italic).
- removeContainedTracks (bool): If contained tracks within tracks should be removed. Defaults to true.
- isMarker (bool): If markers should be displayed. Defaults to false.

Returns:

labeledImg – Image with all tracks present labeled.

Return type:

(array, NxM)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateTimeSeriesImageMatrix(this, halfWindowLength)¶

GENERATETIMESERIESIMAGEMATRIX Generates and saves an image series for each track and image frame of the experimet. Each track is labeled with its segmentation mask and centered.

Parameters:

this (object) – ImageProcessing instance
halfWindowLength (int, 1x1) – Half window side length around cell center to be used for each image frame.

Returns:

Resulting images are written to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generate4DImageStack(this, imageFilePath, segmentationResultDir, imageFileNameArray, trackerResultMaskArray, coiFrameArray, cellCenterXArray, cellCenterYArray, halfWindowLength, imageFrameArray, trackIndexArray, trackOI, trackContainedInTrack)¶

GENERATE4DIMAGESTACK Generates 2D images with single precision in either greyscale or RGB into 4D stack 4th dimension here is time. To save memory, images are converted with im2uint8 from >8bit to 8bit images.

Parameters:

this (object) – ImageProcessing instance
imageFilePath (str) – Path to image location
segmentationResultDir (str) – Path to segmentation result files.
imageFileNameArray (str 1xN) – Cell array with image file names
trackerResultMaskArray (str 1xN) – Cell array with tracker mask file names.
coiFrameArray (int 1xN) – Array with frame number for cell of interest.
cellCenterXArray (int 1xN) – Array with x coordinates for the cell of interest.
cellCenterYArray (int 1xN) – Array with y coordinates for the cell of interest.
halfWindowLength (int) – Half window length of a square around cell center to cut out from the total image matrix.
imageFrameArray (int 1xN) – Array of image frames where a tracked cell is present.
trackIndexArray (int 1xN) – Array with track indices
trackOI – selected Track (current track of interest)
trackContainedInTrack (int 1xN) – Array with track indices contained in other tracks (due to discarded miss segmented objects)

Returns:

ImgStack – 4D Stack containing the image of cell of interest windowed around its cell center.

Return type:

array WxHx3xN

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.getFieldCMap(this, property)¶

GETFIELDCMAP Returns a colormap based on a specific property. Where as each track_index is colored by a unique color. For track_parent each parent gets a unique_color that changes over time to longer the time distance to cell division. All other properties get a unique time invariant color.

Parameters:

this (object) – ImageProcessing instance
property (str) – SegmentationData property

Returns:

cMap float Kx3 – Color map for track indices
cMapFull float Kx3 – Full color map
cLim float 1x2 – Min and max property values

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generatePoleAgeControlImageFrame(this, fontSize, frameNumber)¶

GENERATEPOLEAGECONTROLIMAGEFRAME Generates a control image with labeled cell poles for all cell tracks found on an image frame with their pole age overlayed onto a (Brightfield) image.

Parameters:

this (object) – ImageProcessing instance
fontSize (float) – Font size of track indicies labels.
frameNumber (int) – Image frame number.

Returns:

Raw image with all tracks present labeled with their cell pole ages.

Return type:

labeledImg double NxM

Authors:

Andreas P. Cuny - initial implementation

class TracX.@ImageProcessing.ImageProcessing¶

ImageProcessing Class for processing image matrices. It implements methods to generate various control images.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

ImageProcessing(io, configuration, data, utils, lineage)¶

Constructor of an ImageProcessing object

Parameters:

io (object) – TracX.@IO instance.
configuration (object) – TracX.@TrackerConfiguration instance.
data (object) – TracX.@TrackerData instance.
utils (object) – TracX.@Utils instance.
lineage (object) – TracX.@Lineage instance.

Returns:

ImageProcessing instance

Return type:

obj (object)

Authors:

Andreas P. Cuny - initial implementation

Property Summary

configuration¶: TracX.@TrackerConfiguration instance with the tracking parameters and project metadata

data¶: TracX.@TrackerData instance stores all segmentation, quantification and lineage data.

io¶: TracX.@IO instance implementing read/write methods

lineage¶: TracX.@Lineage instance implementing lineage methods

utils¶: TracX.@Utils instance implementing utility methods

Method Summary

addTimestampScalebar(this, img, imageFrequency, frame, varargin)¶

ADDTIMESTAMPSCALEBAR Adds a timestamp (frame number or time in units time as well as a scale bar to an image.

Parameters:

this (object) – ImageProcessing instance
img (uint8 NxNx1 uint8, 16, 32, 64) – Image matrix
imageFrequency (float) – Image frequency in hours
frame (int) – Image frame number
varargin (str varchar) –
- scaleBarLength (float): Length of scalebar in terms of unit.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Options are pixel, px, pixels.

Returns:

Image matrix including timestamp and scalebar.

Return type:

img unit8 NxM

Authors:

Andreas P. Cuny - initial implementation

computeCLAHE(image, claheBlockSize, claheClipLimit)¶

COMPUTECLAHE Computes the Contrast Limited Adaptive Histogram Equalization (CLAHE) to enhance the local contrast of an image.

Parameters:

image (str) – Path to image file.
claheBlockSize (int [M, N]) – The size of the local region around a pixel for which the histogram is equalized. This size should be larger than the size of features to be preserved.
claheClipLimit (float [0-1]) – Real scalar that specifies a contrast enhancement limit. Higher numbers result in more contrast.

Returns:

Image matrix with enhanced contrast.

Return type:

claheImage ddouble NxM

Authors:

Sotiris Dimopoulos - initial implementation in CellX

Authors:

Andreas P. Cuny - adaptation for TracX

generate4DImageStack(this, imageFilePath, segmentationResultDir, imageFileNameArray, trackerResultMaskArray, coiFrameArray, cellCenterXArray, cellCenterYArray, halfWindowLength, imageFrameArray, trackIndexArray, trackOI, trackContainedInTrack)¶

Parameters:

this (object) – ImageProcessing instance
imageFilePath (str) – Path to image location
segmentationResultDir (str) – Path to segmentation result files.
imageFileNameArray (str 1xN) – Cell array with image file names
trackerResultMaskArray (str 1xN) – Cell array with tracker mask file names.
coiFrameArray (int 1xN) – Array with frame number for cell of interest.
cellCenterXArray (int 1xN) – Array with x coordinates for the cell of interest.
cellCenterYArray (int 1xN) – Array with y coordinates for the cell of interest.
halfWindowLength (int) – Half window length of a square around cell center to cut out from the total image matrix.
imageFrameArray (int 1xN) – Array of image frames where a tracked cell is present.
trackIndexArray (int 1xN) – Array with track indices
trackOI – selected Track (current track of interest)
trackContainedInTrack (int 1xN) – Array with track indices contained in other tracks (due to discarded miss segmented objects)

Returns:

ImgStack – 4D Stack containing the image of cell of interest windowed around its cell center.

Return type:

array WxHx3xN

Authors:

Andreas P. Cuny - initial implementation

generate4DImageStackMarker(this, imageFilePath, segmentationResultDir, imageFileNameArray, trackerResultMaskArray, cycleMarker, halfWindowLength, trackOI, fontSize, isPlotMarkerSignal)¶

Parameters:

this (object) – ImageProcessing instance
imageFilePath (str) – Path to image location
segmentationResultDir (str) – Path to segmentation result files.
imageFileNameArray (str 1xN) – Cell array with image file names
trackerResultMaskArray (str 1xN) – Cell array with tracker mask file names.
cycleMarker (array 1x2) – Cell array with marker file identifiers i.e {‘mKate’, ‘mKO’}
halfWindowLength (int) – Half window length of a square around cell center to cut out from the total image matrix.
trackOI – selected Track (current track of interest)
fontSize (int 1x1) – Fontsize for labels.
isPlotMarkerSignal (bool) – Flag if cell cycle marker signal shold be plotted as additional layer. Default to false.

Returns:

ImgStack – 4D Stack containing the image of cell of interest windowed around its cell center.

Return type:

array WxHx3xN

Authors:

Andreas P. Cuny - initial implementation

generateAnnotatedControlImageFrame(this, frameNumber, varargin)¶

Parameters:

this (obj) – ImageProcessing object
frameNumber (int) – Image frame number.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- highlightFieldNameVal (int): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- fontSize (str): Font size of property to be displayed. Defaults to 14.
  - fontName (str): Font name of property to be displayed. Defaults to Arial.
  - fontEmphasis (int): Font emphasis of property to be displayed. Defaults to 0 (regular). Options 1 (bold), 2 (italic).
- removeContainedTracks (bool): If contained tracks within tracks should be removed. Defaults to true.
- isMarker (bool): If markers should be displayed. Defaults to false.

Returns:

labeledImg – Image with all tracks present labeled.

Return type:

(array, NxM)

Authors:

Andreas P. Cuny - initial implementation

generateFingerprintControlImageFrame(this, fontSize, rectHalfSideLength, frameNumber)¶

GENERATEFINGERPRINTCONTROLIMAGEFRAME Generates a control image where all cell tracks found on an image frame are labeled with their track indicies overlayed onto a (Brightfield) image. Additionally the fingerprint windows are displayed to estimate the size of the cell neighbourhood.

Parameters:

this (obj) – ImageProcessing object
fontSize (int) – Font size of track indicies labels.
rectHalfSideLength (int) – fingerprintWindowHalfSideLength
frameNumber (int) – Image frame number.

Returns:

labeledImg – Image with the fingerprint window for all tracks present labeled.

Return type:

(array, NxM)

Authors:

Andreas P. Cuny - initial implementation

generateLineageFrame(this, rootTrack, imageFrequency, frame, varargin)¶

Parameters:

this (object) – ImageProcessing instance
rootTrack (int) – Track index of the lineage root to be visualized.
imageFrequency (float) – Image frequency in hours
frame (int) – Image frame number
varargin (str varchar) –
- figurePosition (float): Figure position and size (x,y, width, height) array for the movie generation. Default is: [10 10 1350 600]
- scaleBarLength (float): Length of scalebar in terms of unit.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Opthons are pixel, px, pixels.

Returns:

Figure handle.

Return type:

fh object

Authors:

Andreas P. Cuny - initial implementation

generateLineageMovie(this, rootTrack, imageFrequency, movieName, varargin)¶

GENERATELINEAGEMOVIE Generates a video displaying the cell lineage, labeled image and quantified signals over time.

Parameters:

this (object) – ImageProcessing instance
rootTrack (int) – Track index of the lineage root to be visualized.
imageFrequency (float) – Image frequency in hours
movieName (str) – Name of the movie
varargin (str varchar) –
- figurePosition (float): Figure position and size (x,y, width, height) array for the movie generation. Default is: [10 10 1350 600]
- videoQuality (int 0-100): Quality (0:100) of exported movie; Defaults to 100.
- videoFrameRate (int ): Frame per second in exported movie; Defaults to 5.
- videoProfile (str ): Compression format that should be used for the exported move; Defautls to ‘MPEG-4’; help VideoWriter in cmd for more help.
- scaleBarLength (float): Length of scalebar in terms of unit.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Opthons are pixel, px, pixels.

Returns:

Writes movie to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

generateMarkerControlImageFrame(this, frameNumber)¶

GENERATEMARKERCONTROLIMAGEFRAME Generates a marker tracking control image to visualize i.e budneck marker tracking.

Parameters:

this (object) – ImageProcessing instance
frameNumber (int) – Image frame number

Returns:

Image matrix including segmentation mask of cell cycle marker.

Return type:

labeledMask array NxM

Authors:

Andreas P. Cuny - initial implementation

generateMarkerTimeSeriesImage(this, varargin)¶

GENERATEMARKERTIMESERIESIMAGE Generates and saves an image series for each track and image frame of the experimet. Each track is labeled with its segmentation mask and centered.

Parameters:

this (object) – ImageProcessing instance
img (uint8 NxNx1 uint8, 16, 32, 64) – Image matrix
imageFrequency (float) – Image frequency in hours
frame (int) – Image frame number
varargin (str varchar) –
- fontSize (float): Fontsize of labeles. Defaults to 12.
- halfWindowLength (int): Half window side length around cell center to be used for each image frame. Defaults to 50.
- cycleMarker (array): Cell array with flourescence channel identifiers depicting cell cycle markers i.e {‘mKO’, ‘mKate’}.
- isPlotMarkerSignal (bool): Flag to plot cell cycle marker ‘raw’ signal as additional overlay; Defaults to false.

Returns:

Resulting images are written to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

generateMaskForMatrixCorners(img)¶

GENERATEMASKFORMATRIXCORNERS Creates a mask of the same size of a 2D (image) matrix(NxM) with all corners are labeled by a square.

Parameters:: img (array, NxM) – Image / mask matrix
Returns:: Matrix with edges labeled starting top left with 1.
Return type:: mask array NxM
Authors:: Andreas P. Cuny - initial implementation

generateMergedMask(this)¶

GENERATEMERGEDMASK Merges the bud mask with the mother mask prior cell division if exists (i.e. with CellX segmentation it does).

Parameters:: this (object) – ImageProcessing instance
Returns:: void – Corrected masks are saved directly to disk.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

generateMergedMaskForReSegmentation(this, tracks2Merge)¶

Parameters:

this (object) – ImageProcessing instance
tracks2Merge (array kx1) – Image matrix

Returns:

Writes new massks to disk directly into a tmp folder. segmentationResultDir

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

generateMultiTrackControlMovie(this, fromImageFrame, toImageFrame, movieFileName, varargin)¶

GENERATEMULTITRACKCONTROLMOVIE Exports a movie for all detected and tracked cells in the indicated image frame range. The movie helps the user to visually inspect the tracking accuracy.

Parameters:

this (object) – ImageProcessing instance
fromImageFrame (int) – Frame (image) number to start movie from.
toImageFrame (int) – Frame (image) number to end movie.
movieFileName (str) – Name for the resulting movie to save.
varargin (str varchar) –
- fieldname (str): Field name for which to create color map. Defaults to ‘track_index’; Any SegmentationData property
- videoQuality (int 0-100): Quality (0:100) of exported movie; Defaults to 100.
- videoFrameRate (int ): Frame per second in exported movie; Defaults to 5.
- videoProfile (str ): Compression format that should be used for the exported move; Defautls to ‘MPEG-4’; help VideoWriter in cmd for more help.
- scaleBarLength (float): Length of scalebar in terms of unit. Defaults to 10.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Options are pixel, px, pixels.
- imageFrequency (int): Images aquired per hour.
- roi (array, 1x4): Region of interest to export defined as crop array [x, y, h, w]. Default is empty.
- tracksOfInterest (array,): Array of track indices to be labeled.

Returns:

A movie with all cells in a track labeled is written to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

generatePoleAgeControlImageFrame(this, fontSize, frameNumber)¶

GENERATEPOLEAGECONTROLIMAGEFRAME Generates a control image with labeled cell poles for all cell tracks found on an image frame with their pole age overlayed onto a (Brightfield) image.

Parameters:

this (object) – ImageProcessing instance
fontSize (float) – Font size of track indicies labels.
frameNumber (int) – Image frame number.

Returns:

Raw image with all tracks present labeled with their cell pole ages.

Return type:

labeledImg double NxM

Authors:

Andreas P. Cuny - initial implementation

generateSingleTrackControlMovie(this, fromImageFrame, toImageFrame, trackOfInterest, movieFileName, varargin)¶

GENERATESINGLETRACKCONTROLMOVIE Exports a movie for one selected cell in the indicated image frame range labeled with tracking accuray information encoded in the edges of the movie frames. The movies are intended to help the user to inspect the tracking but also segmentation accuracy for a selected cell of interst.

Parameters:

this (object) – ImageProcessing instance
fromImageFrame (int) – Frame (image) number to start movie from.
toImageFrame (int) – Frame (image) number to end movie.
trackOfInterest (int) – Track of interest for which a control movie should be generated.
movieFileName (str) – Name for the resulting movie to save.
varargin (str varchar) –
- videoQuality (int 0-100): Quality (0:100) of exported movie; Defaults to 100.
- videoFrameRate (int ): Frame per second in exported movie; Defaults to 5.
- videoProfile (str ): Compression format that should be used for the exported move; Defautls to ‘MPEG-4’; help VideoWriter in cmd for more help.
- scaleBarLength (float): Length of scalebar in terms of unit. Defaults to 10.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Options are pixel, px, pixels.
- imageFrequency (int): Images aquired per hour.

Returns:

Movie will be written directly to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

generateTimeSeriesImageMatrix(this, halfWindowLength)¶

GENERATETIMESERIESIMAGEMATRIX Generates and saves an image series for each track and image frame of the experimet. Each track is labeled with its segmentation mask and centered.

Parameters:

this (object) – ImageProcessing instance
halfWindowLength (int, 1x1) – Half window side length around cell center to be used for each image frame.

Returns:

Resulting images are written to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

generateTrackControlImageFramePadded(this, trackOfInterest, frameNumber, varargin)¶

GENERATETRACKCONTROLIMAGEFRAMEPADDED Generates a control image where all cell tracks found on that frame are labeled with the tracked segmentation mask as overlay to the raw (Brightfield) image. The final image is padded to keep the original image size i.e. for cells at image boundary. In the corners of the generated control image frame information about tracking accuracy is encoded as mentioned in the note below.

Parameters:

this (object) – ImageProcessing instance
trackOfInterest (int 1x1) – Track number of a cell of interest
frameNumber (int 1x1) – Image frame number
varargin (str varchar) –
- showImageIfTrackAbsent (bool): Shows real image for image frames where a track is absent using its last position. Otherwise a black image is shown.

Returns:

Image where the track of interest is labeled with additional tracking accuracy information at the image corners.

Return type:

labeledImg array NxM

Note

TopLeft = green := track_index and track_index_qc are identical
TopRight = red := track was put to VeryOld
BottomLeft = red := Mask identity low (bad segmentation but still tracked.
BottomRight = red := track_index and and mask identity ok but qc > thres

Authors:: Andreas P. Cuny - initial implementation

generateTrackerControlMaskImageFrame(this, frameNumber, varargin)¶

GENERATETRACKERCONTROLMASKIMAGEFRAME Generates a tracker control image where the labeled tracker mask are overlayed onto the raw image. Optionaly the label color can be set using a cmap.

Parameters:

this (object) – ImageProcessing instance
frameNumber (int) – Image frame number
varargin (str varchar) –
- useTrackIndices (bool): If track indices should be used. Defaults to true. Othewise cell indices are used.
- customCMap (array kx3): Use custom colormat to color the cell segmentation masks. Otherwise auto generates one.

Returns:

Image matrix with tracked cell segmentation masks.

Return type:

labeledMask array NxM

Authors:

Andreas P. Cuny - initial implementation

getFieldCMap(this, property)¶

Parameters:

this (object) – ImageProcessing instance
property (str) – SegmentationData property

Returns:

cMap float Kx3 – Color map for track indices
cMapFull float Kx3 – Full color map
cLim float 1x2 – Min and max property values

Authors:

Andreas P. Cuny - initial implementation

getTextOnJavaImage(~, image, string, position, fontColor, fontName, fontSize, fontEmphasis)¶

GETTEXTONJAVAIMAGE Outputs image with string label at position for a Java BufferedImage.

Parameters:

ignoredArg (object) – ImageProcessing instance
image (array NxM) – Image matrix where the text string should be inserted. Note: Needs to be a BufferedImage (java).
string (str) – Text that should be added to the image
position (array 2x1) – Position with x and y coordinates to place the string onto the image
fontColor (str) – Font color. Defaults to green (green, red, blue)
fontName (str) – Font name. Defaults to Arial.
fontSize (int) – Font size. Defaults to 14.
fontEmphasis (int) – Font emphasis. Defaults to regular.

Returns:

Image

Return type:

image array NxM

Note

This array (image) can be used in a loop if multiple text strings need to be placed on an image.

Example:

>>> image = im2java2d(rand([100,100,3]));
>>> % Label the image with the text only in the green channel
>>> image = getTextOnJavaImage(image, 'Hello World!', [9,50], 'blue', 'Arial', 16, 1);
>>> % Convert Java BufferedImage back to Matlab array
>>> nrows = image.getHeight;
>>> ncols = image.getWidth;
>>> channel = image.getRaster.getNumBands;
>>> pixelsData = reshape(typecast(image.getData.getDataStorage, 'uint8'), ...
>>>              channel, ncols, nrows);
>>> labeledImg = cat(channel, ...
>>>     transpose(reshape(pixelsData(1, :, :), ncols, nrows)), ...
>>>     transpose(reshape(pixelsData(2, :, :), ncols, nrows)), ...
>>>     transpose(reshape(pixelsData(3, :, :), ncols, nrows)));
>>> figure; imshow(labeledImg)

Authors:: Andreas P. Cuny - initial implementation

labelImageTrackMasks(this, trackToLabelArray, frameNumber, varargin)¶

Parameters:

this (object) – ImageProcessing instance
trackToLabelArray (array 1xK) – Array of track numbers which should be labeled with their segmentation mask on an image.
frameNumber (int 1x1) – Image frame number
varargin (str varchar) –
- maskOverlayAlpha (float 0-1): Sets the transparency of the mask in the range[0,1].
- imageBrightness (float 0-1): Sets the brightness of the image in the range [0,1].
- customColorMap (array, Kx3): Applies a custom colormap of the size [K,3], with K = max(track_index) number

Returns:

labeledImg – RGB image with all tracks of interest are labeled with their masks..

Return type:

array NxM

Authors:

Andreas P. Cuny - initial implementation

mergeBudPriorDivision(this)¶

MERGEBUDPRIORDIVISION Merges the bud mask with the mother mask prior cell division if exists (i.e. with CellX segmentation it does).

Parameters:: this (object) – ImageProcessing instance
Returns:: void – Corrected masks are saved directly to disk.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

normalizeImage(~, imageMatrix)¶

NORMALIZEIMAGE Normalizes image between 0 and 1.

Input:: ignoredArg (object): ImageProcessing instance imageMatrix (array NxM): Image matrix to be normalized.

Returns:: imageMatrixNorm – Normalized image matrix.
Return type:: array NxM
Authors:: Sotiris Dimopoulos - initial implementation in CellX
Authors:: Andreas P. Cuny - adapation for TracX

overlayMaskOnImage(this, image, mask, varargin)¶

OVERLAYMASKONIMAGE Overlays a mask file on an image where as the transparency of the overlay is set trough the optional maskOverlayAlpha argument.

Parameters:

this (object) – ImageProcessing instance
image (array NxM) – Image matrix
mask (array) – the specified channel with the in alpha specified transparency.
varargin (str varchar) –
- maskOverlayAlpha (float 0-1): Sets the transparency of the mask in the range[0,1].
- imageBrightness (float 0-1): Sets the brightness of the image in the range [0,1].
- customColorMap (array, Kx3): Applies a custom colormap of the size [K,3], with K = max(track_index) number

Returns:

Image with mask overlayed onto image with user defined transparency.

Return type:

labeledImg double NxM

Authors:

Andreas P. Cuny - initial implementation

relabelMaskIndices(~, mask, newLabelArray, oldLabelArray)¶

RELABELMASKINDICES Relabels indices on a 2D mask [NxM].

Parameters:

ignoredArg (object) – ImageProcessing instance
mask (uint16 NxM) – Matrix with numerical labels
newLabelArray (int 1xN) – Array containing the new numerical labels to replace the old ones with.
oldLabelArray (int 1xN) – Array containing all the numerical labels of mask.

Returns:

Matrix with labels replaced.

Return type:

maskRelabeled double NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateSingleTrackControlMovie(this, fromImageFrame, toImageFrame, trackOfInterest, movieFileName, varargin)¶

Parameters:

this (object) – ImageProcessing instance
fromImageFrame (int) – Frame (image) number to start movie from.
toImageFrame (int) – Frame (image) number to end movie.
trackOfInterest (int) – Track of interest for which a control movie should be generated.
movieFileName (str) – Name for the resulting movie to save.
varargin (str varchar) –
- videoQuality (int 0-100): Quality (0:100) of exported movie; Defaults to 100.
- videoFrameRate (int ): Frame per second in exported movie; Defaults to 5.
- videoProfile (str ): Compression format that should be used for the exported move; Defautls to ‘MPEG-4’; help VideoWriter in cmd for more help.
- scaleBarLength (float): Length of scalebar in terms of unit. Defaults to 10.
- pxToUnit (float): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- unit (str): Unit of scalebar. Defaults to micron. Options are pixel, px, pixels.
- imageFrequency (int): Images aquired per hour.

Returns:

Movie will be written directly to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.mergeBudPriorDivision(this)¶

MERGEBUDPRIORDIVISION Merges the bud mask with the mother mask prior cell division if exists (i.e. with CellX segmentation it does).

Parameters:: this (object) – ImageProcessing instance
Returns:: void – Corrected masks are saved directly to disk.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.getTextOnJavaImage(~, image, string, position, fontColor, fontName, fontSize, fontEmphasis)¶

GETTEXTONJAVAIMAGE Outputs image with string label at position for a Java BufferedImage.

Parameters:

ignoredArg (object) – ImageProcessing instance
image (array NxM) – Image matrix where the text string should be inserted. Note: Needs to be a BufferedImage (java).
string (str) – Text that should be added to the image
position (array 2x1) – Position with x and y coordinates to place the string onto the image
fontColor (str) – Font color. Defaults to green (green, red, blue)
fontName (str) – Font name. Defaults to Arial.
fontSize (int) – Font size. Defaults to 14.
fontEmphasis (int) – Font emphasis. Defaults to regular.

Returns:

Image

Return type:

image array NxM

Note

This array (image) can be used in a loop if multiple text strings need to be placed on an image.

Example:

>>> image = im2java2d(rand([100,100,3]));
>>> % Label the image with the text only in the green channel
>>> image = getTextOnJavaImage(image, 'Hello World!', [9,50], 'blue', 'Arial', 16, 1);
>>> % Convert Java BufferedImage back to Matlab array
>>> nrows = image.getHeight;
>>> ncols = image.getWidth;
>>> channel = image.getRaster.getNumBands;
>>> pixelsData = reshape(typecast(image.getData.getDataStorage, 'uint8'), ...
>>>              channel, ncols, nrows);
>>> labeledImg = cat(channel, ...
>>>     transpose(reshape(pixelsData(1, :, :), ncols, nrows)), ...
>>>     transpose(reshape(pixelsData(2, :, :), ncols, nrows)), ...
>>>     transpose(reshape(pixelsData(3, :, :), ncols, nrows)));
>>> figure; imshow(labeledImg)

Authors:: Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.normalizeImage(~, imageMatrix)¶

NORMALIZEIMAGE Normalizes image between 0 and 1.

Input:: ignoredArg (object): ImageProcessing instance imageMatrix (array NxM): Image matrix to be normalized.

Returns:: imageMatrixNorm – Normalized image matrix.
Return type:: array NxM
Authors:: Sotiris Dimopoulos - initial implementation in CellX
Authors:: Andreas P. Cuny - adapation for TracX

TracX.@ImageProcessing.generateTrackControlImageFramePadded(this, trackOfInterest, frameNumber, varargin)¶

Parameters:

this (object) – ImageProcessing instance
trackOfInterest (int 1x1) – Track number of a cell of interest
frameNumber (int 1x1) – Image frame number
varargin (str varchar) –
- showImageIfTrackAbsent (bool): Shows real image for image frames where a track is absent using its last position. Otherwise a black image is shown.

Returns:

Image where the track of interest is labeled with additional tracking accuracy information at the image corners.

Return type:

labeledImg array NxM

Note

TopLeft = green := track_index and track_index_qc are identical
TopRight = red := track was put to VeryOld
BottomLeft = red := Mask identity low (bad segmentation but still tracked.
BottomRight = red := track_index and and mask identity ok but qc > thres

Authors:: Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateFingerprintControlImageFrame(this, fontSize, rectHalfSideLength, frameNumber)¶

Parameters:

this (obj) – ImageProcessing object
fontSize (int) – Font size of track indicies labels.
rectHalfSideLength (int) – fingerprintWindowHalfSideLength
frameNumber (int) – Image frame number.

Returns:

labeledImg – Image with the fingerprint window for all tracks present labeled.

Return type:

(array, NxM)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageProcessing.generateMaskForMatrixCorners(img)¶

GENERATEMASKFORMATRIXCORNERS Creates a mask of the same size of a 2D (image) matrix(NxM) with all corners are labeled by a square.

Parameters:: img (array, NxM) – Image / mask matrix
Returns:: Matrix with edges labeled starting top left with 1.
Return type:: mask array NxM
Authors:: Andreas P. Cuny - initial implementation

ImageVisualization ¶

TracX.@ImageVisualization.plotLineageTree(this, varargin)¶

PLOTLINEAGETREE Plot a lineage tree for one or multiple root cells (i.e cells on the first frame). The tree is plotted to the console by default. With ‘plotToFigure’ set to true plots the tree to a figure.

Parameters:

this (obj) – ImageVisualization object
varargin (str varchar) –
- rootIndicies (int): The lineage root; Any ‘track_index’ number.
- divisionType (int): Cell division type. Set automatically but can be change.
- plotToFigure (bool): Flag if lineage tree should be plotted to a figure. Defaults to false.

Returns:

Prints the tree to the command window. Optionally the lineage tree is visualized in a figure.

Return type:

figureHandles (object)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageVisualization.plotFingerprintEvalSummary(this, pathToResults)¶

PLOTFINGERPRINTEVALSUMMARY Plots fingerprint evaluation results as contour plots for varied parameters for resizing, freq bins and windowing. Additionally a plot visualizing the window on the real data is displayed.

Parameters:

this (obj) – ImageVisualization object
pathToResults (str) – Full path to fingerprintEvaluation result file.

Returns:

Displays figures.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageVisualization.visualise3DCells(this, varargin)¶

VISUALISE3DCELLS Function to visualize 3D cells / type of data. Optional inputs alow for customization regarding track to display, colormap, image limits, if only reduced alpha shapes should be used, if an image sould be returned, if a movie should be generated, what the pixel per micron factor is and if the image should be rotated.

Parameters:

ignoredArg (obj) – ImageVisualization object
varargin (str varchar) –
- PropertyToVisualise (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- Track (int): Track number which should be highlighed.
- Frames (array): Image frames array
- ColorMap (array kx3): Colormap to be used
- DelayTime (float 1x1): Deleay time. Defaults to 0.3.
- NameOnly (bool 1x1): Flag if name only. Defaults to false.
- FileName (str 1x1): Filename of output file.
- XLim (array, 1x2): Plot x limits.
- YLim (array, 1x2): Plot y limits.
- ZLim (array, 1x2): Plot z limits.
- ReducedShapes (bool): Flag; if redunced alpha shapes should be used. Defaults to false.
- ReturnImage (bool): Flag; if image should be returned. Defaults to false.
- NumbersHidden (bool): Flag, if numbers should be shown. Defaults to false.
- OutputType (str): Type of output. Defaults to ‘Movie’.
- PixelsPerMicrometer (float): Pixels per micrometer. Defaults to 0.
- Rotation (bool): Flag, if rotation should be applied. Defaults to 0.
- Colorbar (bool): Flag, if colobar should be shown. Defaults to false.

Returns:

Image is visualized in a figure.

Return type:

returnValue (array)

Authors:

Thomas Kuending - initial implementation

TracX.@ImageVisualization.plotSummaryTracksAboveFPThreshold(this, varargin)¶

PLOTSUMMARYTRACKSABOVEFPTHRESHOLD Creates a summary plot track ids vs image frames with tracks and image frames above the fingerprint threshold marked. Gives an overview which linkages have to be inspected manually.

Parameters:

this (obj) – ImageVisualization object
varargin (str varchar) –
- threshold (str): CRF fraction threshold. Defaults to 0.

Returns:

Image is visualized in a figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageVisualization.plotDifferenceAlphaShapeVsReducedAlphaShape(this, cellIdxArray)¶

PLOTDIFFERENCEALPHASHAPEVSREDUCEDALPHASHAPE Displays a control image for the differences in alpha shapes vs reduced alpha shapes.

Parameters:

this (obj) – ImageVisualization instance.
cellIdxArray (array) – Array of cell indices to plot.

Returns:

Image is visualized in figure.

Return type:

void (-)

Authors:

Tomas Kuendig - initial implementation

TracX.@ImageVisualization.plotFingerprintControlImageFrame(this, fontSize, rectHalfSideLength, frameNumber)¶

PLOTFINGERPRINTCONTROLIMAGEFRAME Displays a control image where all cell tracks found on an image frame are labeled with their track indicies overlayed onto a (Brightfield) image. Additionally the fingerprint windows are displayed.

Parameters:

this (obj) – ImageVisualization object
fontSize (int) – Font size of track indicies labels.
rectHalfSideLength (int) – Half side length of rectangle around cell centroids (i.e. fingerprintWindowHalfSideLength)
frameNumber (int) – Image frame number.

Returns:

Labeled image is visualized in figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageVisualization.plotAnnotatedControlImageFrame(this, frameNumber, varargin)¶

PLOTANNOTATEDCONTROLIMAGEFRAME Displays a control image where all data found on an image frame for a given property are overlayed onto a (Brightfield) image at their cell position. Default plotted property is ‘track_index’ and the image cropped to the segmented window.

Parameters:

this (obj) – ImageVisualization object
frameNumber (int) – Image frame number.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- highlightFieldNameVal (int): Property value that should be highlighted.
- fontSize (str): Font size of property to be displayed.
- removeContainedTracks (bool): Flag, if contained tracks within tracks should be removed. Defaults to true.
- figure (object): Figure handle of existing figure to plot result in.

Returns:

Image is visualized in figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageVisualization.plotPoleAgeControlImageFrame(this, fontSize, frameNumber)¶

PLOTPOLEAGECONTROLIMAGEFRAME Displays a control image with the cell poles for all cell tracks found on an image frame labeled with their pole age overlayed onto a (Brightfield) image.

Parameters:

this (obj) – ImageVisualization object
fontSize (int) – Font size of track indicies labels.
frameNumber (int) – Image frame number.

Returns:

Image is visualized in a figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

class TracX.@ImageVisualization.ImageVisualization¶

IMAGEVISUALIZATION Class handles all the image visualization aspects of TracX. i.e. control images displayed to the user.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

ImageVisualization(data, configuration, imageProcessing, lineage)¶

Constructor of an ImageVisualization object. Class handles all the image visualization aspects of TracX. i.e. control images displayed to the user.

Parameters:

data (obj) – TrackerData instance
configuration (obj) – TrackerConfiguration instance
imageProcessing (obj) – ImageProcessing instance
lineage (obj) – Lineage instance

Returns:

ImageVisualization instance

Return type:

obj (obj)

Authors:

Andreas P. Cuny - initial implementation

Property Summary

configuration¶: TracX.@TrackerConfiguration instance implementing configuration methods.

data¶: TracX.@TrackerData instance stores all segmentation, quantification and lineage data.

imageProcessing¶: TracX.@ImageProcessing instance implementing image processing methods.

lineage¶: TracX.@Lineage instance implementing lineage methods.

Method Summary

plotAnnotatedControlImageFrame(this, frameNumber, varargin)¶

Parameters:

this (obj) – ImageVisualization object
frameNumber (int) – Image frame number.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- highlightFieldNameVal (int): Property value that should be highlighted.
- fontSize (str): Font size of property to be displayed.
- removeContainedTracks (bool): Flag, if contained tracks within tracks should be removed. Defaults to true.
- figure (object): Figure handle of existing figure to plot result in.

Returns:

Image is visualized in figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

plotDifferenceAlphaShapeVsReducedAlphaShape(this, cellIdxArray)¶

PLOTDIFFERENCEALPHASHAPEVSREDUCEDALPHASHAPE Displays a control image for the differences in alpha shapes vs reduced alpha shapes.

Parameters:

this (obj) – ImageVisualization instance.
cellIdxArray (array) – Array of cell indices to plot.

Returns:

Image is visualized in figure.

Return type:

void (-)

Authors:

Tomas Kuendig - initial implementation

plotFPVsDeltaDistPlot(~, xFPDistAssigned, xFPDistAssignedToCompare, yDeltaDistAssigned, yDeltaDistToCompare, fpDistThreshold, lowerQuantile, varargin)¶

PLOTFPVSDELTADISTPLOT Displays a scatter plot figure with fingerprint distance vs. delta distance plotted. Additional histograms show the distributions of the main cathegory along the respective axes.

Parameters:

ignoredArg (object) – ImageVisualization instance
xFPDistAssigned (array 1xk) – Fingerprint distance of all assignments
xFPDistAssignedToCompare (array 1xj) – Fingerprint distances of neighbouring cells for each assigned cell.
yDeltaDistAssigned (array 1xk) – Delta distance of all assignments to the minimal FPdist of all possible assignments for each cell.
yDeltaDistToCompare (array 1xj) – Delta distance of all assignments to their comparator (i.e. its direct neighbours or all other cells)
fpDistThreshold (fluat 1x1) – Fingerprint distance threshold.
lowerQuantile (float 1x1) – Lower quantile [0,1] used for fpDistThreshold determination.
varargin (str varchar) –
- lowXLim (float): Lower plot x limit.
- upXLim (float): Upper plot x limit.
- lowYLim (float): Lower plot y limit.
- upYLim (float): Upper plot y limit.
- plotThreshold (float): Flag; if threhsold should be plotted. Defaults to true.
- plotTitle (float): Flag; if title should be plotted. Defaults to true.
- markerFaceAlpha (float): The transparency of the scatter dots in the range [0,1]. Defaults to 0.2.
- markerSize (float): The size of the scatter dots [>0]. Defaults to 32.

Returns:

fh – Figure handle.

Return type:

object 1xM

Authors:

Andreas P. Cuny - initial implementation

plotFingerprintControlImageFrame(this, fontSize, rectHalfSideLength, frameNumber)¶

Parameters:

this (obj) – ImageVisualization object
fontSize (int) – Font size of track indicies labels.
rectHalfSideLength (int) – Half side length of rectangle around cell centroids (i.e. fingerprintWindowHalfSideLength)
frameNumber (int) – Image frame number.

Returns:

Labeled image is visualized in figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

plotFingerprintEvalSummary(this, pathToResults)¶

Parameters:

this (obj) – ImageVisualization object
pathToResults (str) – Full path to fingerprintEvaluation result file.

Returns:

Displays figures.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

plotLineageTree(this, varargin)¶

Parameters:

this (obj) – ImageVisualization object
varargin (str varchar) –
- rootIndicies (int): The lineage root; Any ‘track_index’ number.
- divisionType (int): Cell division type. Set automatically but can be change.
- plotToFigure (bool): Flag if lineage tree should be plotted to a figure. Defaults to false.

Returns:

Prints the tree to the command window. Optionally the lineage tree is visualized in a figure.

Return type:

figureHandles (object)

Authors:

Andreas P. Cuny - initial implementation

plotPoleAgeControlImageFrame(this, fontSize, frameNumber)¶

PLOTPOLEAGECONTROLIMAGEFRAME Displays a control image with the cell poles for all cell tracks found on an image frame labeled with their pole age overlayed onto a (Brightfield) image.

Parameters:

this (obj) – ImageVisualization object
fontSize (int) – Font size of track indicies labels.
frameNumber (int) – Image frame number.

Returns:

Image is visualized in a figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

plotSummaryTracksAboveFPThreshold(this, varargin)¶

Parameters:

this (obj) – ImageVisualization object
varargin (str varchar) –
- threshold (str): CRF fraction threshold. Defaults to 0.

Returns:

Image is visualized in a figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

plotTrackControlImageFrame(this, frameNumber, varargin)¶

PLOTTRACKCONTROLIMAGEFRAME Displays a control image where all cell tracks found on an image frame are labeled with their track indicies overlayed onto a (Brightfield) image.

Parameters:

frameNumber (int) – Image frame number.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- highlightFieldNameVal (int): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- fontSize (str): Font size of property to be displayed.
- removeContainedTracks (bool): If contained tracks within tracks should be removed. Defaults to true.
- isMarker (bool): If markers should be displayed. Defaults to false.

Returns:

Image is visualized in a figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

visualise3DCells(this, varargin)¶

Parameters:

ignoredArg (obj) – ImageVisualization object
varargin (str varchar) –
- PropertyToVisualise (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- Track (int): Track number which should be highlighed.
- Frames (array): Image frames array
- ColorMap (array kx3): Colormap to be used
- DelayTime (float 1x1): Deleay time. Defaults to 0.3.
- NameOnly (bool 1x1): Flag if name only. Defaults to false.
- FileName (str 1x1): Filename of output file.
- XLim (array, 1x2): Plot x limits.
- YLim (array, 1x2): Plot y limits.
- ZLim (array, 1x2): Plot z limits.
- ReducedShapes (bool): Flag; if redunced alpha shapes should be used. Defaults to false.
- ReturnImage (bool): Flag; if image should be returned. Defaults to false.
- NumbersHidden (bool): Flag, if numbers should be shown. Defaults to false.
- OutputType (str): Type of output. Defaults to ‘Movie’.
- PixelsPerMicrometer (float): Pixels per micrometer. Defaults to 0.
- Rotation (bool): Flag, if rotation should be applied. Defaults to 0.
- Colorbar (bool): Flag, if colobar should be shown. Defaults to false.

Returns:

Image is visualized in a figure.

Return type:

returnValue (array)

Authors:

Thomas Kuending - initial implementation

TracX.@ImageVisualization.plotTrackControlImageFrame(this, frameNumber, varargin)¶

PLOTTRACKCONTROLIMAGEFRAME Displays a control image where all cell tracks found on an image frame are labeled with their track indicies overlayed onto a (Brightfield) image.

Parameters:

frameNumber (int) – Image frame number.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of TracX.SegmentationData.
- highlightFieldNameVal (int): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- fontSize (str): Font size of property to be displayed.
- removeContainedTracks (bool): If contained tracks within tracks should be removed. Defaults to true.
- isMarker (bool): If markers should be displayed. Defaults to false.

Returns:

Image is visualized in a figure.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@ImageVisualization.plotFPVsDeltaDistPlot(~, xFPDistAssigned, xFPDistAssignedToCompare, yDeltaDistAssigned, yDeltaDistToCompare, fpDistThreshold, lowerQuantile, varargin)¶

Parameters:

ignoredArg (object) – ImageVisualization instance
xFPDistAssigned (array 1xk) – Fingerprint distance of all assignments
xFPDistAssignedToCompare (array 1xj) – Fingerprint distances of neighbouring cells for each assigned cell.
yDeltaDistAssigned (array 1xk) – Delta distance of all assignments to the minimal FPdist of all possible assignments for each cell.
yDeltaDistToCompare (array 1xj) – Delta distance of all assignments to their comparator (i.e. its direct neighbours or all other cells)
fpDistThreshold (fluat 1x1) – Fingerprint distance threshold.
lowerQuantile (float 1x1) – Lower quantile [0,1] used for fpDistThreshold determination.
varargin (str varchar) –
- lowXLim (float): Lower plot x limit.
- upXLim (float): Upper plot x limit.
- lowYLim (float): Lower plot y limit.
- upYLim (float): Upper plot y limit.
- plotThreshold (float): Flag; if threhsold should be plotted. Defaults to true.
- plotTitle (float): Flag; if title should be plotted. Defaults to true.
- markerFaceAlpha (float): The transparency of the scatter dots in the range [0,1]. Defaults to 0.2.
- markerSize (float): The size of the scatter dots [>0]. Defaults to 32.

Returns:

fh – Figure handle.

Return type:

object 1xM

Authors:

Andreas P. Cuny - initial implementation

IO ¶

TracX.@IO.readSegmentationMask(this, pathToFile)¶

READSEGMENTATIONMASK Loads an segmentation mask file stored in a .mat or .tif file. Each segment should consist of a positive integer value. A segment can span any number of pixel, at least one at max all.

Parameters:

ignoredArg (obj) – IO instance.
pathToFile (str) – Path to mask file.

Returns:

Segmentation mask matrix.

Return type:

mask (array, NxM)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.orientationCompressor(~, vector3D)¶

ORIENTATIONCOMPRESSOR Compresses the orientation vector into a single number. Note: Vector should be already of unit length!

Parameters:

ignoredArg (obj) – IO instance.
vector3D (array) – 3D vector

Returns:

tag – Orientation incompressed format.

Return type:

int

Authors:

Thomas Kuendig - initial implementation

TracX.@IO.writeToMAT(~, data, resultFilePath, resultFileName, varargin)¶

WRITETOMAT Writes tracker results to disk in mat format.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData.
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file

Returns:

Writes text file to disk

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.readImageToGrayScale(~, pathToFile, varargin)¶

READIMAGETOGRAYSCALE loads an image and converts it to gray scale if it has 3 channels (RGB). Gray conversion is performed as follows: img = (R+G+B)/3

Parameters:

ignoredArg (obj) – IO instance.
pathToFile (str) – Path to image file.
varargin – [x, y, w-1, h-1] imageCropCoordinateArray used to crop theloaded image to this size.

Returns:

image (:obj:`array`, NxM) – the size given by imageCropCoordinateArray

Return type:

Image matrix, optionally cropped to

Authors:

Sotiris Dimopoulos - initial implementation in CellX Andreas P. Cuny - Adaptation for TracX

TracX.@IO.convertXLSToCSV(this, fullFileName, dataDelimiter)¶

CONVERTXLSTOCSV Convert a excel spreadsheet to csv table from a file.

Parameters:

this (obj) – IO instance.
fullFileName (str) – Full path and name of file as string.
dataDelimiter (str) – Name or symbol of delimiter

Returns:

Writes text file to disk

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeToPNG(~, image, fullPath)¶

WRITETOPNG Writes an image matrix as png file to disk.

Parameters:

ignoredArg (obj) – IO instance.
image (array, NxM) – Image matrix
fullPath (str) – Path to where the image will be saved.

Returns:

Writes image file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.maskInterface3D(this, frameNumber, segmentationFile, imageFile, resultPath, pxPerZInterval, fluoTags, fluoImagePaths)¶

MASKINTERFACE3D Interface to import 3D segmentation data from mask files into TracX internal data format.

Parameters:

ignoredArg (obj) – IO instance.
frameNumber (int) – Image frame number
segmentationFile (str) – Name of segmentation file
imageFile (str) – Name of image file
resultPath (str) – Path to where output should be saved. Defaults to experiment folder.
pxPerZInterval (int) – Conversion factor pixel to z interval
fluoTags (str) – Fluorescent channel identifiers (optional).
fluoImagePaths (str) – Path to fluorescent images

Returns:

Data written directly to disk.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

TracX.@IO.readCellXParameters(~, file)¶

READCELLXPARAMETERS Reads a CellX parameter xml file and stores and returns them as struct. To be used for automatic project configuration such as i.e. image crop.

Parameters:

ignoredArg (obj) – IO instance.
file (str) – Path to CellX parameter xml file

Returns:

ret (:obj:`struct`)

Return type:

CellX parameter as struct.

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeToXLS(~, data, resultFilePath, resultFileName, varargin)¶

WRITETOXLS Writes tracker results to disk as excel spreadsheet.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData instance..
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
varargin (str varchar) –
- sheetName (str): Name of the excel sheet.
- rangeStartCol (str): Range start column. Has to be capital characters i.e. A, B, C, AA.
- rangeStartRow (int): Range start row. Has to be integers i.e. 1,2,3.
- writeVariableNames (bool): Flag, if table variable names (header) should be written. Defaults to true.

Returns:

Writes excel file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

class TracX.@IO.IO¶

Bases: handle

IO class to deal with TracX input and output while reading or writing data to disk.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

IO(utils)¶

IO Constructor of an TracX.IO class to deal with TracX input and output while reading or writing data to disk.

Parameters:: utils (obj) – UTILS instance.
Returns:: Returns a IO object instance.
Return type:: obj (obj)
Authors:: Andreas P. Cuny - initial implementation

Property Summary

convertedImageFileNameArray¶: Converted image file name array

rawImageFileNameArray¶: Raw image file name array

utils¶: TracX.@Utils instance implementing utility methods

Method Summary

convertChallengeFilesToParseable(~, path, setName)¶

CONVERTCHALLENGEFILESTOPARSEABLE Converts files from the tracker challenge into parseable format.

Parameters:

ignoredArg (obj) – IO instance.
path (str) – Path to the images
setName (str) – Name of the dataset.

Returns:

Converted set saved to disk directly.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

convertImageFileNames(this, imageFilePath)¶

CONVERTIMAGEFILENAMES Converts a previously parsed list of raw image file names to a new format. Therby it copies the raw images to a ‘RawImages subfolder and keeps the newly renamed files in the imageFilePath.

Parameters:

ignoredArg (obj) – IO instance.
imageFilePath (str) – Path to the images to be paresed

Returns:

Directly acts on images on the filesystem.

Return type:

void (-)

Note

Run Tracker.io.imageFileNameParser() first.

Authors:: Andreas P. Cuny - initial implementation

convertXLSToCSV(this, fullFileName, dataDelimiter)¶

CONVERTXLSTOCSV Convert a excel spreadsheet to csv table from a file.

Parameters:

this (obj) – IO instance.
fullFileName (str) – Full path and name of file as string.
dataDelimiter (str) – Name or symbol of delimiter

Returns:

Writes text file to disk

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

destackTimepoints(this, inputFilePath, fileRegEx, nTimepoints, nPlanes, direction)¶

DESTACKTIMEPOINTS Destacks a 3D (multipage tiff) stack into single files per time point.

Parameters:

this (obj) – IO instance.
inputFilePath (str) – Path to files.
fileRegEx (str) – File name identifier regular expression
nTimepoints (int) – Number of time points in stack
nPlanes (int) – Number of planes in stack
direction (int) – Direction to destack either planes (0) or timepoints (1).

Returns:

Writes destacked files to disk directly.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

filenameSorterForCellXinput(~, fileNameArray)¶

FILENAMESORTERFORCELLXINPUT Sorts CellX output file names and returns them as well as the number of time points and planes.

Parameters:

this (obj) – IO instance.
fileNameArray (str, 1xK) – Array with filenames to be sorted.
dataDelimiter (str) – Name or symbol of delimiter

Returns:

sortedFilenames ((array, 1xK)) – Array with sorted file names.
checkMatrix ((array, 3xK)) – Matrix sorted by frame with timepoints, plane and well position.
nTimePoints ((int, 1xK)) – Number of time points.
nPlanes ((int, 1xK)) – Number of z planes.

Authors:

Thomas Kuendig - initial implementation

imageFileNameParser(this, imageFilePath, imageFileType, varargin)¶

IMAGEFILENMAEPARSER Parses any image file name to convert them to the filename format which is used by Cellx as a standard: :obj: ChannelIdentifier_WellPositionWellPlane_Timepoint.FileType Using regular experssions part in an image name can be identified and converted to a default or custom value.

Parameters:

ignoredArg (obj) – IO instance.
imageFilePath (str) – Path to the images to be paresed
imageFileType (str) – Image file type. Supported are [‘tif’, ‘TIF’, ‘TIFF’, ‘tiff’, ‘png’, … ‘PNG’, ‘JPG’, ‘jpg’]
varargin (str varchar) –
- channelRE (str): Regular expression to identify the image channel.
- positionRE (str): Regular expression to identify the well position.
- planeRE (str): Regular expression to identify the image plane.
- timeRE (bool): Regular expression to identify the image frame number.
- customChannel (str): Custom name for the channel.
- customPosition (str): Custom position name.
- customZIndex (str): Custom image plane index.
- channelNameDict (bool): Channel name dictionary.

Returns:

IO object with the result filled into rawImageFileNameArray and convertedImageFileNameArray.

Return type:

void (-)

Example:

>>> Tracker.io.imageFileNameParser( 'Path\to\folder', 'JPG', 'timeRE', '(?<=time)\d*', 'positionRE', '(?<=Position\()\d*')

Authors:: Andreas P. Cuny - initial implementation

maskInterface3D(this, frameNumber, segmentationFile, imageFile, resultPath, pxPerZInterval, fluoTags, fluoImagePaths)¶

MASKINTERFACE3D Interface to import 3D segmentation data from mask files into TracX internal data format.

Parameters:

ignoredArg (obj) – IO instance.
frameNumber (int) – Image frame number
segmentationFile (str) – Name of segmentation file
imageFile (str) – Name of image file
resultPath (str) – Path to where output should be saved. Defaults to experiment folder.
pxPerZInterval (int) – Conversion factor pixel to z interval
fluoTags (str) – Fluorescent channel identifiers (optional).
fluoImagePaths (str) – Path to fluorescent images

Returns:

Data written directly to disk.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

orientationCompressor(~, vector3D)¶

ORIENTATIONCOMPRESSOR Compresses the orientation vector into a single number. Note: Vector should be already of unit length!

Parameters:

ignoredArg (obj) – IO instance.
vector3D (array) – 3D vector

Returns:

tag – Orientation incompressed format.

Return type:

int

Authors:

Thomas Kuendig - initial implementation

readCellXParameters(~, file)¶

READCELLXPARAMETERS Reads a CellX parameter xml file and stores and returns them as struct. To be used for automatic project configuration such as i.e. image crop.

Parameters:

ignoredArg (obj) – IO instance.
file (str) – Path to CellX parameter xml file

Returns:

ret (:obj:`struct`)

Return type:

CellX parameter as struct.

Authors:

Andreas P. Cuny - initial implementation

readFromXML(~, configuration, file)¶

READFROMXML Reads a TracX configuration xml file and stores the parameters in the ParameterConfiguration object.

Parameters:

ignoredArg (obj) – IO instance.
configuration (obj) – TrackerConfiguration object.
file (str) – Path to parameter xml file

Returns:

configuration (:obj:`obj`) – object directly and returns it parametrized.

Return type:

Configuration. Acts on TrackerConfiguration

Authors:

Andreas P. Cuny - initial implementation

readImageToGrayScale(~, pathToFile, varargin)¶

READIMAGETOGRAYSCALE loads an image and converts it to gray scale if it has 3 channels (RGB). Gray conversion is performed as follows: img = (R+G+B)/3

Parameters:

ignoredArg (obj) – IO instance.
pathToFile (str) – Path to image file.
varargin – [x, y, w-1, h-1] imageCropCoordinateArray used to crop theloaded image to this size.

Returns:

image (:obj:`array`, NxM) – the size given by imageCropCoordinateArray

Return type:

Image matrix, optionally cropped to

Authors:

Sotiris Dimopoulos - initial implementation in CellX Andreas P. Cuny - Adaptation for TracX

readImageToRGB(~, imageFilePath, varargin)¶

READIMAGETORGB loads an image as RGB matrix

Parameters:

ignoredArg (obj) – IO instance.
imageFilePath (str) – Path to image file.
varargin – [x, y, w-1, h-1] imageCropCoordinateArray used to crop the loaded image to this size.

Returns:

Image matrix, optionally cropped to the size specified by imageCropCoordinateArray.

Return type:

image (array, NxM)

Authors:

Andreas P. Cuny - initial implementation

readSegmentationData(this, pathName, fileNameArray, varargin)¶

READSEGMENTATIONDATA Reads segmentation data. Currently it supports the CellX format where segmentation data is split into a file per image frame.

Parameters:

this (obj) – IO instance.
pathName (str) – The path to where the data is stored.
fileNameArray (str) – Array of filename(s) of the data to import.
varargin (str varchar) –
- maxNrOfFrames (str): Max number of files to import (if not full experimental data of a time series should be imported.
- dataDelimiter (str): Data delimiter (‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’).

Returns:

data (struct) – Returns segmentation data as stuct, with fieldnames corresponding to column headers of raw data.
dataMatrix (array) – Data as matrix in a cell for each frame in fileNameArray
fieldNameArray (array) – Array of cell arrays with the column header names of the imported data for each frame.

Authors:

Andreas P. Cuny - initial implementation

readSegmentationMask(this, pathToFile)¶

Parameters:

ignoredArg (obj) – IO instance.
pathToFile (str) – Path to mask file.

Returns:

Segmentation mask matrix.

Return type:

mask (array, NxM)

Authors:

Andreas P. Cuny - initial implementation

stackZPlanes(~, inputFilePath, fileRegEx, planeRegEx, convert)¶

STACKZPLANES Stacks single file z planes into one multipage tiff.

Parameters:

ignoredArg (obj) – IO instance.
inputFilePath (str) – File path to images
fileRegEx (str) – File identifier regular expression
planeRegEx (str) – File z plane identifier regular expression
convert (bool) – Bool if stack should be converted.

Returns:

uRemnants – Unique remnants.

Return type:

str

Authors:

Thomas Kuendig - initial implementation

writeBudNeckCellSegmentationMaskImage(~, maskDilated, foundEdgesFilled, trackIndexArray, cellCenterXArray, cellCenterYArray, segmentationResultDir, frameNumber, imageCropCoordinateArray)¶

WRITEBUDNECKCELLSEGMENTATIONMASKIMAGE Detect bud neck marker from fluorescence images. A ROF denoising is first applied and then an edge detection to get an array of pixel that each bud covers.

Parameters:

ignoredArg (obj) – IO instance.
maskDilated (array, NxM) – Segmentation mask. Dilated such that cells touch each others.
foundEdgesFilled (array, NxM) – Budneck segmentation mask.
trackIndexArray (array, 1xK) – Track index array
cellCenterXArray (array, 1xK) – Cell center x array
cellCenterYArray (array, 1xK) – Cell center y array
segmentationResultDir (str) – Path to segmentation results.
frameNumber (int) – Image frame number
imageCropCoordinateArray (array) – Image crop coordinates

Returns:

Writes the output image directly to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToCSV(~, data, resultFilePath, resultFileName, dataDelimiter)¶

WRITETOCSV Writes tracker results to disk in csv format.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData instance..
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
dataDelimiter (str) – Name or symbol of delimiter

Returns:

Writes text file to disk

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToMAT(~, data, resultFilePath, resultFileName, varargin)¶

WRITETOMAT Writes tracker results to disk in mat format.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData.
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file

Returns:

Writes text file to disk

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToPNG(~, image, fullPath)¶

WRITETOPNG Writes an image matrix as png file to disk.

Parameters:

ignoredArg (obj) – IO instance.
image (array, NxM) – Image matrix
fullPath (str) – Path to where the image will be saved.

Returns:

Writes image file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToTIF(~, image, fullPath)¶

WRITETOTIF Writes an image matrix as tif file to disk.

Parameters:

ignoredArg (obj) – IO instance.
image (array, NxM) – Image matrix
fullPath (str) – Path to where the image will be saved.

Returns:

Writes image file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToTXT(~, data, resultFilePath, resultFileName, dataDelimiter)¶

WRITETOTEXT Writes tracker results to disk in txt format.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData instance..
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
dataDelimiter (str) – Name or symbol of delimiter

Returns:

Writes text file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToXLS(~, data, resultFilePath, resultFileName, varargin)¶

WRITETOXLS Writes tracker results to disk as excel spreadsheet.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData instance..
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
varargin (str varchar) –
- sheetName (str): Name of the excel sheet.
- rangeStartCol (str): Range start column. Has to be capital characters i.e. A, B, C, AA.
- rangeStartRow (int): Range start row. Has to be integers i.e. 1,2,3.
- writeVariableNames (bool): Flag, if table variable names (header) should be written. Defaults to true.

Returns:

Writes excel file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeToXML(~, configuration, file)¶

WRITETOXML Writes a TracX configuration xml file with all the parameters stored in the ParameterConfiguration and ProjectConfiguration object.

Parameters:

ignoredArg (obj) – IO instance. instance
configuration (obj) – TrackerConfiguration object.
file (str) – Path to TracX configuration xml file and its name.

Returns:

Writes to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

writeTrackerDataToDisk(this, joinedTrackerDataTable, resultFilePath, resultFileName, varargin)¶

WRITETRACKERDATATODISK Writes tracker results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (object) – IO instance..
joinedTrackerDataTable (table) – Table with joined TrackerData
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
varargin (str varchar) –
- fileType (str): Save tracker results with specific file types (‘txt’, ‘csv’, ‘mat’).
- dataDelimiter (str): Data delimiter (‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’).

Returns:

Writes data file to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.readImageToRGB(~, imageFilePath, varargin)¶

READIMAGETORGB loads an image as RGB matrix

Parameters:

ignoredArg (obj) – IO instance.
imageFilePath (str) – Path to image file.
varargin – [x, y, w-1, h-1] imageCropCoordinateArray used to crop the loaded image to this size.

Returns:

Image matrix, optionally cropped to the size specified by imageCropCoordinateArray.

Return type:

image (array, NxM)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeToTIF(~, image, fullPath)¶

WRITETOTIF Writes an image matrix as tif file to disk.

Parameters:

ignoredArg (obj) – IO instance.
image (array, NxM) – Image matrix
fullPath (str) – Path to where the image will be saved.

Returns:

Writes image file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.imageFileNameParser(this, imageFilePath, imageFileType, varargin)¶

Parameters:

ignoredArg (obj) – IO instance.
imageFilePath (str) – Path to the images to be paresed
imageFileType (str) – Image file type. Supported are [‘tif’, ‘TIF’, ‘TIFF’, ‘tiff’, ‘png’, … ‘PNG’, ‘JPG’, ‘jpg’]
varargin (str varchar) –
- channelRE (str): Regular expression to identify the image channel.
- positionRE (str): Regular expression to identify the well position.
- planeRE (str): Regular expression to identify the image plane.
- timeRE (bool): Regular expression to identify the image frame number.
- customChannel (str): Custom name for the channel.
- customPosition (str): Custom position name.
- customZIndex (str): Custom image plane index.
- channelNameDict (bool): Channel name dictionary.

Returns:

IO object with the result filled into rawImageFileNameArray and convertedImageFileNameArray.

Return type:

void (-)

Example:

>>> Tracker.io.imageFileNameParser( 'Path\to\folder', 'JPG', 'timeRE', '(?<=time)\d*', 'positionRE', '(?<=Position\()\d*')

Authors:: Andreas P. Cuny - initial implementation

TracX.@IO.filenameSorterForCellXinput(~, fileNameArray)¶

FILENAMESORTERFORCELLXINPUT Sorts CellX output file names and returns them as well as the number of time points and planes.

Parameters:

this (obj) – IO instance.
fileNameArray (str, 1xK) – Array with filenames to be sorted.
dataDelimiter (str) – Name or symbol of delimiter

Returns:

sortedFilenames ((array, 1xK)) – Array with sorted file names.
checkMatrix ((array, 3xK)) – Matrix sorted by frame with timepoints, plane and well position.
nTimePoints ((int, 1xK)) – Number of time points.
nPlanes ((int, 1xK)) – Number of z planes.

Authors:

Thomas Kuendig - initial implementation

TracX.@IO.destackTimepoints(this, inputFilePath, fileRegEx, nTimepoints, nPlanes, direction)¶

DESTACKTIMEPOINTS Destacks a 3D (multipage tiff) stack into single files per time point.

Parameters:

this (obj) – IO instance.
inputFilePath (str) – Path to files.
fileRegEx (str) – File name identifier regular expression
nTimepoints (int) – Number of time points in stack
nPlanes (int) – Number of planes in stack
direction (int) – Direction to destack either planes (0) or timepoints (1).

Returns:

Writes destacked files to disk directly.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

TracX.@IO.writeToTXT(~, data, resultFilePath, resultFileName, dataDelimiter)¶

WRITETOTEXT Writes tracker results to disk in txt format.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData instance..
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
dataDelimiter (str) – Name or symbol of delimiter

Returns:

Writes text file to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.convertImageFileNames(this, imageFilePath)¶

Parameters:

ignoredArg (obj) – IO instance.
imageFilePath (str) – Path to the images to be paresed

Returns:

Directly acts on images on the filesystem.

Return type:

void (-)

Note

Run Tracker.io.imageFileNameParser() first.

Authors:: Andreas P. Cuny - initial implementation

TracX.@IO.readSegmentationData(this, pathName, fileNameArray, varargin)¶

READSEGMENTATIONDATA Reads segmentation data. Currently it supports the CellX format where segmentation data is split into a file per image frame.

Parameters:

this (obj) – IO instance.
pathName (str) – The path to where the data is stored.
fileNameArray (str) – Array of filename(s) of the data to import.
varargin (str varchar) –
- maxNrOfFrames (str): Max number of files to import (if not full experimental data of a time series should be imported.
- dataDelimiter (str): Data delimiter (‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’).

Returns:

data (struct) – Returns segmentation data as stuct, with fieldnames corresponding to column headers of raw data.
dataMatrix (array) – Data as matrix in a cell for each frame in fileNameArray
fieldNameArray (array) – Array of cell arrays with the column header names of the imported data for each frame.

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.readFromXML(~, configuration, file)¶

READFROMXML Reads a TracX configuration xml file and stores the parameters in the ParameterConfiguration object.

Parameters:

ignoredArg (obj) – IO instance.
configuration (obj) – TrackerConfiguration object.
file (str) – Path to parameter xml file

Returns:

configuration (:obj:`obj`) – object directly and returns it parametrized.

Return type:

Configuration. Acts on TrackerConfiguration

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeTrackerDataToDisk(this, joinedTrackerDataTable, resultFilePath, resultFileName, varargin)¶

WRITETRACKERDATATODISK Writes tracker results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (object) – IO instance..
joinedTrackerDataTable (table) – Table with joined TrackerData
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
varargin (str varchar) –
- fileType (str): Save tracker results with specific file types (‘txt’, ‘csv’, ‘mat’).
- dataDelimiter (str): Data delimiter (‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’).

Returns:

Writes data file to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeToCSV(~, data, resultFilePath, resultFileName, dataDelimiter)¶

WRITETOCSV Writes tracker results to disk in csv format.

Parameters:

ignoredArg (obj) – IO instance.
data (table) – Table of TrackerData instance..
resultFilePath (str) – Path to where tracker results should be saved.
resultFileName (str) – Name of result file
dataDelimiter (str) – Name or symbol of delimiter

Returns:

Writes text file to disk

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeToXML(~, configuration, file)¶

WRITETOXML Writes a TracX configuration xml file with all the parameters stored in the ParameterConfiguration and ProjectConfiguration object.

Parameters:

ignoredArg (obj) – IO instance. instance
configuration (obj) – TrackerConfiguration object.
file (str) – Path to TracX configuration xml file and its name.

Returns:

Writes to disk directly.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.writeBudNeckCellSegmentationMaskImage(~, maskDilated, foundEdgesFilled, trackIndexArray, cellCenterXArray, cellCenterYArray, segmentationResultDir, frameNumber, imageCropCoordinateArray)¶

WRITEBUDNECKCELLSEGMENTATIONMASKIMAGE Detect bud neck marker from fluorescence images. A ROF denoising is first applied and then an edge detection to get an array of pixel that each bud covers.

Parameters:

ignoredArg (obj) – IO instance.
maskDilated (array, NxM) – Segmentation mask. Dilated such that cells touch each others.
foundEdgesFilled (array, NxM) – Budneck segmentation mask.
trackIndexArray (array, 1xK) – Track index array
cellCenterXArray (array, 1xK) – Cell center x array
cellCenterYArray (array, 1xK) – Cell center y array
segmentationResultDir (str) – Path to segmentation results.
frameNumber (int) – Image frame number
imageCropCoordinateArray (array) – Image crop coordinates

Returns:

Writes the output image directly to disk.

Return type:

void (-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@IO.stackZPlanes(~, inputFilePath, fileRegEx, planeRegEx, convert)¶

STACKZPLANES Stacks single file z planes into one multipage tiff.

Parameters:

ignoredArg (obj) – IO instance.
inputFilePath (str) – File path to images
fileRegEx (str) – File identifier regular expression
planeRegEx (str) – File z plane identifier regular expression
convert (bool) – Bool if stack should be converted.

Returns:

uRemnants – Unique remnants.

Return type:

str

Authors:

Thomas Kuendig - initial implementation

TracX.@IO.convertChallengeFilesToParseable(~, path, setName)¶

CONVERTCHALLENGEFILESTOPARSEABLE Converts files from the tracker challenge into parseable format.

Parameters:

ignoredArg (obj) – IO instance.
path (str) – Path to the images
setName (str) – Name of the dataset.

Returns:

Converted set saved to disk directly.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

LAP ¶

TracX.@LAP.computeAssignmentCostMatrix(this, oldFrame, newFrame, maxCellCenterDisplacement, maxMajorAxisRotation, individualFunctionPenalty, maxCellSizeDecrease, averageCellSizeGrowth, maxCellSizeIncrease, usedFunctionsForCostMatrix, meanCellDiameter, maxTrackFrameSkipping, displacementWeightingMode, is3DData)¶

COMPUTEASSIGNMENTCOSTMATRIX computes the individual assignement costs for spatial (position), size (area) and rotation (orientation) differences as well as frame skipping and returns the matrices for each cost individually (positionCost: frameSkippingCost) as well as the sum of all costs (totalCost).

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance
newFrame (object) – newFrame TemporaryTrackingData instance
maxCellCenterDisplacement (int, 1x1) – Maximal frame to frame segmentation centroid displacement
maxMajorAxisRotation (float 1x1) – Max allowed major axis rotation in degree.
individualFunctionPenalty (int 1x1) – Individual function penalty
maxCellSizeDecrease (float 1x1) – Maximal allowed frame to frame cell size decrease fraction.
averageCellSizeGrowth (float 1x1) – Average allowed frame to frame cell size growth fraction.
maxCellSizeIncrease (float 1x1) – Maximal allowed frame to frame cell size increase fraction.
usedFunctionsForCostMatrix (array 1x4) – Logical array to select which of the four penalty functions should be used to build the cost matrix.
meanCellDiameter (float 1x1) – Mean segmentation object diameter (cell diameter).
maxTrackFrameSkipping (int 1x1) – Max number of frames a cell is allowed to be missing from a track
displacementWeightingMode (bool) – For quadratic (default) or 1 for linear displacement cost calculation.
is3DData (bool) – Is data 3D. Defaults to 0 for 2D data.

Returns:

totalCost (float IxJ) – Costmatrix with the sum of cost matricies positionCost to frameSkippingCost
positionCost (float IxJ) – Costmatrix for spatial position.
areaCost (float IxJ) – Costmatrix for size difference (area).
rotationCost (float IxJ) – Costmatrix for rotation difference (orientation).
frameSkippingCost (float IxJ) – Costmatrix for frame skipping (segmented object not present/detected on current image frame).

Authors:

Markus Duerr - initial implementation in R (weight_age)

Authors:

Urs Kuechler - translation to Matlab (weight_age)

Authors:

Andreas P. Cuny - Re-implementation and new design for computation of individual cost functions with real physical meaning.

TracX.@LAP.computeOrientationDifference(~, a, b)¶

COMPUTEORIENTATIONDIFFERENCE Calculates the central angle between two orientation vectors

Parameters:

ignoredArg (object) – LAP instance.
a (array) – Orientation vector a
b (array) – Orientation vector b

Returns:

result – Resulting orientation difference

Return type:

double

Authors:

Thomas Kuendig - initial implementation

TracX.@LAP.computeFFPCostMatrix(~, oldFrame, newFrame, individualFunctionPenalty, radius, dCRFM)¶

COMPUTEFFPCOSTMATRIX computes the individual assignement costs for an FFP based tracker based on spatial (position), differences and returns the matrices for each cost individually (positionCost: frameSkippingCost) as well as the sum of all costs (totalCost) to keep the existing structure.

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
individualFunctionPenalty (int 1x1) – Individual function penalty
radius (int 1x1) – Radius for neighbourhood
dCRFM (array NxM) – Cell region fingerprint distances.

Returns:

totalCost (float IxJ) – Costmatrix with the sum of cost matricies
positionCost (float IxJ) – Costmatrix for dCRF
areaCost (float IxJ) – Costmatrix placeholder
rotationCost (float IxJ) – Costmatrix placeholder
frameSkippingCost (float IxJ) – Costmatrix placeholder

Authors:

Andreas P. Cuny - Initial implementation

TracX.@LAP.computeNeighbourhoodMotionCostMatrix(~, oldFrame, newFrame, displacementOfAssignedTracks, maxExpectedMovement, cellCloseNeighbours, individualFunctionPenalty, maxCellSizeDecrease, averageCellSizeGrowth, maxCellSizeIncrease)¶

COMPUTENEIGHBOURHOODMOTIONCOSTMATRIX Computes the individual assignement costs for spatial (position), size (area) differences and returns the matrices for each weighted cost component individually (weightedPositionCost, weightedAreaCost, weightedTotalCost). For computing the individual spatial differences, the individual neighbourhood is considered and the indivudial spatial differeces are compenstated by the minimal difference of its neighbourhood. For the area weight an averageCellSizeGrowth is assumed and the maximal cell size decrease and increase can be specified individually.

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
displacementOfAssignedTracks (array, Kx3) – Displacement of assigned tracks in x,y,z
maxExpectedMovement (float) – Maximum expected segmented centroid movement
cellCloseNeighbours (array) – Array of cell close neighbours
individualFunctionPenalty (int 1x1) – Individual function penalty
maxCellSizeDecrease (float 1x1) – Maximal allowed frame to frame cell size decrease as fraction.
averageCellSizeGrowth (float 1x1) – Average allowed frame to frame cell size growth as fraction.
maxCellSizeIncrease (float 1x1) – Maximal allowed frame to frame cell size increase as fraction.

Returns:

weightedTotalCosts (float nxm) – Costmatrix with the sum of cost matrices weightedpositionCost to weightedAreaCost
weightedPositionCost (float nxm) – Weighted cost matrix for spatial differences (position).
weightedAreaCost (float nxm) – Weighted cost matrix for size differences (area).

Authors:

Ricard Delgado-Gonzalo - initial description of neighbourhood preserved motion https://doi.org/10.1109/ISBI.2010.5490288

Authors:

Cristian Vesari - Implementation of idea above in MATLAB http://dx.doi.org/10.1098/rsif.2016.0705

Authors:

Andreas P. Cuny - Neighbourhood preserved motion implementation for TracX.

TracX.@LAP.fingperprintCostMatrixRefinement(~, newFrame, oldFrame, costMatrix, fingerprintDistThreshold)¶

FINGERPRINTCOSTMATRIXREFINEMENT Refines the cost matrix by setting costs for confirmed/trusted assignments (below fingerprint distance threshold) to 0 and detection of invalid costMatrix rows (all costs above max individual function penalty.

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
costMatrix (double, NxM) – Cost matrix for assignments between old- and newFrame.
fingerprintDistThreshold (float) – fingerprintDistThreshold

Returns:

costMatrix (double NxM) – Refined cost matrix
excludeFromAssignmentIdx (array Nx1) – Logical indicies of rows to exclude from costMatrix.

Authors:

Andreas P. Cuny - initial implementation

TracX.@LAP.mammalianLineageCost(~, oldFrameData, newFrameData, daughterpairTracks, parentTracks, daughterpairTypes, parentTypes)¶

MAMMALIANLINEAGECOST Cost matrix function for mammalian lineage reconstruction in 2 & 3D.

Parameters:

ignoredArg (object) – LAP instance.
oldFrameData (object) – oldFrame TemporaryTrackingData instance.
newFrameData (object) – newFrame TemporaryTrackingData instance.
daughterpairTracks (int, 1xK) – Array of daughterpair tracks
parentTracks (int, 1xJ) – Array of parent tracks
daughterpairTypes (int, 1x1) – Type of daughter pairs (I or II)
parentTypes (int, 1x1) – Type of parents (I or II)

Returns:

cost – Cost matrix

Return type:

array

Authors:

Thomas Kuendig - initial implementation

class TracX.@LAP.LAP¶

LAP class to create cost matricies and solve linear assignment problem.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

LAP()¶

LAP Constructs a TemporaryTrackingData object to create cost matricies and solve linear assignment problem.

Returns:: obj
Return type:: object Returns a TemporaryTrackingData instance.
Authors:: Andreas P. Cuny - initial implementation

Method Summary

computeAssignmentCostMatrix(this, oldFrame, newFrame, maxCellCenterDisplacement, maxMajorAxisRotation, individualFunctionPenalty, maxCellSizeDecrease, averageCellSizeGrowth, maxCellSizeIncrease, usedFunctionsForCostMatrix, meanCellDiameter, maxTrackFrameSkipping, displacementWeightingMode, is3DData)¶

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance
newFrame (object) – newFrame TemporaryTrackingData instance
maxCellCenterDisplacement (int, 1x1) – Maximal frame to frame segmentation centroid displacement
maxMajorAxisRotation (float 1x1) – Max allowed major axis rotation in degree.
individualFunctionPenalty (int 1x1) – Individual function penalty
maxCellSizeDecrease (float 1x1) – Maximal allowed frame to frame cell size decrease fraction.
averageCellSizeGrowth (float 1x1) – Average allowed frame to frame cell size growth fraction.
maxCellSizeIncrease (float 1x1) – Maximal allowed frame to frame cell size increase fraction.
usedFunctionsForCostMatrix (array 1x4) – Logical array to select which of the four penalty functions should be used to build the cost matrix.
meanCellDiameter (float 1x1) – Mean segmentation object diameter (cell diameter).
maxTrackFrameSkipping (int 1x1) – Max number of frames a cell is allowed to be missing from a track
displacementWeightingMode (bool) – For quadratic (default) or 1 for linear displacement cost calculation.
is3DData (bool) – Is data 3D. Defaults to 0 for 2D data.

Returns:

totalCost (float IxJ) – Costmatrix with the sum of cost matricies positionCost to frameSkippingCost
positionCost (float IxJ) – Costmatrix for spatial position.
areaCost (float IxJ) – Costmatrix for size difference (area).
rotationCost (float IxJ) – Costmatrix for rotation difference (orientation).
frameSkippingCost (float IxJ) – Costmatrix for frame skipping (segmented object not present/detected on current image frame).

Authors:

Markus Duerr - initial implementation in R (weight_age)

Authors:

Urs Kuechler - translation to Matlab (weight_age)

Authors:

Andreas P. Cuny - Re-implementation and new design for computation of individual cost functions with real physical meaning.

computeFFPCostMatrix(~, oldFrame, newFrame, individualFunctionPenalty, radius, dCRFM)¶

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
individualFunctionPenalty (int 1x1) – Individual function penalty
radius (int 1x1) – Radius for neighbourhood
dCRFM (array NxM) – Cell region fingerprint distances.

Returns:

totalCost (float IxJ) – Costmatrix with the sum of cost matricies
positionCost (float IxJ) – Costmatrix for dCRF
areaCost (float IxJ) – Costmatrix placeholder
rotationCost (float IxJ) – Costmatrix placeholder
frameSkippingCost (float IxJ) – Costmatrix placeholder

Authors:

Andreas P. Cuny - Initial implementation

computeNeighbourhoodMotionCostMatrix(~, oldFrame, newFrame, displacementOfAssignedTracks, maxExpectedMovement, cellCloseNeighbours, individualFunctionPenalty, maxCellSizeDecrease, averageCellSizeGrowth, maxCellSizeIncrease)¶

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
displacementOfAssignedTracks (array, Kx3) – Displacement of assigned tracks in x,y,z
maxExpectedMovement (float) – Maximum expected segmented centroid movement
cellCloseNeighbours (array) – Array of cell close neighbours
individualFunctionPenalty (int 1x1) – Individual function penalty
maxCellSizeDecrease (float 1x1) – Maximal allowed frame to frame cell size decrease as fraction.
averageCellSizeGrowth (float 1x1) – Average allowed frame to frame cell size growth as fraction.
maxCellSizeIncrease (float 1x1) – Maximal allowed frame to frame cell size increase as fraction.

Returns:

weightedTotalCosts (float nxm) – Costmatrix with the sum of cost matrices weightedpositionCost to weightedAreaCost
weightedPositionCost (float nxm) – Weighted cost matrix for spatial differences (position).
weightedAreaCost (float nxm) – Weighted cost matrix for size differences (area).

Authors:

Ricard Delgado-Gonzalo - initial description of neighbourhood preserved motion https://doi.org/10.1109/ISBI.2010.5490288

Authors:

Cristian Vesari - Implementation of idea above in MATLAB http://dx.doi.org/10.1098/rsif.2016.0705

Authors:

Andreas P. Cuny - Neighbourhood preserved motion implementation for TracX.

computeNewFrameAssignment(this, oldFrame, newFrame, maxCellCenterDisplacement, maxMajorAxisRotation, maxTrackFrameSkipping, individualFunctionPenalty, maxCellSizeDecrease, averageCellSizeGrowth, maxCellSizeIncrease, usedFunctionsForCostMatrix, fingerprintDistThreshold, meanCellDiameter, is3DData)¶

COMPUTENEWFRAMEASSIGNMENT Computes linear assignment and returns track indicies for the subsequent frame (‘newFrame’).

Parameters:

this (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
maxCellCenterDisplacement (int, 1x1) – Maximal frame to frame segmentation centroid displacement
maxMajorAxisRotation (float 1x1) – Max allowed major axis rotation in degree.
maxTrackFrameSkipping (int 1x1) – Max number of frames a cell is allowed to be missing from a track
individualFunctionPenalty (int 1x1) – Individual function penalty
maxCellSizeDecrease (float 1x1) – Maximal allowed frame to frame cell size decrease in percent.
averageCellSizeGrowth (float 1x1) – Average allowed frame to frame cell size growth in percent.
maxCellSizeIncrease (float 1x1) – Maximal allowed frame to frame cell size increase in percent.
usedFunctionsForCostMatrix (array 1x4) – Logical array to select which of the four penalty functions should be used to build the cost matrix.
fingerprintDistThreshold (float 1x1) – CRF threshold
meanCellDiameter (float 1x1) – Mean segmentation object diameter (cell diameter).
is3DData (bool) – Is data 3D. Defaults to 0 for 2D data.

Returns:

newTrackIndex (array) – New track indices array
totalCost (float IxJ) – Costmatrix with the sum of cost matricies positionCost to frameSkippingCost
positionCost (float IxJ) – Costmatrix for spatial position.
areaCost (float IxJ) – Costmatrix for size difference (area).
rotationCost (float IxJ) – Costmatrix for rotation difference (orientation).
frameSkippingCost (float IxJ) – Costmatrix for frame skipping (segmented object not present/detected on current image frame).

Authors:

Andreas P. Cuny - initial implementation

computeOrientationDifference(~, a, b)¶

COMPUTEORIENTATIONDIFFERENCE Calculates the central angle between two orientation vectors

Parameters:

ignoredArg (object) – LAP instance.
a (array) – Orientation vector a
b (array) – Orientation vector b

Returns:

result – Resulting orientation difference

Return type:

double

Authors:

Thomas Kuendig - initial implementation

computeOrientationDifferenceMatrix(this, A, B)¶

COMPUTEORIENTATIONDIFFERENCEMATRIX Computes the orientation difference matrix.

Parameters:

this (object) – LAP instance.
A (array) – Orientation matrix A
B (array) – Orientation matrix B

Returns:

resultMatrix – Resulting matrix

Return type:

double

Authors:

Thomas Kuendig - initial implementation

fingperprintCostMatrixRefinement(~, newFrame, oldFrame, costMatrix, fingerprintDistThreshold)¶

Parameters:

ignoredArg (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
costMatrix (double, NxM) – Cost matrix for assignments between old- and newFrame.
fingerprintDistThreshold (float) – fingerprintDistThreshold

Returns:

costMatrix (double NxM) – Refined cost matrix
excludeFromAssignmentIdx (array Nx1) – Logical indicies of rows to exclude from costMatrix.

Authors:

Andreas P. Cuny - initial implementation

lapjv(~, costMat, varargin)¶

LAPJV Wrapper around the Jonker-Volgenant Algorithm for Linear Assignment Problem. Returns the optimal column indices, ROWSOL, assigned to row in solution, and the minimum COST based on the assignment problem represented by the COSTMAT, where the (i,j)th element represents the cost to assign the jth job to the ith worker.

Parameters:

ignoredArg (object) – LAP instance.
costMat (array, IxJ) – [IxJ, Float] Cost matrix, where the (i,j)th element represents the cost to assign the jth job to the ith worker.
varargin (int, 1x1) – ‘resolution’ (Optional) input can be used to define data resolution to accelerate speed.

Returns:

rowsol (array) – The optimal column indices
cost (array) – Minimum COST based on the assignment problem
v (array) – Dual variables, column reduction numbers.
u (array) – Dual variables, row reduction numbers.
costMat (array) – The reduced cost matrix.

Authors:

Andreas P. Cuny - initial implementation

mammalianLineageCost(~, oldFrameData, newFrameData, daughterpairTracks, parentTracks, daughterpairTypes, parentTypes)¶

MAMMALIANLINEAGECOST Cost matrix function for mammalian lineage reconstruction in 2 & 3D.

Parameters:

ignoredArg (object) – LAP instance.
oldFrameData (object) – oldFrame TemporaryTrackingData instance.
newFrameData (object) – newFrame TemporaryTrackingData instance.
daughterpairTracks (int, 1xK) – Array of daughterpair tracks
parentTracks (int, 1xJ) – Array of parent tracks
daughterpairTypes (int, 1x1) – Type of daughter pairs (I or II)
parentTypes (int, 1x1) – Type of parents (I or II)

Returns:

cost – Cost matrix

Return type:

array

Authors:

Thomas Kuendig - initial implementation

orientationDecompressor(~, tag)¶

ORIENTATIONDECOMPRESSOR Decompresses the linearized orientation vector to its 3D format.

Parameters:

ignoredArg (object) – LAP instance.
tag (array) – Compressed and linearized orientation 3D vector

Returns:

vec – Decompressed orientation vector

Return type:

array Kx3

Authors:

Thomas Kuendig - initial implementation

solveLAP(this, costMatrix, varargin)¶

SOLVELAP Computes linear assignment and returns the assignments for the row and columns of the costMatrix (i.e. oldFrame and newFrame) and the linear assignement location indicies of the costMatrix directly.

Parameters:

this (object) – LAP instance.
costMatrix (float, IxJ) – costMatrix with the total cost of all individual weighting functions.
varargin (float, IxJ) – (Optional) individual weighted costs matrix for i.e. position, area.

Returns:

assignmentRowIdx (int Ix1) – Optimal row indicies
assignmentColIdx (int Ix1) – Optimal column indicies
assignmentLocIdx (int Ix1) – Linear indicies for optimal row and column indicies
assignmentCosts array IxJ – Costs of the final assignment
varargout int – An array for each varargin with the assignmentLocIdx applied of same size.

Authors:

Andreas P. Cuny - initial implementation

TracX.@LAP.lapjv(~, costMat, varargin)¶

Parameters:

ignoredArg (object) – LAP instance.
costMat (array, IxJ) – [IxJ, Float] Cost matrix, where the (i,j)th element represents the cost to assign the jth job to the ith worker.
varargin (int, 1x1) – ‘resolution’ (Optional) input can be used to define data resolution to accelerate speed.

Returns:

rowsol (array) – The optimal column indices
cost (array) – Minimum COST based on the assignment problem
v (array) – Dual variables, column reduction numbers.
u (array) – Dual variables, row reduction numbers.
costMat (array) – The reduced cost matrix.

Authors:

Andreas P. Cuny - initial implementation

TracX.@LAP.solveLAP(this, costMatrix, varargin)¶

Parameters:

this (object) – LAP instance.
costMatrix (float, IxJ) – costMatrix with the total cost of all individual weighting functions.
varargin (float, IxJ) – (Optional) individual weighted costs matrix for i.e. position, area.

Returns:

assignmentRowIdx (int Ix1) – Optimal row indicies
assignmentColIdx (int Ix1) – Optimal column indicies
assignmentLocIdx (int Ix1) – Linear indicies for optimal row and column indicies
assignmentCosts array IxJ – Costs of the final assignment
varargout int – An array for each varargin with the assignmentLocIdx applied of same size.

Authors:

Andreas P. Cuny - initial implementation

TracX.@LAP.orientationDecompressor(~, tag)¶

ORIENTATIONDECOMPRESSOR Decompresses the linearized orientation vector to its 3D format.

Parameters:

ignoredArg (object) – LAP instance.
tag (array) – Compressed and linearized orientation 3D vector

Returns:

vec – Decompressed orientation vector

Return type:

array Kx3

Authors:

Thomas Kuendig - initial implementation

TracX.@LAP.computeOrientationDifferenceMatrix(this, A, B)¶

COMPUTEORIENTATIONDIFFERENCEMATRIX Computes the orientation difference matrix.

Parameters:

this (object) – LAP instance.
A (array) – Orientation matrix A
B (array) – Orientation matrix B

Returns:

resultMatrix – Resulting matrix

Return type:

double

Authors:

Thomas Kuendig - initial implementation

TracX.@LAP.computeNewFrameAssignment(this, oldFrame, newFrame, maxCellCenterDisplacement, maxMajorAxisRotation, maxTrackFrameSkipping, individualFunctionPenalty, maxCellSizeDecrease, averageCellSizeGrowth, maxCellSizeIncrease, usedFunctionsForCostMatrix, fingerprintDistThreshold, meanCellDiameter, is3DData)¶

COMPUTENEWFRAMEASSIGNMENT Computes linear assignment and returns track indicies for the subsequent frame (‘newFrame’).

Parameters:

this (object) – LAP instance.
oldFrame (object) – oldFrame TemporaryTrackingData instance.
newFrame (object) – newFrame TemporaryTrackingData instance.
maxCellCenterDisplacement (int, 1x1) – Maximal frame to frame segmentation centroid displacement
maxMajorAxisRotation (float 1x1) – Max allowed major axis rotation in degree.
maxTrackFrameSkipping (int 1x1) – Max number of frames a cell is allowed to be missing from a track
individualFunctionPenalty (int 1x1) – Individual function penalty
maxCellSizeDecrease (float 1x1) – Maximal allowed frame to frame cell size decrease in percent.
averageCellSizeGrowth (float 1x1) – Average allowed frame to frame cell size growth in percent.
maxCellSizeIncrease (float 1x1) – Maximal allowed frame to frame cell size increase in percent.
usedFunctionsForCostMatrix (array 1x4) – Logical array to select which of the four penalty functions should be used to build the cost matrix.
fingerprintDistThreshold (float 1x1) – CRF threshold
meanCellDiameter (float 1x1) – Mean segmentation object diameter (cell diameter).
is3DData (bool) – Is data 3D. Defaults to 0 for 2D data.

Returns:

newTrackIndex (array) – New track indices array
totalCost (float IxJ) – Costmatrix with the sum of cost matricies positionCost to frameSkippingCost
positionCost (float IxJ) – Costmatrix for spatial position.
areaCost (float IxJ) – Costmatrix for size difference (area).
rotationCost (float IxJ) – Costmatrix for rotation difference (orientation).
frameSkippingCost (float IxJ) – Costmatrix for frame skipping (segmented object not present/detected on current image frame).

Authors:

Andreas P. Cuny - initial implementation

Lineage ¶

TracX.@Lineage.evaluateNewMammalianRoots(this, varargin)¶

EVALUATENEWMAMMALIANROOTS Determination of best lineage for given root cells for mammalian lineage reconstruction.

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- roots (array): Array of lineage roots.

Returns:

Prints reslut to console.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

TracX.@Lineage.getLineageSummary(this)¶

GETLINEAGESUMMARY Returns a condensed version of the cell lineage as a table. Each row is a division event with the columns mother_start_frame, trackindex_mother, daughter_start_frame, trackindex_daughter, division_frame.

Parameters:: this (object) – Lineage instance
Returns:: Lineage summary as table.
Return type:: summaryTable table
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.setParentAndHasBud(this)¶

SETPARENTANDHASBUD Sets the track parent, the probability of the parent being correct and the parent score as well as during which frames the cell has a bud.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.getTreeNodeDurations(this, lineageTree, firstFrame, lastFrame, imageFreq)¶

GETTREENODEDURATIONS Returns a tree object containing the cell cycle duration until cell division.

Parameters:

this (object) – Lineage instance.
lineageTree (obj) – Lineage tree
firstFrame (int) – First frame of experiment
lastFrame (int) – Last frmae of experiment
imageFreq (float) – Image frequency [h].

Returns:

durationTreeObj obj – Duration tree object.
phaseStartIdxNew array – Array with cell cycle phase start indices.
phaseEndIdxNew array – Array with cell cycle phase end indices.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.getTracks2Merge(this)¶

GETTRACKS2MERGE Returns a matrix with the mothers and buds to be merged prior division.

Parameters:: this (object) – Lineage instance.
Returns:: Array with the tracks to merge. Colums are frame_number, mother track_index daughter track_index, mother uuid, daughter uuid
Return type:: tracks2Merge array
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.getRootTrackRelatedDaughterArray(~, trackIndexArray, trackParentArray, rootTrack)¶

GETROOTTRACKRELATEDDAUGHTERARRAY Finds all SegmentationData.track_index directly and indirectly related to a certain track_index of interest (e.g. root of a lineage).

Parameters:

ignoredArg (object) – Lineage instance.
trackIndexArray (array, kx1) – Array with all track indicies track_index
trackParentArray (array, kx1) – Array with all track parents track_parent
rootTrack (int, 1x1) – The lineage tree root track

Returns:

Array containing track_index numbers of to rootTrack related cells. (For all those track indicies the initial cell_parent track_index (rootTrack) can be added to track_lineage

Return type:

rootTrackRelatedCellArray array

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.getRootTrackTreeObject(~, trackIndexArray, trackParentArray, rootTrack, rootTrackRelatedCellArray)¶

GETROOTTRACKTREEOBJECT Constructs a tree lineage tree object for a specified rootTrack (SegmentationData.track_index typically of the first image frame) and all its relatives.

Parameters:

ignoredArg (object) – Lineage instance.
trackIndexArray (array, kx1) – Array with all track indicies track_index
trackParentArray (array, kx1) – Array with all track parents track_parent
rootTrack (int, 1x1) – The lineage tree root track
rootTrackRelatedCellArray (int, jx1) – Related track indices with parent parent == rootTrack

Returns:

Lineage tree object for rootTrack and all its relatives. Can be visualized as cmd text output using lineageTree.tostring or graphically using lineageTree.plotBinaryTree( [], ‘Parent’, figureHandle ‘TextRotation’, 360).

Return type:

lineageTree object

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.detectBudNeckMarkerPixelArray(this, imageDir, fluoLineageFileName, imageCropCoordinateArray, segMaskDilated, divisionMarkerDenoising, divisionMarkerEdgeSensitivityThresh, divisionMarkerConvexAreaLowerThresh, divisionMarkerConvexAreaUpperThresh)¶

DETECTBUDNECKMARKERPIXELARRAY Detect bud neck marker from fluorescence images. A ROF denoising is first applied and then an edge detection to get an array of pixel covered by each bud.

Parameters:

this (object) – Lineage instance
imageDir (str) – Path to image directory
fluoLineageFileName (str) – Fluorescence image file names for the given channel and frame.
imageCropCoordinateArray (array, 1x4) – Array with crop coordinates used during segmentation. Needed to map segmentation cell cennters to correct position within the raw images.
segMaskDilated (array, NxM) – Dilated cell segmentation mask where masks touch each others.
divisionMarkerDenoising (float) – divisionMarkerDenoising
divisionMarkerEdgeSensitivityThresh (float) – divisionMarkerEdgeSensitivityThresh
divisionMarkerConvexAreaLowerThresh (float) – divisionMarkerConvexAreaLowerThresh
divisionMarkerConvexAreaUpperThresh (float) – divisionMarkerConvexAreaUpperThresh

Returns:

budPixelIndiciesArray array – Array of all pixels belonging to a bud.
foundEdgesFilled array NxM – Image after edge detection with filled holes
fluoImgDenoised array NxM – Denoised image

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.generateLineageTreeObject(this, varargin)¶

GENERATELINEAGETREEObject Generates a lineage tree object for one or multiple root cells (i.e. cells on the first image frame).

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- rootIndicies (array): Array of lineage
  root track indices.

Returns:

Array containing a lineage tree object for each rood index.

Return type:

lineageTreeArray (array)

Note

The returned tree object can be visualized in a figure or as text in the console with i.e lineageTreeArray{1}.tostring.

Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.recursiveTrackParentColoring(this, root, color, colormap, trackIndexArray, trackParentArray)¶

RECURSIVETRACKPARENTCOLORING Returns a colormap for recursive track parent coloring.

Parameters:

this (object) – Lineage instance.
root (int) – Root track index.
color (array) – Color.
colormap (array) – Colormap
trackIndexArray (array) – Track index array.
trackParentArray (array) – Track parent array.

Returns:

Colormap

Return type:

colormap array kx3

Authors:

Thomas Kuendig - initial implementation

TracX.@Lineage.getDivisionFrames(this, toRootTrackRelatedCellArray)¶

GETDIVISIONFRAMES Returns an array of the division frames for an array of track indicies such as i.e. lineage root related tracks. It is assumed that the first element is allways the rote of the lineage tree.

Parameters:

this (object) – Lineage instance
toRootTrackRelatedCellArray (int) – Array with to root related track indices.

Returns:

Indices of joined non empty splitted track indices and joined track indices.

Return type:

divisionFrameArray array

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.runMarkerTracking(this, varargin)¶

RUNMARKERTRACKING Runs the tracker algorithm for cell cycle marker channels. To track i.e a bud neck marker.

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- divisionMarkerMaxTrackFrameSkipping (int): Max frame skipping for segmented division marker.
- divisionMarkerMaxObjCenterDisplacement (float): Max displacement for segmented division marker.
- divisionMarkerMaxObjSizeIncrease (float): Max object size increase for segmented division marker.
- divisionMarkerFingerprintHalfWindowSideLength (int): Fingerprint half window side length.
- qc (str): Flag, if quality control images should be written. Defaults to false.

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.setTrackAge(this)¶

SETTRACKAGE Sets the cell age for each track after lineage reconstruction.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.getCellCyclePhaseTable(this)¶

GETCELLCYCLEPHASETABLE Returns the full cell cycle phase table.

Parameters:: this (object) – Lineage instance
Returns:: Full cell cycle table with columns ‘track’, ‘parent’, ‘daughter’, ‘tree’ … ‘generation’, ‘age’, ‘pole1_age’, ‘pole2_age’, ‘g1_st’, ‘g1_e’, … ‘g1_dur’, ‘g2_st’, ‘g2_e’, ‘g2_dur’, ‘div’, ‘seg_st_track’, ‘seg_st_daughter’. Abbreviations st, start, e, end, dur, duration, div, division, seg_st, segmentation start.
Return type:: t table
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.setSignalInNucleus(this, channel, qc, varargin)¶

SETSIGNALINNUCLEUS Quantifies if a signal is in the nucleus when it is larger than the mean + 0.5 * mad.

Parameters:

this (object) – Lineage instance
channel (int) – Number of the fluorescent channel to read.
qc (bool) – Flag if quality control images should be generated.
varargin (str varchar) –
- minSignalLength (int): Minimal length of signal [frames]. Defaults to 2.

Returns:

Binary array. 1 if signal is in nucleus, 0 otherwise.

Return type:

sigInNuc array

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.setBirthToDivPhase(this)¶

SETBIRTHTODIVPHASE Sets the phase between birth and cell division, also known as G2 or S/G2/M phase in budding yeast.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.setTrackGeneration(this)¶

SETTRACKGENERATION Sets the cell generation for each track after lineage reconstruction.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.getLineProfileVerification(~, img, x, y, resizeFactor, divisionMarkerLineProfileLength, divisionMarkerLineProfilePeakLowerBound, divisionMarkerLineProfilePeakUpperBound)¶

GETLINEPROFILEVERIFICATION Computes a line profile between two centroids and returns true if a peak in the line profile above a given threshold is is found. Additionaly the retrived line profile is returned in its raw and resampled form.

Parameters:

ignoredArg (object) – Lineage instance.
img (array, NxM) – Image matrix.
x (array, kx1) – Spatial coordinates of start and endpoint for line profile in x.
y (array, kx1) – Spatial coordinates of start and endpoint for line profile in y.
resizeFactor (int, 1x1) – Number used to resize the image matrix to increase processing speed. Attention: To high downscaleing can result in false positive line profiles since only a few pixel remain.
divisionMarkerLineProfileLength (int) – Max length to resample the profiles to.
divisionMarkerLineProfilePeakLowerBound (int) – Lower bound to accept a peak in the Line profile.
divisionMarkerLineProfilePeakUpperBound (int) – Upper bound to accept a peak in the Line profile.

Returns:

validPair bool – Binarization of the result. 1 if at least one peak was detected. 0 if no peak was detected.
lineProfileResampled array Array of resampled line profile.
lineProfileRaw array Array of raw line profile – with applied resizing.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.setParentMamDivCells(this, startFrame, endFrame, imageFrameNumberArray, joinTracks, printOutput)¶

SETPARENTMAMDIVCELLS Determines the relationship between daughter and mother cell of symmetricaly dividing cells.

Parameters:

this (object) – Lineage instance
startFrame (int) – Number of the first frame of the project where to start the mother daughter assignment.
endFrame (int) – Number of the last frame of the project where to end the mother daughter assignment.
imageFrameNumberArray (object) – Array with all image frame numbers for current project. This function evaluates this array in the range startFrame to endFrame.
joinTracks (bool) – Flag to join tracks. Defaults to true.
printOutput (bool) – Flag, if output should be printed to console.

Returns:

Indices of joined non empty splitted track indices and joined track indices.

Return type:

stable array

Authors:

Andreas P. Cuny - initial implementation

TracX.@Lineage.resolveCircAssignment(this)¶

RESOLVECIRCASSIGNMENT Aims to resove circular mother-daugher assignments where each track assignes each other as parent. The incorect assignment will be deleted.

Parameters:: this (object) – Lineage instance.
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.splitSurvivingParentTracks(this)¶

SPLITSURVIVINGPARENTTRACKS Splits surviving parent tracks during mammalian lineage reconstruction.

Parameters:: this (object) – Tracker instance
Return type:: void -
Authors:: Thomas Kuendig - initial implementation

TracX.@Lineage.getNewickFormat(this, varargin)¶

GETNEWICKFORMAT Converts the LineageTreeObject/Summary to a phytree object or to the Newick format.

Parameters:

this (obj) – Lineage object
varargin (str varchar) –
- rootIndicies (int): The lineage root; Any ‘track_index’ number.
- plotToFigure (bool): Flag if lineage tree should be plotted to a figure. Defaults to false.

Returns:

B ((array, nx2)) – Numeric array of size [NUMBRANCHES X 2] in which every row represents a branch of the tree. It contains two pointers to the branch or leaf nodes, which are its children.
nwk ((str):) – NEWICK tree string format.
phyStruct ((stuct):) – Phytree struct.
figH ((object):) – Phytree figure handle.
Authors: – Andreas P. Cuny - initial implementation Eline Y. Bijman - initial implementation

TracX.@Lineage.getBkgCorrSig(~, x, y, track, minSigLength, qc)¶

GETBKGCURRSIG Returns a background corrected nuclear signal for G1 determination.

Parameters:

ignoredArg (object) – Lineage instance
x (array) – Array of frame numbers of signal.
y (array) – Array with raw signal
track (int) – Current track index. track indices.
minSigLength (int) – Minimal length of signal to be considered.
qc (bool) – Flag, if quality control images should be written.

Returns:

bkgCorrSig array – Array with background corrected signal.
validSigL array – Logical array for valid signal.
fh handle – Figure handle of quality control image

Authors:

Andreas P. Cuny - initial implementation

class TracX.@Lineage.Lineage¶

Bases: handle

LINEAGE Implements functionalities to reconstruct the cell lineage for asymmetrically and symetrically dividing cell types.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

Lineage(data, config)¶

LINEAGE Constructs a Lineage object to reconstruct the generalogy for asymmetric and symmetric dividing cells.

Returns:: Returns a Lineage object instance.
Return type:: obj (-)
Authors:: Andreas P. Cuny - initial implementation

Property Summary

cellCyclePhaseTable¶: Cell cycle phases

configuration¶: TracX.@TrackerConfiguration TrackerConfiguration instance with the tracking parameters and project metadata.

data¶: TracX.@TrackerData instance stores all segmentation, quantification and lineage data.

fingerprint¶: TracX.@Fingerprint instance implementing fingerprinting methods.

io¶: TracX.@IO instance implementing read/write methods.

lap¶: TracX.@LAP instance implementing tracking methods.

lineageData¶: TracX.@LineageData instance implementing temporary lineage data storage.

lineageTable¶: Lineage summary table.

motion¶: TracX.@Motion instance implementing motion methods.

tracks2Merge¶: Matrix with info about mother and buds to merge prior division

unresolvedTempLinAss¶: TracX.@TemporaryLineageAssignment instance implementing temporary assignments methods.

utils¶: TracX.@Utils instance implementing utility methods.

Method Summary

asymmetricalLineageReconstruction(this)¶

ASYMMETRICALLINEAGERECONSTRUCTION Runs the asymmetrical lineage reconstruction i.e for budding yeast.

Parameters:: this (object) – Lineage instance
Return type:: void (-)

detectBudNeckMarkerPixelArray(this, imageDir, fluoLineageFileName, imageCropCoordinateArray, segMaskDilated, divisionMarkerDenoising, divisionMarkerEdgeSensitivityThresh, divisionMarkerConvexAreaLowerThresh, divisionMarkerConvexAreaUpperThresh)¶

DETECTBUDNECKMARKERPIXELARRAY Detect bud neck marker from fluorescence images. A ROF denoising is first applied and then an edge detection to get an array of pixel covered by each bud.

Parameters:

this (object) – Lineage instance
imageDir (str) – Path to image directory
fluoLineageFileName (str) – Fluorescence image file names for the given channel and frame.
imageCropCoordinateArray (array, 1x4) – Array with crop coordinates used during segmentation. Needed to map segmentation cell cennters to correct position within the raw images.
segMaskDilated (array, NxM) – Dilated cell segmentation mask where masks touch each others.
divisionMarkerDenoising (float) – divisionMarkerDenoising
divisionMarkerEdgeSensitivityThresh (float) – divisionMarkerEdgeSensitivityThresh
divisionMarkerConvexAreaLowerThresh (float) – divisionMarkerConvexAreaLowerThresh
divisionMarkerConvexAreaUpperThresh (float) – divisionMarkerConvexAreaUpperThresh

Returns:

budPixelIndiciesArray array – Array of all pixels belonging to a bud.
foundEdgesFilled array NxM – Image after edge detection with filled holes
fluoImgDenoised array NxM – Denoised image

Authors:

Andreas P. Cuny - initial implementation

evaluateNewMammalianRoots(this, varargin)¶

EVALUATENEWMAMMALIANROOTS Determination of best lineage for given root cells for mammalian lineage reconstruction.

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- roots (array): Array of lineage roots.

Returns:

Prints reslut to console.

Return type:

void (-)

Authors:

Thomas Kuendig - initial implementation

generateLineageTreeObject(this, varargin)¶

GENERATELINEAGETREEObject Generates a lineage tree object for one or multiple root cells (i.e. cells on the first image frame).

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- rootIndicies (array): Array of lineage
  root track indices.

Returns:

Array containing a lineage tree object for each rood index.

Return type:

lineageTreeArray (array)

Note

The returned tree object can be visualized in a figure or as text in the console with i.e lineageTreeArray{1}.tostring.

Authors:: Andreas P. Cuny - initial implementation

getBkgCorrSig(~, x, y, track, minSigLength, qc)¶

GETBKGCURRSIG Returns a background corrected nuclear signal for G1 determination.

Parameters:

ignoredArg (object) – Lineage instance
x (array) – Array of frame numbers of signal.
y (array) – Array with raw signal
track (int) – Current track index. track indices.
minSigLength (int) – Minimal length of signal to be considered.
qc (bool) – Flag, if quality control images should be written.

Returns:

bkgCorrSig array – Array with background corrected signal.
validSigL array – Logical array for valid signal.
fh handle – Figure handle of quality control image

Authors:

Andreas P. Cuny - initial implementation

getCellCyclePhaseTable(this)¶

GETCELLCYCLEPHASETABLE Returns the full cell cycle phase table.

Parameters:: this (object) – Lineage instance
Returns:: Full cell cycle table with columns ‘track’, ‘parent’, ‘daughter’, ‘tree’ … ‘generation’, ‘age’, ‘pole1_age’, ‘pole2_age’, ‘g1_st’, ‘g1_e’, … ‘g1_dur’, ‘g2_st’, ‘g2_e’, ‘g2_dur’, ‘div’, ‘seg_st_track’, ‘seg_st_daughter’. Abbreviations st, start, e, end, dur, duration, div, division, seg_st, segmentation start.
Return type:: t table
Authors:: Andreas P. Cuny - initial implementation

getDivisionFrames(this, toRootTrackRelatedCellArray)¶

Parameters:

this (object) – Lineage instance
toRootTrackRelatedCellArray (int) – Array with to root related track indices.

Returns:

Indices of joined non empty splitted track indices and joined track indices.

Return type:

divisionFrameArray array

Authors:

Andreas P. Cuny - initial implementation

getLineProfileVerification(~, img, x, y, resizeFactor, divisionMarkerLineProfileLength, divisionMarkerLineProfilePeakLowerBound, divisionMarkerLineProfilePeakUpperBound)¶

Parameters:

ignoredArg (object) – Lineage instance.
img (array, NxM) – Image matrix.
x (array, kx1) – Spatial coordinates of start and endpoint for line profile in x.
y (array, kx1) – Spatial coordinates of start and endpoint for line profile in y.
resizeFactor (int, 1x1) – Number used to resize the image matrix to increase processing speed. Attention: To high downscaleing can result in false positive line profiles since only a few pixel remain.
divisionMarkerLineProfileLength (int) – Max length to resample the profiles to.
divisionMarkerLineProfilePeakLowerBound (int) – Lower bound to accept a peak in the Line profile.
divisionMarkerLineProfilePeakUpperBound (int) – Upper bound to accept a peak in the Line profile.

Returns:

validPair bool – Binarization of the result. 1 if at least one peak was detected. 0 if no peak was detected.
lineProfileResampled array Array of resampled line profile.
lineProfileRaw array Array of raw line profile – with applied resizing.

Authors:

Andreas P. Cuny - initial implementation

getLineageSummary(this)¶

Parameters:: this (object) – Lineage instance
Returns:: Lineage summary as table.
Return type:: summaryTable table
Authors:: Andreas P. Cuny - initial implementation

getNewickFormat(this, varargin)¶

GETNEWICKFORMAT Converts the LineageTreeObject/Summary to a phytree object or to the Newick format.

Parameters:

this (obj) – Lineage object
varargin (str varchar) –
- rootIndicies (int): The lineage root; Any ‘track_index’ number.
- plotToFigure (bool): Flag if lineage tree should be plotted to a figure. Defaults to false.

Returns:

B ((array, nx2)) – Numeric array of size [NUMBRANCHES X 2] in which every row represents a branch of the tree. It contains two pointers to the branch or leaf nodes, which are its children.
nwk ((str):) – NEWICK tree string format.
phyStruct ((stuct):) – Phytree struct.
figH ((object):) – Phytree figure handle.
Authors: – Andreas P. Cuny - initial implementation Eline Y. Bijman - initial implementation

getRootTrackRelatedDaughterArray(~, trackIndexArray, trackParentArray, rootTrack)¶

GETROOTTRACKRELATEDDAUGHTERARRAY Finds all SegmentationData.track_index directly and indirectly related to a certain track_index of interest (e.g. root of a lineage).

Parameters:

ignoredArg (object) – Lineage instance.
trackIndexArray (array, kx1) – Array with all track indicies track_index
trackParentArray (array, kx1) – Array with all track parents track_parent
rootTrack (int, 1x1) – The lineage tree root track

Returns:

Array containing track_index numbers of to rootTrack related cells. (For all those track indicies the initial cell_parent track_index (rootTrack) can be added to track_lineage

Return type:

rootTrackRelatedCellArray array

Authors:

Andreas P. Cuny - initial implementation

getRootTrackTreeObject(~, trackIndexArray, trackParentArray, rootTrack, rootTrackRelatedCellArray)¶

GETROOTTRACKTREEOBJECT Constructs a tree lineage tree object for a specified rootTrack (SegmentationData.track_index typically of the first image frame) and all its relatives.

Parameters:

ignoredArg (object) – Lineage instance.
trackIndexArray (array, kx1) – Array with all track indicies track_index
trackParentArray (array, kx1) – Array with all track parents track_parent
rootTrack (int, 1x1) – The lineage tree root track
rootTrackRelatedCellArray (int, jx1) – Related track indices with parent parent == rootTrack

Returns:

Return type:

lineageTree object

Authors:

Andreas P. Cuny - initial implementation

getTracks2Merge(this)¶

GETTRACKS2MERGE Returns a matrix with the mothers and buds to be merged prior division.

Parameters:: this (object) – Lineage instance.
Returns:: Array with the tracks to merge. Colums are frame_number, mother track_index daughter track_index, mother uuid, daughter uuid
Return type:: tracks2Merge array
Authors:: Andreas P. Cuny - initial implementation

getTreeNodeDurations(this, lineageTree, firstFrame, lastFrame, imageFreq)¶

GETTREENODEDURATIONS Returns a tree object containing the cell cycle duration until cell division.

Parameters:

this (object) – Lineage instance.
lineageTree (obj) – Lineage tree
firstFrame (int) – First frame of experiment
lastFrame (int) – Last frmae of experiment
imageFreq (float) – Image frequency [h].

Returns:

durationTreeObj obj – Duration tree object.
phaseStartIdxNew array – Array with cell cycle phase start indices.
phaseEndIdxNew array – Array with cell cycle phase end indices.

Authors:

Andreas P. Cuny - initial implementation

mammalianLineageReconstruction(this)¶

MAMMALIANLINEAGERECONSTRUCTION Runs the symmetrical lineage reconstruction for mammalian cells with convex shapes.

Parameters:: this (object) – Lineage instance
Return type:: void (-)

recursiveTrackParentColoring(this, root, color, colormap, trackIndexArray, trackParentArray)¶

RECURSIVETRACKPARENTCOLORING Returns a colormap for recursive track parent coloring.

Parameters:

this (object) – Lineage instance.
root (int) – Root track index.
color (array) – Color.
colormap (array) – Colormap
trackIndexArray (array) – Track index array.
trackParentArray (array) – Track parent array.

Returns:

Colormap

Return type:

colormap array kx3

Authors:

Thomas Kuendig - initial implementation

resolveCircAssignment(this)¶

RESOLVECIRCASSIGNMENT Aims to resove circular mother-daugher assignments where each track assignes each other as parent. The incorect assignment will be deleted.

Parameters:: this (object) – Lineage instance.
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

runLineageReconstruction(this, varargin)¶

RUNLINEAGERECONSTRUCTION Starts lineage reconstruction based on tracking results for symmetrically and asymmetrically dividing cells.

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- symmetricalDivision (bool): Flag, defining which lineage reconstruction approach to use. Defaults to is asymmetrical divison (0).
- writeControlImages (bool): Flag, to save lineage control images segmentation are written out. Defaults to false.
- nuclearMarkerChannel (int): Fluorescent channel number depicting a nuclear marker.
- maxFrameEvalAfterBirth (int): Max number of frames after brith to consider a MD pair.

Return type:

void (-)

runMarkerTracking(this, varargin)¶

RUNMARKERTRACKING Runs the tracker algorithm for cell cycle marker channels. To track i.e a bud neck marker.

Parameters:

this (object) – Lineage instance
varargin (str varchar) –
- divisionMarkerMaxTrackFrameSkipping (int): Max frame skipping for segmented division marker.
- divisionMarkerMaxObjCenterDisplacement (float): Max displacement for segmented division marker.
- divisionMarkerMaxObjSizeIncrease (float): Max object size increase for segmented division marker.
- divisionMarkerFingerprintHalfWindowSideLength (int): Fingerprint half window side length.
- qc (str): Flag, if quality control images should be written. Defaults to false.

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

setBirthToDivPhase(this)¶

SETBIRTHTODIVPHASE Sets the phase between birth and cell division, also known as G2 or S/G2/M phase in budding yeast.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

setLineageTable(this)¶

SETLINEAGETABLE Sets the lineage summary table.

Parameters:: this (object) – Lineage instance
Return type:: void (-)

setParentAndHasBud(this)¶

SETPARENTANDHASBUD Sets the track parent, the probability of the parent being correct and the parent score as well as during which frames the cell has a bud.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

setParentMamDivCells(this, startFrame, endFrame, imageFrameNumberArray, joinTracks, printOutput)¶

SETPARENTMAMDIVCELLS Determines the relationship between daughter and mother cell of symmetricaly dividing cells.

Parameters:

this (object) – Lineage instance
startFrame (int) – Number of the first frame of the project where to start the mother daughter assignment.
endFrame (int) – Number of the last frame of the project where to end the mother daughter assignment.
imageFrameNumberArray (object) – Array with all image frame numbers for current project. This function evaluates this array in the range startFrame to endFrame.
joinTracks (bool) – Flag to join tracks. Defaults to true.
printOutput (bool) – Flag, if output should be printed to console.

Returns:

Indices of joined non empty splitted track indices and joined track indices.

Return type:

stable array

Authors:

Andreas P. Cuny - initial implementation

setSignalInNucleus(this, channel, qc, varargin)¶

SETSIGNALINNUCLEUS Quantifies if a signal is in the nucleus when it is larger than the mean + 0.5 * mad.

Parameters:

this (object) – Lineage instance
channel (int) – Number of the fluorescent channel to read.
qc (bool) – Flag if quality control images should be generated.
varargin (str varchar) –
- minSignalLength (int): Minimal length of signal [frames]. Defaults to 2.

Returns:

Binary array. 1 if signal is in nucleus, 0 otherwise.

Return type:

sigInNuc array

Authors:

Andreas P. Cuny - initial implementation

setTrackAge(this)¶

SETTRACKAGE Sets the cell age for each track after lineage reconstruction.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

setTrackGeneration(this)¶

SETTRACKGENERATION Sets the cell generation for each track after lineage reconstruction.

Parameters:: this (object) – Lineage instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

splitSurvivingParentTracks(this)¶

SPLITSURVIVINGPARENTTRACKS Splits surviving parent tracks during mammalian lineage reconstruction.

Parameters:: this (object) – Tracker instance
Return type:: void -
Authors:: Thomas Kuendig - initial implementation

symmetricalLineageReconstruction(this)¶

SYMMETRICALLINEAGERECONSTRUCTION Runs the symmetrical lineage reconstruction (rod shaped cells).

Parameters:: this (object) – Lineage instance
Return type:: void (-)

validateTmpLinAss(this)¶

VALIDATETMPLINASS Validates temporary mother daughter (MD) assignments based on how often an overlapping assignment was found and with which budneck marker track. Assignments where a marker track is used for different MD pairs will be modified by keeping the one pair with the most detections. The others will get the second longest assignment or if there is none these will be deleted.

Parameters:: this (object) – Tracker instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

TracX.@Lineage.validateTmpLinAss(this)¶

Parameters:: this (object) – Tracker instance
Return type:: void -
Authors:: Andreas P. Cuny - initial implementation

LineageData ¶

TracX.@LineageData.moveToVeryOld(this, selectedTrackArray, neighbourhoodSearchRadius)¶

MOVETOVERYOLD Moves temporary data stored in OldFrame to VeryOld.

Parameters:

this (object) – LineageData instance
selectedTrackArray (array, kx1) – Array of selected track indicies to move.
neighbourhoodSearchRadius (int) – Radius in pixel within an other point defined by the coordinate arrays x and y is considered to be a neighbour of (x_i,y_i). neighbourhoodSearchRadius

Returns:

Array of track idndicies to change.

Return type:

trackIdxToChange array NxM

Authors:

Andreas P. Cuny - initial implementation

TracX.@LineageData.getCloseCellNeighbourIdx(~, xCoordinateArray, yCoordinateArray, neighbourhoodSearchRadius)¶

GETCLOSECELLNEIGHBOURIDX Returns a square logical matrix of size length(x) where as 1 corresponds to a neighbour within the neighbourhoodSearchRadius.

Parameters:

ignoredArg (object) – LineageData instance
xCoordinateArray (array, kx1) – Array with x coordinates
yCoordinateArray (array, kx1) – Array with y coordinates
neighbourhoodSearchRadius (int) – Radius in pixel within an other point defined by the coordinate arrays x and y is considered to be a neighbour of (x_i,y_i). neighbourhoodSearchRadius

Returns:

Square logical matrix selecting the neighbours within neighbourhoodSearchRadius.

Return type:

closeNeighboursIdx array NxM

Authors:

Andreas P. Cuny - initial implementation

class TracX.@LineageData.LineageData¶

Bases: handle

LINEAGEDATA Creates an object to store data generated during lineage reconstruction such as i.e. segmentation and quantification of bud neck marker Myo1 in S. cerevisiae.

Authors:: Andreas P. Cuny - initial implementation

Property Summary

NewFrame¶: NewFrame to keep obj frame properties for tracking

OldFrame¶: OldFrame to keep obj frame properties for tracking

VeryOld¶: VeryOld to keep obj frame properties for tracking

numberOfTracks¶: Max number of tracks

obj_area¶: Area of segmented object.

obj_center_x¶: X component of segmented object center.

obj_center_y¶: Y component of segmented object center.

obj_center_z¶: Z component of segmented object center.

obj_channel_id¶: Image channel id of segmented object.

obj_close_neighbour¶: Neighbourhood of each object

obj_dif_x¶: old to newFrame displacement in x.

obj_dif_y¶: old to newFrame displacement in y.

obj_dif_z¶: old to newFrame displacement in z.

obj_filtered_dif_x¶: Filtered old to newFrame displacement in x.

obj_filtered_dif_y¶: Filtered old to newFrame displacement in x.

obj_filtered_dif_z¶: Filtered old to newFrame displacement in x.

obj_fluoImgDenoised¶

chl_n}.

Type:: Denoised image of obj_channel_id {obj1
Type:: obj_n, chl_1

obj_fluo_mean¶: Mean denoised signal of segmented object.

obj_fluo_total¶: Total denoised signal of segmented object.

obj_frame¶: Image frame number of segmented object.

obj_index¶: Unique segmentation object label for each frame.

obj_major_axis¶: Major axis of segmented object.

obj_minor_axis¶: Minor axis of segmented object.

obj_orientation¶: Orientation of segmented object.

obj_parent_fluo_mean¶: Mean denoised signal of parent cell of segmented object (i.e. background).

obj_parent_fluo_total¶: Total denoised signal of parent cell of segmented object (i.e. background).

obj_parent_seg_mask_id¶: Cell segmentation mask id overlaping with object.

obj_parent_track_index¶: Trackindex of parent cell.

obj_parent_uuid¶: UUID of parent cell.

obj_perimeter¶: Perimeter of segmented object.

obj_pixelIdxList¶

chl_n}.

Type:: Pixel indicies list of segmented object {obj1
Type:: obj_n, chl_1

obj_track_age¶: Track age of each obj

obj_track_fingerprint_real¶: Track fingerprint real

obj_track_index¶: Track index of obj

track_fingerprint_real_distance¶: Track fingerprint read distance

uuid¶: Primary key (unique identifier for each object).

Method Summary

InitializeVeryOld(this, assignmentRowIdx, maxTrackFrameSkipping)¶

INITIALIZEVERYOLD Initailizes the VeryOld property of the Tracker with data from OldFrame.

Parameters:

this (object) – LineageData instance
assignmentRowIdx (int) – Row index of track assignment.
maxTrackFrameSkipping (int) – Max tolerated frames a track is allowed to be missing.

Returns:

LineageData instance.

Return type:

this object

clearMarkerTracking(this)¶

CLEANMARKGERTRACKING Deletes all previous assignments made during marker trakcing (for cell cycle determination of asymmetrically dividing cells).

Parameters:: this (object) – LineageData instance
Return type:: void (-)

copyResultsToTrackerData(this, dataToSave, fieldName, emptyDataLocIdx, oldFrameLocIdx, frameNumber)¶

COPYRESULTSTOTRACKERDATA Copies results of the frame by frame tracking to the data store TracX.TrackerData.

Parameters:

this (object) – LineageData instance
dataToSave (str) – Empty array (cell, nan) of the correct size to hold the data to save.
fieldName (str) – String with fieldname where to add new values.
emptyDataLocIdx (array) – Location indicies of empty data.
oldFrameLocIdx (array) – OldFrame location indicies for track_index.
frameNumber (int) – Frame number for which the fieldName data should be added.

Return type:

void (-)

evaluateObjSigAroundTrustedFrames(this, trustedFrames, currDaughter, currMother)¶

EVALUATEOBJSIGAROUNDTRUSTEDFRAMES Evaluates the signal of the detected object around the trusted frames of mother daughter candidate pairs.

Parameters:

this (object) – LineageData instance
trustedFrames (array, kx1) – Array of trusted frames.
currDaughter (int) – Track index of current daughter.
currMother (int) – Track index of current mother.

Returns:

LineageData instance.

Return type:

this object

getCloseCellNeighbourIdx(~, xCoordinateArray, yCoordinateArray, neighbourhoodSearchRadius)¶

GETCLOSECELLNEIGHBOURIDX Returns a square logical matrix of size length(x) where as 1 corresponds to a neighbour within the neighbourhoodSearchRadius.

Parameters:

ignoredArg (object) – LineageData instance
xCoordinateArray (array, kx1) – Array with x coordinates
yCoordinateArray (array, kx1) – Array with y coordinates
neighbourhoodSearchRadius (int) – Radius in pixel within an other point defined by the coordinate arrays x and y is considered to be a neighbour of (x_i,y_i). neighbourhoodSearchRadius

Returns:

Square logical matrix selecting the neighbours within neighbourhoodSearchRadius.

Return type:

closeNeighboursIdx array NxM

Authors:

Andreas P. Cuny - initial implementation

getConditionalFieldArray(this, fieldName, fieldNameCond, Condition)¶

GETCONDITIONALFIELDARRAY Returns an array with all the data for a given fieldName (SegmentationData property) matching a given condition for the fieldNameCon (SegmentationData property).

Parameters:

this (object) – LineageData instance
fieldName (str) – String with fieldname where to get values from.
fieldNameCond (str) – String with fieldname to match the condition
Condition (array) – : Array with condition to match the match with the fieldNameCond.

Returns:

Array of selected data.

Return type:

ret array

getFieldArrayForFrame(this, fieldName, frameNumber)¶

GETFIELDARRAYFORFRAME Returns an array with all the data for a given fieldName (LineageData property) for a given frameNumber (image frame).

Parameters:

this (object) – LineageData instance
fieldName (str) – String with fieldname where to get values from.
frameNumber (int) – Frame number for which the fieldName data should be returned.

Returns:

Array of selected data.

Return type:

ret array

getNumberOfRowsFromFrame(this, frameNumber)¶

GETNUMBEROFROWSFORFRAME Returns the number of rows in the SegmentationData object for the selected frameNumber.

Parameters:

this (object) – LineageData instance
frameNumber (int) – Frame number for which the data should be retrieved.

Returns:

Number of rows in LineageData for frameNumber.

Return type:

nRows (int)

getTrackIndexStorageIndicies(this)¶

GETTRACKINDEXSTORAGEINDICIES Returns indicies of track_index where to store them.

Parameters:

this (object) – LineageData instance

Returns:

oldFrameIdx (array) – OldFrame indicies for track_index.
emptyDataIdx (array) – Indicies of empty data.

initializeCellCloseNeighbours(this, neighbourRadius, nUniqueFrames)¶

INITIALIZECELLCLOSENEIGHBOURS Initializes the cell neighbourhood index matrix for all cells within neighbourRadius related fields of the LineageData object.

Parameters:

this (object) – LineageData instance
neighbourRadius (int) – Distance in pixel to consider other cells to be a neighbouring cell.
nUniqueFrames (int) – Max number of frames to initialize neighbourhood.

Returns:

LineageData instance.

Return type:

this object

initializeNewFrame(this, frameNumber)¶

INITIALIZENEWFRAME Initailizes the NewFrame property of the Tracker with data from the Tracker.Data object for the current image frame (frameNumber).

Parameters:

this (object) – LineageData instance
frameNumber (int) – Frame number of subsequent image frame.

Returns:

Initializes the LineageData.NewFrame object and returns LineageData.

Return type:

this object

initializeOldFrame(this)¶

INITIALIZEOLDFRAME Initailizes the OldFrame property for Lineage marker tracker with data from the LineageData object for the first image frame (frameNumber i.e. 1).

Parameters:: this (object) – LineageData instance
Returns:: LineageData instance.
Return type:: this object

moveToVeryOld(this, selectedTrackArray, neighbourhoodSearchRadius)¶

MOVETOVERYOLD Moves temporary data stored in OldFrame to VeryOld.

Parameters:

this (object) – LineageData instance
selectedTrackArray (array, kx1) – Array of selected track indicies to move.
neighbourhoodSearchRadius (int) – Radius in pixel within an other point defined by the coordinate arrays x and y is considered to be a neighbour of (x_i,y_i). neighbourhoodSearchRadius

Returns:

Array of track idndicies to change.

Return type:

trackIdxToChange array NxM

Authors:

Andreas P. Cuny - initial implementation

saveTrackingAssignmentsToTrackerData(this, frameNumber, dataToSave)¶

SAVETRACKINGASSIGNMENTSTOTRACKERDATA Update the temporary data (oldFrame) by joining newFrame and veryOld for the next frame track assignment iteration.

Parameters:

this (object) – LineageData instance
frameNumber (int) – Frame number for which the data should be saved.
dataToSave (array) – New tracking assignment data to be saved.

Return type:

void (-)

setFieldArrayForFrame(this, fieldName, frameNumber, fieldDataArray)¶

SETFIELDARRAYFORFRAME Sets data for a particular fieldname in the SegmentationData object of TrackerData.

Parameters:

this (object) – LineageData instance
fieldName (str) – String with fieldname where to add new values.
frameNumber (int) – Frame number for which the fieldName data should be added.
fieldDataArray (array) – Data to add to fieldName.

Return type:

void (-)

setObjParent(this, daughters, mothers, motherCandidates, frameOccurance)¶

SETOBJPARENT Sets the parent (cell) of the current segmented object (budneck marker signal).

Parameters:

this (object) – LineageData instance
daughters (array) – Array of Track indices for the daughters.
mothers (array) – Array of Track indices for the mothers.
motherCandidates (array) – Array of Track indices for the mother candidates.
frameOccurance (array) – Array of frame numbers for mother daughter pairs.

Returns:

LineageData instance.

Return type:

this object

setUUID(this)¶

SETUUID Sets a unique id for each object in LineageData over the whole project to facilitate the selection of data. :param this: LineageData instance :type this: object

Returns:: LineageData instance.
Return type:: this object

updateTemporaryTrackingDataForNextFrameEvaluation(this, neighbourhoodSearchRadius)¶

UPDATETEMPORARYTRACKINGDATAFORNEXTFRAMEEVALUATION Update the temporary data (oldFrame) by joining newFrame and veryOld for the next frame track assignment iteration.

Parameters:

this (object) – LineageData instance
neighbourRadius (int) – Distance in pixel to consider other cells to be a neighbouring cell.

Return type:

void (-)

Motion ¶

TracX.@Motion.getInvalidVectors(~, x, y, z, dx, dy, dz, neighbourMatrix, meanCellDiameter, nStd)¶

GETINVALIDVECTORS Tries to find invalid vectors based on an exceptional long vector distance (due to miss assignment). Vector lengths above n times the standard deviation from the mean are identified as invalid.

Parameters:

ignoredArg (int) – Motion instance
x (array, Nx1) – Array of X coordinates of the vectors.
y (array, Nx1) – Array of Y coordinates of the vectors.
dx (array, Nx1) – Array of dX coordinates of the vectors.
dy (array, Nx1) – Array of dY coordinates of the vectors.
neighbourMatrix (bool, NxN) – Logical matrix of neighbours of x and y.
meanCellDiameter (float, 1x1) – TracX.ParameterConfiguration.meanCellDiameter
nStd (int, 1x1) – : Nr of standard deviations to keep from the mean vector length of the vector field.

Returns:

invalidVectorsIdx (array Nx1) – Logical indicies of invalid vector lengths.
vecLength (array Nx1) – Array of common vector lengths.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Motion.filterVectorField(~, X, Y, Z, dX, dY, dZ, radiusSupportX, radiusSupportY, radiusSupportZ)¶

FILTERVECTORFIELD Filters a vector field by calculating a Gaussian-weighted average of neighboring vector components at each position in the vector field.

The support of the Gaussian weighting kernel is defined as the radius of the 2D Gaussian from the center to the location where the support falls to a 1% of the central value.

Parameters:

ignoredArg (object) – Motion instance
X (array, Nx1) – Array of X coordinates of the vector field.
Y (array, Nx1) – Array of Y coordinates of the vector field.
dX (array, Nx1) – Array of X components at each position in the vector field.
dY (array, Nx1) – Array of Y components at each position in the vector field.
radiusSupportX (int) – Radius of the Gaussian weighting function support in X direction
radiusSupportY (int) – Radius of the Gaussian weighting function support in Y direction

Returns:

wdX (array Nx1) – Filtered components ate the X positions with calculated Gaussian weights
wdY (array Nx1) – Filtered components ate the Y positions with calculated Gaussian weights.

Authors:

Aaron Ponti - initial implementation in Python

Authors:

Andreas P. Cuny - Translation to Matlab

class TracX.@Motion.Motion¶

MOTION class to deal with cell motion and filter vectorns on consecutive images.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

Motion()¶

MOTION Constructs a Motion object to deal with cell motion and filter vectorns on consecutive images.

Returns:: obj – Returns a Motion instance
Return type:: object
Authors:: Andreas P. Cuny - initial implementation

Method Summary

filterVectorField(~, X, Y, Z, dX, dY, dZ, radiusSupportX, radiusSupportY, radiusSupportZ)¶

FILTERVECTORFIELD Filters a vector field by calculating a Gaussian-weighted average of neighboring vector components at each position in the vector field.

The support of the Gaussian weighting kernel is defined as the radius of the 2D Gaussian from the center to the location where the support falls to a 1% of the central value.

Parameters:

ignoredArg (object) – Motion instance
X (array, Nx1) – Array of X coordinates of the vector field.
Y (array, Nx1) – Array of Y coordinates of the vector field.
dX (array, Nx1) – Array of X components at each position in the vector field.
dY (array, Nx1) – Array of Y components at each position in the vector field.
radiusSupportX (int) – Radius of the Gaussian weighting function support in X direction
radiusSupportY (int) – Radius of the Gaussian weighting function support in Y direction

Returns:

wdX (array Nx1) – Filtered components ate the X positions with calculated Gaussian weights
wdY (array Nx1) – Filtered components ate the Y positions with calculated Gaussian weights.

Authors:

Aaron Ponti - initial implementation in Python

Authors:

Andreas P. Cuny - Translation to Matlab

getInvalidVectors(~, x, y, z, dx, dy, dz, neighbourMatrix, meanCellDiameter, nStd)¶

Parameters:

ignoredArg (int) – Motion instance
x (array, Nx1) – Array of X coordinates of the vectors.
y (array, Nx1) – Array of Y coordinates of the vectors.
dx (array, Nx1) – Array of dX coordinates of the vectors.
dy (array, Nx1) – Array of dY coordinates of the vectors.
neighbourMatrix (bool, NxN) – Logical matrix of neighbours of x and y.
meanCellDiameter (float, 1x1) – TracX.ParameterConfiguration.meanCellDiameter
nStd (int, 1x1) – : Nr of standard deviations to keep from the mean vector length of the vector field.

Returns:

invalidVectorsIdx (array Nx1) – Logical indicies of invalid vector lengths.
vecLength (array Nx1) – Array of common vector lengths.

Authors:

Andreas P. Cuny - initial implementation

interpolateVectorComponents(~, x, y, fdX, fdY, fdZ, Lia, neighbourLocIdxMatrix)¶

INTERPOLATEVECTORCOMPONENTS Averages vector components by its neighbourhood.

Parameters:

ignoredArg (object) – Motion instance
x (array, Nx1) – Array of X coordinates of all cells.
y (array, Nx1) – Array of Y coordinates of all cells.
fdX (array, Nx1) – Array of Gaussian filtered X components at matching position (identical cells) in the vector field.
fdY (array, Nx1) – Array of Gaussian filtered Y components at matching position (identical cells) in the vector field.
Lia (array, Nx1) – Location indicies for dfX and dfY into X and Y.
neighbourLocIdxMatrix (array, Nx1) – Location indicies of X,Y neighbourhood

Returns:

wdX (array Nx1) – Filtered components ate the X positions with averaged components.
wdY (array Nx1) – Filtered components ate the Y positions with averaged components.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Motion.interpolateVectorComponents(~, x, y, fdX, fdY, fdZ, Lia, neighbourLocIdxMatrix)¶

INTERPOLATEVECTORCOMPONENTS Averages vector components by its neighbourhood.

Parameters:

ignoredArg (object) – Motion instance
x (array, Nx1) – Array of X coordinates of all cells.
y (array, Nx1) – Array of Y coordinates of all cells.
fdX (array, Nx1) – Array of Gaussian filtered X components at matching position (identical cells) in the vector field.
fdY (array, Nx1) – Array of Gaussian filtered Y components at matching position (identical cells) in the vector field.
Lia (array, Nx1) – Location indicies for dfX and dfY into X and Y.
neighbourLocIdxMatrix (array, Nx1) – Location indicies of X,Y neighbourhood

Returns:

wdX (array Nx1) – Filtered components ate the X positions with averaged components.
wdY (array Nx1) – Filtered components ate the Y positions with averaged components.

Authors:

Andreas P. Cuny - initial implementation

NonAssignedTracks ¶

class TracX.@NonAssignedTracks.NonAssignedTracks¶

Bases: handle

NONASSIGNEDTRACKS This class holds the minimal required information of the non assigned tracks after each round of tracking improvement evaluation.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

NonAssignedTracks()¶

NONASSIGNEDTRACKS Constructs a NonAssignedTracks object instance to keep teporary frame data during tracking.

Returns:: obj – Returns NonAssignedTracks instance.
Return type:: object
Authors:: Andreas P. Cuny - initial implementation

Property Summary

cell_area¶: cell_area

cell_center_x¶: cell_center_x

cell_center_y¶: cell_center_y

cell_center_z¶: cell_center_z

cell_filtered_dif_x¶: cell_filtered_dif_x

cell_filtered_dif_y¶: cell_filtered_dif_y

cell_filtered_dif_z¶: cell_filtered_dif_z

cell_orientation¶: cell_orientation

maxTrackFrameSkipping¶: ParameterConfigurationmaxTrackFrameSkipping

track_age¶: track_age

track_assignment_fraction¶: track_assignment_fraction

track_fingerprint_real¶: track_fingerprint_real

track_fingerprint_real_distance¶: track_fingerprint_real_distance

track_index¶: track_index

Method Summary

addCell(this, data, varargin)¶

ADDCELL Adds a cell to TracX.NonAssignedTracks instance to keep teporary the data of non assigned tracks.

Parameters:

this (object) – NonAssignedTracks instance.
data (array) – Data array in order of properties
varargin (array) – Optional input

Returns:

Adds data to NonAssignedTracks directly.

Return type:

void (-)

evaluateTrackAge(this)¶

EVALUTATETRACKAGE Evaluates track age and removes cell above maxTrackFrameSkipping threshold.

Parameters:: this (object) – NonAssignedTracks instance.
Returns:: Adds data to NonAssignedTracks directly.
Return type:: void (-)

getCellStruct(this)¶

GETCELLSTRUCT Returns data as struct.

Parameters:: this (object) – NonAssignedTracks instance.
Returns:: Data from TracX.NonAssignedTracks as formated struct.
Return type:: ret (struct)

increaseTrackAge(this)¶

INCREASETRACKAGE Increases track age by one.

Parameters:: this (object) – NonAssignedTracks instance.
Returns:: Acts on NonAssignedTracks directly
Return type:: void (-)

merge(~, structA, structB)¶

MERGE Merges two structs.

Parameters:

ignoredArg (object) – NonAssignedTracks instance.
structA (struct) – Struct A
structB (struct) – Struct B

Returns:

Merged data

Return type:

merged (struct)

removeCell(this, track_index)¶

REMOVECELL Removes a cell from TracX.NonAssignedTracks instance.

Parameters:

this (object) – NonAssignedTracks instance.
track_index (array) – Track indices of data to be removed

Returns:

Removes data from NonAssignedTracks directly.

Return type:

void (-)

setMaxTrackFrameSkipping(this, maxTrackFrameSkipping)¶

SETMAXTRACKFRAMESKIPPING Sets the max track frame skipping threshold.

Parameters:

this (object) – NonAssignedTracks instance.
maxTrackFrameSkipping (int) – Max track frame skipping threshold

Returns:

Acts on NonAssignedTracks directly

Return type:

void (-)

ProjectConfiguration ¶

class TracX.@ProjectConfiguration.ProjectConfiguration¶

Bases: handle

PROJECTCONFIGURATION This class creates an object containing all information required for a tracking an experiment such as path to image files, segmentation results and where to save tracking results for the Tracker. It tries to identify the number and type of image channels as well as well positions from the image filenames directly. The convention used is the following: ChannelID_WellPosition_ImageFrameNumber.FileType. Where as the ChannelID defines the different image modalities such as BrightField, Fluorescence channels such as e.g. GFP, YFP, PC (phase contrast) etc. WellPosition is 000000 if only one position was imaged or if a multi well experiment was performet it is based on well plate derived format in decimal system e.g. 030200 (e.g. C2; C = ‘03’ and 2 = ‘02’ and no z level = ‘00’). ImageFrameNumber is the number describing the image frame in a long term experiment. FileType is the file type used. Default is tiff. (YouScope naming convenction).

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

ProjectConfiguration()¶

PROJECTCONFIGURATION Constructs an empty ProjectConfiguration object.

Returns:: ProjectConfiguration instance
Return type:: this (object)

Property Summary

cellDivisionType¶: Cell division type

controlPrefix¶: Prefix for segmentation control files.

fluoFileArray¶: Array of all fluorescent image file names

fluoImageIdentifier¶: Identifiers for fluorescence images (e.g. gfp, yfp).

fluoLineageFileArray¶: Array of all fluorescent image file names needed to reconstruct the cell lineage

fontSize¶: Default fontsize for plotting.

imageBitDepth¶: Image bit depth

imageCropCoordinateArray¶: Array with crop coordinates used during segmentation. Needed to map segmentation cell centers to correct position within the raw images (for CellX segmentation data).

imageCropCoordinatePriorReversionArray¶: Array with crop coordinates used during segmentation as given previous to reversion mapping to raw data size.

imageDepth¶: Image number of Z planes

imageDir¶: Image directory to be used in the current project.

imageFileArray¶: Array of all image file names

imageFileFormat¶: Default imageFileFormat for image and mask import / export.

imageFingerprintFileArray¶: Array of (ideally) out-of-focus Brigthfield image file names to be used to compute unique fingerprints. In fact any channel can be used.

imageFrameNumberArray¶: All image frame numbers of the experiment identifying each existing timepoint.

imageHeight¶: Image height

imageMaxSampleValue¶: Image max sample value

imageMinSampleValue¶: Image min sample value

imagePositionArray¶: All experiment positions (based on well plate derived format in decimal system e.g. 0302 (C = ‘03’ and 2 = ‘02’) C2.

imagePrefixArray¶: All image prefixes of the experiment.

imageWidth¶: Image width

maskPrefix¶: Prefix for segmentation mask files.

nFramesToImport¶: Number of frames to import. If for e.g. not all files should be tracked.

projectName¶: Name of ccurrent project (i.e. experiment name).

segmentationControlFileArray¶: Array of all segmentation control image file names

segmentationResultDir¶: Directory containing the segmentation results for the current project. Images in imageDir have to be segmented with e.g. CellX prior to tracking.

segmentationResultFileArray¶: Array of all segmentation result text file names

segmentationResultMaskFileArray¶: Array of all segmentation result mask file names

segmentationResultMatFileArray¶: Array of all segmentation result mat file names

trackerEndFrame¶: End frame number where the tracker should terminate.

trackerPrefix¶: Prefix for tracking outputs.

trackerResultMaskFileArray¶: Array of all tracking result mask file names (relabeled segmentation masks [i.e cell_index -> track_index]).

trackerResultsDir¶: The directory where the tracking results should be saved.

trackerStartFrame¶: Starting frame number of where the tracker should start.

Method Summary

addFluoImage(this, fluoImgFile)¶

ADDFLUOIMAGE Adds the fluo image identifier.

Parameters:

this (object) – ProjectConfiguration instance.
fluoImgFile (str) – Fluorescence image file name.

Return type:

void (-)

addFluoImageTag(this, fluoImgFile, tag)¶

ADDFLUOIMAGETAG Adds the fluorescence channel tags / identifiers to the array.

Parameters:

this (object) – ProjectConfiguration instance.
fluoImgFile (str) – Fluorescence image file name.
tag (str) – Fluorescence image file name channel identifier.

Return type:

void (-)

checkProjectConfiguration(this)¶

CHECKPROJECTCONFIGURATION Checks if all values in the ProjectConfiguration object are defined.

Parameters:: this (object) – ProjectConfiguration instance.
Return type:: void (-)

createProjectConfiguration(this, projectName, imageDir, segmentationResultDir, fileIdentifierFingerprintImages, fileIdentifierWellPositionFingerprint, fileIdentifierCellLineage, imageCropCoordinateArray, varargin)¶

CREATEPROJECTCONFIGURATION creates a ProjectConfiguration object for a given TracX project

Parameters:

this (object) – ProjectConfiguration instance.
projectName (str) – Name of project/experiment.
imageDir (str) – Image directory to be used in the current project.
segmentationResultDir (str) – Directory containing the segmentation results for the current project.
fileIdentifierFingerprintImages (str) – File name identifier for raw Brightfield images.
fileIdentifierWellPositionFingerprint (str) – File name identifier specifing the well position (of a multi well experiment).
fileIdentifierCellLineage (str) – File name identifier of the fluorescent channel images to be used to reconstruct the cell lineage (i.e. bud neck marker)
imageCropCoordinateArray (array, 1x4) – Array with crop coordinates used during segmentation.
varargin (str varchar) –
- nFramesToImport (int): Number of frames to import.
- setCellDivisionType (str): Type of cell division.

Note

The images used for fingerprinting (image filenames) can be specified explicitly (full path) and do not need to reside within the segmentation results dir.

Returns:: ProjectConfiguration instance with all the information needed for tracking.
Return type:: this (object)

ensureResultsDirExists(this)¶

ENSURERESULTSDIREXISTS Tests if project result dir exists. If not it creates the directory.

Parameters:: this (object) – ProjectConfiguration instance.
Return type:: void (-)

getControlImageFormat(this)¶

GETCONTROLIMAGEFORMAT Returns the image file format of the segmentation control images.

Parameters:: this (object) – ProjectConfiguration instance.
Returns:: Retunrs the image format.
Return type:: fmt (str)

getFluoID(this, fluoIdx)¶

GETFLUOID Returns the fluorescence channel identifier at the given index.

Parameters:

this (object) – ProjectConfiguration instance
idx (int) – Index of fluorescence channel in this experiment.

Returns:

Name of fluorescence channel at fluoIdx position.

Return type:

fluoID (str)

getFluoImage(this, idx)¶

GETFLUOIMAGE Returns the folorescence image at the given index.

Parameters:

this (object) – ProjectConfiguration instance.
idx (int) – Index of a fuorescence image in the fluoFileArray array.

Returns:

Returns the fluorescence image name at idx.

Return type:

iFluoImage (str)

getNumberOfFluoImages(this)¶

GETNUMBEROFFLUOIMAGES Returns the number of fluorescence channels.

Parameters:: this (object) – ProjectConfiguration instance
Returns:: Number of fluorescence channels in thisexperiment.
Return type:: nfluoImageIdentifier (int)

setCellDivisionType(this, cellDivisionType)¶

SETCELLDIVISIONTYPE Sets the cell division type for the given TracX project. Symmetrical division is denoted as 0 where as asymmetrical division with 1.

Parameters:

this (object) – ProjectConfiguration instance.
cellDivisionType (str) – Cell division type.

Return type:

void (-)

setControlPrefix(this, controlPrefix)¶

SETCONTROLPREFIX Sets control output filename prefix

Parameters:

this (object) – ProjectConfiguration instance.
controlPrefix (str) – Control file name prefix.

Return type:

void (-)

setFingerprintImageNames(this, fileIdentFingerprintImages, fileIdentWellPosFingerPrint)¶

SETFINGERPRINTIMAGENAMES Sets the image file names used for the fingerprint computation.

Parameters:

this (object) – ProjectConfiguration instance.
fileIdentFingerprintImages (str) – File name identifier of images to be used for fingerprint computation
fileIdentWellPosFingerPrint (str) – File name identifier of images to be used for fingerprint computation specifing the position

Return type:

void (-)

setFluoFileArray(this, array)¶

SETFLUOFILEARRAY Sets the fluorescence image array.

Parameters:

this (object) – ProjectConfiguration instance.
array (str) – Array of fluorescence image file names.

Return type:

void (-)

setFluoImageIdentifier(this, tag)¶

SETFLUOIMAGEIDENTIFIER Sets the fluorescence channel tags / identifiers to the array.

Parameters:

this (object) – ProjectConfiguration instance.
tag (str) – Fluorescence image file name channel identifier.

Return type:

void (-)

setFluoLineageFileArray(this, fileIdentifierCellLineage, fileIdentWellPos)¶

SETFLUOLINEAGEFILEARRAY Sets the fluorescence image files used for mother-daughter relationship detection.

Parameters:

this (object) – ProjectConfiguration instance.
fileIdentifierCellLineage (str) – File name prefix/ identifier cell lineage.
fileIdentWellPos (str) – File name prefix/ identifier position.

Return type:

void (-)

setFontSize(this, fontSize)¶

SETFONTSIZE Sets label font size

Parameters:

this (object) – ProjectConfiguration instance.
fontSize (str) – Label font size.

Return type:

void (-)

setImageBitDepth(this, val)¶

SETIMAGEBITDEPTH Sets the image bit depth.

Parameters:

this (object) – ProjectConfiguration instance.
val (int) – BitDepth (imfinfo)

Return type:

void (-)

setImageCropCoordinateArray(this, crop)¶

SETIMAGECROPCOORDINATEARRAY Sets the segmentation image crop coordinates in case not the entire image frame was segmented.

Parameters:

this (object) – ProjectConfiguration instance.
crop (array, 1x4) – Segmentation crop array [x, y, width, height].

Return type:

void (-)

setImageCropCoordinatePriorReversionArray(this, crop)¶

SETIMAGECROPCOORDINATEPRIORREVERSIONARRAY Sets the segmentation image crop coordinates in case not the entire image frame was segmented and the reversion was applied to map them back to the raw data size.

Parameters:

this (object) – ProjectConfiguration instance.
crop (array, 1x4) – Segmentation crop array [x, y, width, height].

Return type:

void (-)

setImageDepth(this, val)¶

SETIMAGEDEPHT Sets the image depth (number of z planes).

Parameters:

this (object) – ProjectConfiguration instance.
val (int) – Depth (imfinfo)

Return type:

void (-)

setImageDir(this, path)¶

SETIMAGEDIR Sets the directory to all the images of the TracX project.

Parameters:

this (object) – ProjectConfiguration instance.
path (str) – Path to project images.

Return type:

void (-)

setImageFileArray(this, varargin)¶

SETIMAGEFILEARRAY Sets all the image names

Parameters:

this (object) – ProjectConfiguration instance.
varargin (array) – Optional array with image filenames.

Return type:

void (-)

setImageFileFormat(this, imageFileFormat)¶

SETIMAGEFILEFORMAT Sets the image file format.

Parameters:

this (object) – ProjectConfiguration instance.
imageFileFormat (str) – Image file format. Defaults to ‘tif’

Return type:

void (-)

setImageFingerprintFileArray(this, fileNames)¶

SETIMAGEFINGERPRINTFILEARRAY Sets all the image names to be used for fingerprint computation.

Parameters:

this (object) – ProjectConfiguration instance.
fileNames (str) – File names.

Return type:

void (-)

setImageFrameNumberArray(this, frameArray)¶

SETIMAGEFRAMENUMBERARRAY Sets all the image frame numbers. According to the file name convention: ChannelID_WellPosition_ImageFrameNumber.FileType

Parameters:

this (object) – ProjectConfiguration instance.
frameArray (int) – Image frame number array.

Return type:

void (-)

setImageHeight(this, val)¶

SETIMAGEHEIGHT Sets the image height.

Parameters:

this (object) – ProjectConfiguration instance.
val (int) – Image height (imfinfo)

Return type:

void (-)

setImageIdentifiers(this)¶

SETIMAGEIDENTIFIERS Sets all the image identifiers. The convention is ChannelID_WellPosition_ImageFrameNumber.FileType.

Parameters:: this (object) – ProjectConfiguration instance

setImageMaxSampleValue(this, val)¶

SETIMAGEMAXSAMPLEVALUE Sets the image max sample value.

Parameters:

this (object) – ProjectConfiguration instance.
val (int) – MaxSampleValue (imfinfo)

Return type:

void (-)

setImageMinSampleValue(this, val)¶

SETIMAGEMINSAMPLEVALUE Sets the image min sample value.

Parameters:

this (object) – ProjectConfiguration instance.
val (int) – MinSampleValue (imfinfo)

Return type:

void (-)

setImagePositionArray(this, pos)¶

SETIMAGEPOSITIONARRAY Sets the image position array of multi well experiments.

Parameters:

this (object) – ProjectConfiguration instance.
pos (str) – Array with well positions names.

Return type:

void (-)

setImagePrefixArray(this, prefixArray)¶

SETIMAGEPREFIXARRAY Sets all the image prefixes. According to the file name convention: ChannelID_WellPosition_ImageFrameNumber.FileType

Parameters:

this (object) – ProjectConfiguration instance.
prefixArray (str) – Image prefix array.

Return type:

void (-)

setImageProperties(this)¶

SETIMAGEPROPERTIES Sets the image properties such as bit depth, image height and width and min/max sample value.

Parameters:: this (object) – ProjectConfiguration instance.
Return type:: void (-)

setImageWidth(this, val)¶

SETIMAGEWIDTH Sets the image width.

Parameters:

this (object) – ProjectConfiguration instance.
val (int) – Image width (imfinfo)

Return type:

void (-)

setMaskPrefix(this, maskPrefix)¶

SETMASKPREFIX Sets mask output filename prefix

Parameters:

this (object) – ProjectConfiguration instance.
maskPrefix (str) – Mask file name prefix.

Return type:

void (-)

setMatFileNames(this)¶

SETMATFILEMANES Sets all the mat file names.

Parameters:: this (object) – ProjectConfiguration instance.
Return type:: void (-)

setNFramesToImport(this, nFrames)¶

SETNFRAMESTOIMPORT Sets max nr of image frames to import.

Parameters:

this (object) – ProjectConfiguration instance.
nFrames (int) – Max image frame number to import.

Return type:

void (-)

setProjectName(this, projectName)¶

SETPROJECTNAME Sets the directory to all the images of the TracX project.

Parameters:

this (object) – ProjectConfiguration instance.
projectName (str) – Name of project/experiment.

Return type:

void (-)

setSegmentationControlFileArray(this, varargin)¶

SETSEGMENTATIONCONTROLFILEARRAY Sets all the segmentation control files.

Parameters:

this (object) – ProjectConfiguration instance.
varargin (array,) – Array with control filenames.

Return type:

void (-)

setSegmentationFiles(this)¶

SETSEGMENTATIONFILES Sets all the segmentation file names in .txt format (based on CellX segmentation software output)

Parameters:: this (object) – ProjectConfiguration instance.
Return type:: void (-)

setSegmentationResultDir(this, path)¶

SETSEGMENTATIONRESULTDIR Sets the directory to all the segmentation results of the TracX project.

Parameters:

this (object) – ProjectConfiguration instance.
path (str) – Path to project images.

Return type:

void (-)

setSegmentationResultFileArray(this, fileNames)¶

SETSEGMENTATIONRESULTFILEARRAY Sets all the text file names of the segmentation results.

Parameters:

this (object) – ProjectConfiguration instance.
fileNames (str) – File names.

Return type:

void (-)

setSegmentationResultMaskFileArray(this, varargin)¶

SETSEGMENTATIONRESULTMASKFILEARRAY Sets all the segmentation mask file names.

Parameters:

this (object) – ProjectConfiguration instance.
varargin (array,) – Array with mask filenames.

Return type:

void (-)

setSegmentationResultMatFileArray(this, fileNames)¶

SETSEGMENTATIONRESULTMATFILEARRAY Sets all the mat file names of the segmentation results.

Parameters:

this (object) – ProjectConfiguration instance.
fileNames (str) – File names.

Return type:

void (-)

setTrackerEndFrame(this, f)¶

SETTRACKERENDFRAME Sets the end frame of the current tracking project.

Parameters:

this (object) – ProjectConfiguration instance.
f (int) – Last image frame number of track.

Return type:

void (-)

setTrackerPrefix(this, trackerPrefix)¶

SETTRACKERPREFIX Sets tracker output filename prefix

Parameters:

this (object) – ProjectConfiguration instance.
trackerPrefix (str) – Tracker output file name prefix.

Return type:

void (-)

setTrackerResultMaskFileArray(this, varargin)¶

SETTRACKERRESULTMASKFILEARRAY Sets all the tracker mask file names.

Parameters:

this (object) – ProjectConfiguration instance.
varargin (array,) – Array with tracker mask filenames.

Return type:

void (-)

setTrackerResultsDirectory(this, path)¶

SETTRACKERRESULTSDIRECTORY Sets the tracker results directory.

Parameters:

this (object) – ProjectConfiguration instance.
path (str) – Path to tracker results dir.

Return type:

void (-)

setTrackerStartFrame(this, f)¶

SETTRACKERSTARTFRAME Sets the end frame of the current tracking project.

Parameters:

this (object) – ProjectConfiguration instance.
f (int) – First image frame number of track.

Return type:

void (-)

ParameterConfiguration ¶

class TracX.@ParameterConfiguration.ParameterConfiguration¶

Bases: handle, matlab.mixin.CustomDisplay

PARAMETERCONFIGURATION This class creates an object containing all the parameters for the Tracker. The class can create and read a Tracer parameter XML file to automize the tracking process.

Authors:: Andreas P. Cuny - initial implementation

Property Summary

active3DFingerprint¶: > is 3D fingerprint used or closest z stack method > optional param

averageCellSizeGrowth¶: > Fractional cell size growth > (Tracker core) > > Average fractional growth of an identical segmented object between > two subsequent image frames (i.e. cell area or nuclear area) > general param

cellThumbSideLength¶: > Thumbnail side length around the center of a segmented object > (i.e a cell) [px] > (Tracker output generation) > > Used for example to cut out all cells contained in a single track > from all image frames for visualization; > optional param

data3D¶: > is data 2D (0) or 3D (1)? > optional param

debugLevel¶: > Parameter defining the debug level [0,1,2] > (Tracker core) > > Parameter defining the debug level. Level 0 shows no output. > level 1 shows general information (info mode) level 2 shows > additional debug info (debug mode). > advanced param

divisionMarkerAverageObjSizeGrowth¶: > Fractional marker size growth > (Lineage reconstruction) > > Average fractionalgrowth of an identical segmented object between > two subsequent image frames (i.e. cell area or nuclear area) > optional param

divisionMarkerConvexAreaLowerThresh¶: > Convex area lower threshold for division marker segmentation. > (Lineage reconstruction) > > Convex area lower threshold used for division marker segmentation > selection to exclude segmentation artefacts. Only segmented > marker object larger than this treshold are used for the mother > daughter assignment. > optional param

divisionMarkerConvexAreaUpperThresh¶: > Convex area upper threshold for division marker segmentation. > (Lineage reconstruction) > > Convex area upper threshold used for division marker segmentation > selection to exclude segmentation artefacts. Only segmented > marker object smaller than this treshold are used for the mother > daughter assignment. > optional param

divisionMarkerDenoising¶: > ROF denoising parameter theta for division marker. > (Lineage reconstruction) > > ROF de-noising parameter theta used for de-noising fluorescent > images. > optional param

divisionMarkerEdgeSensitivityThresh¶: > Edge sensitivity threshold for division marker segmentation > [0-1] > (Lineage reconstruction) > > Edge sensitivity threshold for division marker segmentation > optional param

divisionMarkerFingerprintHalfWindowSideLength¶: > Half window side length of a square around the centroid > coordinates of a segmented object to be used to for fingerprint > computation [px] > (Lineage reconstruction) > > optional param

divisionMarkerFingerprintMaxConsideredFrequencies¶: > Number of DCT frequencies to include for fingerprint computation > (Lineage reconstruction) > > Number of DCT frequencies to include for fingerprint computation; > optional param

divisionMarkerFingerprintResizeFactor¶: > Resize factor for fingerprint calculation > (Lineage reconstruction) > > Resize factor applied to image matrix before fingerprint > calculation; > optional param

divisionMarkerIndividualFunctionPenalty¶: > Individual function penalty > (Lineage reconstruction) > > Individual penalty maximum for each cost function (e.g. for > position, area, rotation, frame skipping); > optional param

divisionMarkerLineProfileLength¶: > Line profile length. > (Lineage reconstruction) > > Maximum length the line profile between two cell centers are > resampled to. Used to be able to compare the profiles. > optional param

divisionMarkerLineProfilePeakLowerBound¶: > Line profile peak lower bound. > (Lineage reconstruction) > > Lower bound where a peak on line profile between two cell > centers is still accepted. Used as threshold. > optional param

divisionMarkerLineProfilePeakUpperBound¶: > Line profile peak upper bound. > (Lineage reconstruction) > > Upper bound where a peak on line profile between two cell > centers is still accepted. Used as threshold. > optional param

divisionMarkerMaxExpectedMovement¶: > Max expected (linear) movement [px] > (Lineage reconstruction) > > Max expected (linear) movement of one or multiple segmented > objects as i.e colony jump in pixel (depends on pixel > size and magnification). By default it is 2.5 > times the average cell diameter but depends on the actual > largest movement. > optional param

divisionMarkerMaxMajorAxisRotation¶: > Major axis rotation [degrees] > (Lineage reconstruction) > > Max allowed major axis rotation (for round objects such as > S.cerevisiae cells the penalty is not telling and should be set > to 0. The paramater might be important for S.pombe (rod shaped) > where the majoraxis is clearly defined); > optional param

divisionMarkerMaxObjCenterDisplacement¶: > Max displacement allowed [px] > (Lineage reconstruction) > > Max displacement of segmented objects in pixel (depends on pixel > size and magnification) allowed in any direction for subsequent > image frames. > optional param

divisionMarkerMaxObjSizeDecrease¶: > Max allowed fractional marker size decrease > (Lineage reconstruction) > > Penalty for maximum fractional segmented object size decrease for > subsequent image frames; > optional param

divisionMarkerMaxObjSizeIncrease¶: > Max allowed fractional marker size increase > (Lineage reconstruction) > > Penalty for maximum fractional segmented object size increase for > subsequent image frames; > optional param

divisionMarkerMaxTrackFrameSkipping¶: > Max number of frames where a segmented object is allowed to be > missing from a track (miss segmentation, out of focus, etc) > [image frames] > (Lineage reconstruction) > > The number of frames where a segmented object is not present; > optional param

divisionMarkerMeanObjDiameter¶: > Mean cell diameter of all segmented objects in > the experiment [px]. > (Lineage reconstruction) > > Mean cell diameter of all segmented objects of all image frames > of the whole experiment; > optional param

divisionMarkerMeanObjDiameterScalingFactor¶: > Mean cell diameter scaling factor. > (Lineage reconstruction) > > Mean cell diameter scaling factor to scale the max allowed linear > motion of cells in respect to the mean cell diameter. > optional param

divisionMarkerNeighbourhoodSearchRadius¶: > Radius around a centroid cooridnates of a segmented object used > to detect the neighbouring cells [px] > (Lineage reconstruction) > > All centroid cooridnates of segmented objects within the > neighbourhoodSearchRadius are counted as neigbours of a selected > segmented object; > optional param

divisionMarkerRadiusVectorFilterX¶: > Radius equals the first standard deviation of a 2D gaussion > distribution around a cell center in X [px]. > (Lineage reconstruction) > > The radius is used calculate the neighbourhood weighted cell > center displacement in X. The larger the radius, the more more > neighbours are used for weighting the vector component; > optional param

divisionMarkerRadiusVectorFilterY¶: > Radius equals the first standard deviation of a 2D gaussion > distribution around a cell center in Y [px]. > (Lineage reconstruction) > > The radius is used calculate the neighbourhood weighted cell > center displacement in Y. The larger the radius, the more more > neighbours are used for weighting the vector component; > optional param

divisionMarkerRadiusVectorFilterZ¶: > Radius equals the first standard deviation of a 2D gaussion > distribution around a cell center in Z [px]. > (Lineage reconstruction) > > The radius is used calculate the neighbourhood weighted cell > center displacement in Z. The larger the radius, the more more > neighbours are used for weighting the vector component; > optional param

divisionMarkerUsedFunctionsForCostMatrix¶: > Logical array to select which of the four cost functions > should be used to build the final cost matrix. [boolean] > (Lineage reconstruction) > > Array specifying which cost functions to consider to build > final cost matrix; > optional param

fingerprintDistThreshold¶: > Fingerprint distance threshhold [a.u.] > (Tracker core) > > Fingerprint distance threshold below which two fingerprints are > considered to be identical. A fingerprint is computed by a > window around the center of a segmented object on an image > frame. Assignments between two objects with a fingerprint > distance above this threshold are deleted; > general param

fingerprintHalfWindowSideLength¶: > Half window side length of a square around the centroid > coordinates of a segmented object to be used to for fingerprint > computation [px]. > (Tracker core) > > general param

fingerprintMaxConsideredFrequencies¶: > Number of DCT frequencies to include for fingerprint computation > (Tracker core) > > Number of DCT frequencies to include for fingerprint computation; > advanced param

fingerprintResizeFactor¶: > Resize factor for fingerprint calculation > (Tracker core) > > Resize factor applied to image matrix before fingerprint > calculation; > general param

individualFunctionPenalty¶: > Individual function penalty > (Tracker core) > > Individual penalty maximum for each cost function (e.g. for > position, area, rotation, frame skipping); > general param

major¶: Current latest version major of TracX.

maskOverlayAlpha¶: > Trasparency (alpha) level for segmentation mask overlay on raw > images [0-1] > (Tracker output generation) > > Transparency (alpha) level for segmentation mask overlay on raw > images for visualization; > optional param

maxCellCenterDisplacement¶: > Max displacement allowed [px] > (Tracker core) > > Max displacement of segmented objects in pixel (depends on pixel > size and magnification) allowed in any direction for subsequent > image frames. > general param

maxCellSizeDecrease¶: > Max allowed fractional cell size decrease > (Tracker core) > > Penalty for maximum fractional segmented object size decrease for > subsequent image frames; > general param

maxCellSizeIncrease¶: > Max allowed fractional cell size increase > (Tracker core) > > Penalty for maximum fractional segmented object size increase for > subsequent image frames; > general param

maxExpectedMovement¶: > Max expected (linear) movement [px] > (Tracker core) > > Max expected (linear) movement of one or multiple segmented > objects as i.e colony jump in pixel (depends on pixel > size and magnification). By default it is 2.5 > times the average cell diameter but depends on the actual > largest movement.

maxMajorAxisRotation¶: > Major axis rotation [degrees] > (Tracker core) > > Max allowed major axis rotation (for round objects such as > S.cerevisiae cells the penalty is not telling and should be set > to 0. The paramater might be important for S.pombe (rod shaped) > where the majoraxis is clearly defined); > general param

maxTrackFrameSkipping¶: > Max number of frames where a segmented object is allowed to be > missing from a track (miss segmentation, out of focus, etc) > [image frames] > (Tracker core) > > The number of frames where a segmented object is not present; > general param

meanCellDiameter¶: > Mean cell diameter of all segmented objects in > the experiment [px]. > (Tracker core) > > Mean cell diameter of all segmented objects of all image frames > of the whole experiment; > general param

meanCellDiameterScalingFactor¶: > Mean cell diameter scaling factor. > (Tracker core) > > Mean cell diameter scaling factor to scale the max allowed linear > motion of cells in respect to the mean cell diameter. > general param

minor¶: Current latest version minor of TracX.

neighbourhoodSearchRadius¶: > Radius around a centroid cooridnates of a segmented object used > to detect the neighbouring cells [px] > (Tracker core, Lineage reconstruction) > > All centroid cooridnates of segmented objects within the > neighbourhoodSearchRadius are counted as neigbours of a selected > segmented object; > general param

patch¶: Current latest version patch of TracX.

pixelsPerZPlaneInterval¶: > The number of pixels that one Z-stack interval is equal to > (Tracker core) > > Number of pixels per Z-stack interval / step. > optional param

radiusVectorFilterX¶: > Radius equals the first standard deviation of a 2D gaussion > distribution around a cell center in X [px]. > (Tracker core) > > The radius is used calculate the neighbourhood weighted cell > center displacement in X. The larger the radius, the more more > neighbours are used for weighting the vector component; > general param

radiusVectorFilterY¶: > Radius equals the first standard deviation of a 2D gaussion > distribution around a cell center in Y [px]. > (Tracker core) > > The radius is used calculate the neighbourhood weighted cell > center displacement in Y. The larger the radius, the more more > neighbours are used for weighting the vector component; > general param

radiusVectorFilterZ¶: > Radius equals the first standard deviation of a 2D gaussion > distribution around a cell center in Z [px]. > (Tracker core) > > The radius is used calculate the neighbourhood weighted cell > center displacement in Z. The larger the radius, the more more > neighbours are used for weighting the vector component; > general param

usedFunctionsForCostMatrix¶: > Logical array to select which of the four cost functions > should be used to build the final cost matrix. [boolean] > (Tracker core) > > Array specifying which cost functions to consider to build > final cost matrix; > general param

Method Summary

checkParameterConfiguration(this)¶

CHECKPARAMETERCONFIGURATION Checks if all values in the ParameterConfiguration object are defined.

Parameters:: this (object) – ParameterConfiguration instance
Return type:: void -

setActive3DFingerprint(this, value)¶

SETACTIVE3DFINGERPRINT Sets value if 3D fingerprint should be activated.

Parameters:

this (object) – ParameterConfiguration instance.
value (bool) – Value if 3D fingerprint should be activated.

Return type:

void (-)

setAverageCellSizeGrowth(this, value)¶

SETAVERAGECELLSIZEGROWTH Sets value for max allowed fractional cell size growth (of the segmented object).

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Sets value for max allowed fractional cell size growth (of the segmented object).

Return type:

void (-)

setCellThumbSideLength(this, value)¶

SETCELLTHUMBSIDELENGTH Sets value for the side length of the image crop around the cell center for single cell trace generation [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the side length of the image crop around the cell center for single cell trace generation [px].

Return type:

void (-)

setData3D(this, value)¶

SETDATA3D Sets value if data is three dimensional.

Parameters:

this (object) – ParameterConfiguration instance.
value (bool) – Value if data is three dimensional.

Return type:

void (-)

setDebugLevel(this, value)¶

SETDEBUGLEVEL Sets value for the debug level.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the debug level.

Return type:

void (-)

setDivisionMarkerAverageObjSizeGrowth(this, value)¶

SETDIVISIONMARKERAVERAGEOBJSIZEGROWTH Sets value for the divisison marker max object size growth.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker average object size growth.

Return type:

void (-)

setDivisionMarkerConvexAreaLowerThresh(this, value)¶

SETDIVISIONMARKERCONVEXAREALOWERTHRESH Sets value for the convex area lower thrshold for division marker segmentation.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the convex area lower threshold for division marker segmentation

Return type:

void (-)

setDivisionMarkerConvexAreaUpperThresh(this, value)¶

SETDIVISIONMARKERCONVEXAREAUPPERTHRESH Sets value for the convex area upper thrshold for division marker segmentation.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the convex area upper threshold for division marker segmentation

Return type:

void (-)

setDivisionMarkerDenoising(this, value)¶

SETDIVISIONMARKERCONVEXAREAUPPERTHRESH Sets value for the ROF denoising parameter theta for division marker.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the ROF denoising parameter theta for division marker.

Return type:

void (-)

setDivisionMarkerEdgeSensitivityThresh(this, value)¶

SETDIVISIONMARKEREDGESENSITIVITYTHRESH Sets value for the edge sensitivity threshold for division marker segmentation [0-1]

Parameters:

this (object) – ParameterConfiguration instance.
value (float, 0-1) – Value for the edge sensitivity threshold for division marker segmentation

Return type:

void (-)

setDivisionMarkerFingerprintHalfWindowSideLength(this, value)¶

SETDIVISIONMARKERFINGERPRINTHALFWINDOWSIDELENGTH Sets value for the divisison half window side length.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker fingerprint half window side length.

Return type:

void (-)

setDivisionMarkerFingerprintMaxConsideredFrequencies(this, value)¶

SETDIVISIONMARKERFINGERPRINTMAXCONSIDEREDFREQUENCIES Sets value for the divisison marker fingerprint max considered frequencies.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker fingerprint max considered frequencies.

Return type:

void (-)

setDivisionMarkerFingerprintResizeFactor(this, value)¶

SETDIVISIONMARKERFINGERPRINTRESIZEFACTOR Sets value for the divisison marker fingerprint resize factor.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker fingerprint resize factor.

Return type:

void (-)

setDivisionMarkerIndividualFunctionPenalty(this, value)¶

SETDIVISIONMARKERINDIVIDUALFUNCTIONPENALTY Sets value for the divisison marker individual function penalty.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker individual function penalty.

Return type:

void (-)

setDivisionMarkerLineProfileLength(this, value)¶

SETDIVISIONMARKERLINEPROFILEPEAKUPPERBOUND Sets value for the line profile length for line profile comparison for different cell pairs.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the line profile length.

Return type:

void (-)

setDivisionMarkerLineProfilePeakLowerBound(this, value)¶

SETDIVISIONMARKERLINEPROFILEPEAKLOWERBOUND Sets value for the line profile peak lower bound for thresholding the detecatble peak region.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the line profile peak lower bound

Return type:

void (-)

setDivisionMarkerLineProfilePeakUpperBound(this, value)¶

SETDIVISIONMARKERLINEPROFILEPEAKUPPERBOUND Sets value for the line profile peak upper bound for thresholding the detecatble peak region.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the line profile peak upper bound

Return type:

void (-)

setDivisionMarkerMaxExpectedMovement(this, value)¶

SETDIVISIONMARKERMAXEXPECTEDMOVEMENT Sets value for the divisison marker max object moviement.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker max object moviement.

Return type:

void (-)

setDivisionMarkerMaxMajorAxisRotation(this, value)¶

SETDIVISIONMARKERMAXMAJORAXISROTATION Sets value for the divisison marker max major axis rotation.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker max major axis rotation.

Return type:

void (-)

setDivisionMarkerMaxObjCenterDisplacement(this, value)¶

SETDIVISIONMARKERMAXOBJCENTERDISPLACEMENT Sets value for the divisison marker max object center displacement.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker max object center displacement.

Return type:

void (-)

setDivisionMarkerMaxObjSizeDecrease(this, value)¶

SETDIVISIONMARKERMAXOBJSIZEDECREASE Sets value for the divisison marker max object size decrease.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker max object size decrease.

Return type:

void (-)

setDivisionMarkerMaxObjSizeIncrease(this, value)¶

SETDIVISIONMARKERMAXOBJSIZEINCREASE Sets value for the divisison marker max object size increase.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker max object size increase.

Return type:

void (-)

setDivisionMarkerMaxTrackFrameSkipping(this, value)¶

SETDIVISIONMARKERMAXTRACKFRAMESKIPPING Sets value for the divisison marker max track frame skipping.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker max track frame skipping.

Return type:

void (-)

setDivisionMarkerMeanObjDiameter(this, value)¶

SETDIVISIONMARKERMEANOBJDIAMETER Sets value for the divisison marker mean object diameter.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker mean object diameter

Return type:

void (-)

setDivisionMarkerMeanObjDiameterScalingFactor(this, value)¶

SETDIVISIONMARKERMEANOBJDIAMETERSCALINGFACTOR Sets value for the divisison marker mean object scaling factor.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the divisison marker mean object scaling factor

Return type:

void (-)

setDivisionMarkerNeighbourhoodSearchRadius(this, value)¶

SETDIVISIONMARKERNEIGHBOURHOODSEARCHRADIUS Sets value for the divisison marker neighbourhood search radius.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker neighbourhood search radius.

Return type:

void (-)

setDivisionMarkerRadiusVectorFilterX(this, value)¶

SETDIVISIONMARKERRADIUSVECTORFILTERX Sets value for the divisison marker radius vector filter x.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker radius vector filter x.

Return type:

void (-)

setDivisionMarkerRadiusVectorFilterY(this, value)¶

SETDIVISIONMARKERRADIUSVECTORFILTERY Sets value for the divisison marker radius vector filter y.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker radius vector filter y.

Return type:

void (-)

setDivisionMarkerRadiusVectorFilterZ(this, value)¶

SETDIVISIONMARKERRADIUSVECTORFILTERZ Sets value for the divisison marker radius vector filter z.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker radius vector filter z.

Return type:

void (-)

setDivisionMarkerUsedFunctionsForCostMatrix(this, value)¶

SETDIVISIONMARKERUSEDFUNCTIONSFORCOSTMATRIX Sets value for the divisison marker used functions for cost matrix.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the divisison marker used functions for cost matrix.

Return type:

void (-)

setFingerprintDistThreshold(this, value)¶

SETFINGERPRINTDISTTHRESHOLD Sets value for the fingerprint distance threshold.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for the fingerprint distance threshold.

Return type:

void (-)

setFingerprintHalfWindowSideLength(this, value)¶

SETFINGERPRINTHALFWINDOWSIDELENGTH Sets value for the half window side length of a square around the centroid coordinates of a segmented cell to be used to for fingerprint computation [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the half window side length of the cell center.

Return type:

void (-)

setFingerprintMaxConsideredFrequencies(this, value)¶

SETFINGERPRINTMAXCONSIDEREDFREQUENCIES Sets value for the maximal DCT frequency to be used to calculate the fingerprint.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the maximal DCT frequency to be used to calculate the fingerprint.

Return type:

void (-)

setFingerprintResizeFactor(this, value)¶

SETFINGERPRINTRESIZEFACTOR Sets value for the image resizing for fingerprint calculation Default is 32.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the image resizing for fingerprint calculation Default is 32.

Return type:

void (-)

setIndividualFunctionPenalty(this, value)¶

SETINDIVIDUALFUNCTIONPENALTY Sets value for all individaul function penalty

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Sets value for all individaul function penalty

Return type:

void (-)

setMaskOverlayAlpha(this, value)¶

SETMASKOVERLAYALPHA Sets value for the transparency (alpha) level of the segmentation mask overlay onto the raw images [0-1].

Parameters:

this (object) – ParameterConfiguration instance.
value (float, 0-1) – Value for the transparency (alpha) level of the segmentation mask overlay onto the raw images.

Return type:

void (-)

setMaxCellCenterDisplacement(this, value)¶

SETMAXEXPECTEDMOVEMENT Sets value for max allowed segmentation object centroid displacement [pixel].

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Sets value for max allowed segmentation object centroid displacement [pixel].

Return type:

void (-)

setMaxCellSizeDecrease(this, value)¶

SETMAXCELLSIZEDECREASE Sets value for max allowed fractional cell size decrease due to segmenation variation (e.g. miss segmentation, focus drift of the segmented object).

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Sets value for max allowed fractional cell size decrease due to segmenation variation.

Return type:

void (-)

setMaxCellSizeIncrease(this, value)¶

SETMAXCELLSIZEINCREASE Sets value for max allowed fractional cell size increase due to segmenation variation (e.g. miss segmentation, focus drift of the segmented object).

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Sets value for max allowed fractional cell size increase due to segmenation variation.

Return type:

void (-)

setMaxExpectedMovement(this, value)¶

SETMAXEXPECTEDMOVEMENT Sets value for max expected movement of a / multiple segmentation object(s) [pixel].

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Sets value for max expected movement of a / multiple segmentation object(s) [pixel].

Return type:

void (-)

setMaxMajorAxisRotation(this, value)¶

SETMAXMAJORAXISROTATION Sets value for majoraxis rotation penalty [degrees].

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Sets value for majoraxis rotation penalty [degrees].

Return type:

void (-)

setMaxTrackFrameSkipping(this, value)¶

SETMAXTRACKFRAMESKIPPING Sets value for max allowed frame skip.

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Sets value for max allowed frame skip.

Return type:

void (-)

setMeanCellDiameter(this, value)¶

SETMEANCELLDIAMETER Sets value for the mean segmentation object (cell) diameter of the experiment in pixel [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for mean segmentation object (cell) diameter of the experiment in pixel [px].

Return type:

void (-)

setMeanCellDiameterScalingFactor(this, value)¶

SETFINGERPRINTHALFWINDOWSIDELENGTH Sets the mean cell diameter scaling factor.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for mean cell diameter scaling factor.

Return type:

void (-)

setNeighbourhoodSearchRadius(this, value)¶

SETNEIGHBOURHOODSEARCHRADIUS Sets value for the neigbourhood half window side length [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the neigbourhood half window side length [px].

Return type:

void (-)

setPixelsPerZPlaneInterval(this, value)¶

SETPIXELSPERZPLANEINTERVAL Sets value for pixels per Z plane interval / step.

Parameters:

this (object) – ParameterConfiguration instance.
value (float) – Value for pixels per Z plane interval / step.

Return type:

void (-)

setRadiusVectorFilterX(this, value)¶

SETRADIUSVECTORFILTERX Sets value for the radius of the vector filter in x [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the radius of the vector filter in x [px].

Return type:

void (-)

setRadiusVectorFilterY(this, value)¶

SETRADIUSVECTORFILTERY Sets value for the radius of the vector filter in z [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the radius of the vector filter in y [px].

Return type:

void (-)

setRadiusVectorFilterZ(this, value)¶

SETRADIUSVECTORFILTERZ Sets value for the radius of the vector filter in z [px].

Parameters:

this (object) – ParameterConfiguration instance.
value (int) – Value for the radius of the vector filter in z [px].

Return type:

void (-)

setUsedFunctionsForCostMatrix(this, value)¶

SETUSEDFUNCTIONSFORCOSTMATRIX Sets value for the selection of which of the four cost functions should be used to build the final cost matrix. 1x4 array [boolean]

Parameters:

this (object) – ParameterConfiguration instance.
value (array, 1x4) – Sets value for the selection of which of the four cost functions should be used.

Return type:

void (-)

QuantificationData ¶

class TracX.@QuantificationData.QuantificationData¶

Bases: handle, dynamicprops

QUANTIFICATIONDATA This class contains all the quantification data of the configured Tracker project for a single experiment (i.e. one well position of a multi well experiment.) The QuantificationData is mapped to the SegmentationData via a primary key stored in the uuid property.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

QuantificationData()¶

QUANTIFICATIONDATA constructs an empty object of type QuantificationData. This object acts as datastorage for fluorescence quantification data for a TracX Project.

Returns:: obj – Returns a QuantificationData instance.
Return type:: object
Authors:: Andreas P. Cuny - initial implementation

Property Summary

fluo_background_mean¶: Fluorescence channel name [string]

fluo_background_std¶: Mean background fluorescence [a.u.]

fluo_bright_euler¶: Quantile 25 brightest pixel fluorescence [a.u.]

fluo_bright_q25¶: Quantile 50 brightest pixel fluorescence [a.u.]

fluo_bright_q50¶: Quantile 75 brightest pixel fluorescence [a.u.]

fluo_bright_q75¶: Brightest pixel of whole cell fluorescence [a.u.]

fluo_bright_total¶: Quantile 25 of cell nucleus fluorescence [a.u.]

fluo_cell_q25¶: Quantile 50 of cell fluorescence [a.u.]

fluo_cell_q50¶: Quantile 75 of cell fluorescence [a.u.]

fluo_cell_q75¶: Total cell fluorescence [a.u.]

fluo_cell_total¶: Standard deviation of background fluorescence [a.u.]

fluo_mem_q25¶: Quantile 50 of cell fluorescence [a.u.]

fluo_mem_q50¶: Quantile 75 cell membrane fluorescence [a.u.]

fluo_mem_q75¶: Total cell membrane fluorescence [a.u.]

fluo_mem_total¶: Quantile 25 of cell fluorescence [a.u.]

fluo_name¶: Id of fluorescence channel [int].

fluo_nuc_q25¶: Quantile 50 of cell nucleus fluorescence [a.u.]

fluo_nuc_q50¶: Quantile 75 of cell nucleus fluorescence [a.u.]

fluo_nuc_q75¶: Total cell nucleus fluorescence [a.u.]

fluo_nuc_total¶: Quantile 25 of cell fluorescence [a.u.]

uuid¶: Primary key

Method Summary

setUUID(this, value)¶

SETUUID Sets a unique id for each segmented cell per image frame such that the QuantificationData is mapped to the SegmentationData object via a primary key stored in the uuid property.

Parameters:

this (object) – QuantificationData instance.
value (int) – Value to be set for uuid

SegmentationData ¶

class TracX.@SegmentationData.SegmentationData¶

Bases: dynamicprops

SegmentationData Creates an object to store imported cell segmentation data. It is structured based on the CellX output, however other segmentation software outputs can be stored as well once converted.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

SegmentationData()¶

SEGMENTATIONDATA Constructs an empty SegmentationData object to save segmentation data as well as tracking results. for a TracX project.

Returns:: SegmentationData instance.
Return type:: obj (object)
Authors:: Andreas P. Cuny - initial implementation

Property Summary

cell_area¶: Orientation of segmented cell.

cell_center_x¶: Unique segmentation cell index for each frame.

cell_center_y¶: X component of segmented cell center.

cell_center_z¶: Y component of segmented cell center

cell_close_neighbour¶: Nucleus area of segmented cell.

cell_dif_x¶: Array of closest cell neighbours of segmented cell.

cell_dif_y¶: X component difference between two subsequent frames of segmented cell.

cell_dif_z¶: Y component difference between two subsequent frames of segmented cell.

cell_eccentricity¶: Perimeter of segmented cell.

cell_filtered_dif_x¶: Z component difference between two subsequent frames of segmented cell.

cell_filtered_dif_y¶: Filtered X component difference between two subsequent frames of segmented cell.

cell_filtered_dif_z¶: Filtered Y component difference between two subsequent frames of segmented cell.

cell_fractionOfGoodMembranePixels¶: Eccentricity of segmented cell.

cell_index¶: Image frame number of segmented cell.

cell_majoraxis¶: Z component of segmented cell center

cell_mask_boundary_points¶: Budneck total fluo signal for the given track

cell_mem_area¶: Fraction of good membrane pixel of segmented cell.

cell_mem_volume¶: Membrane area of segmented cell.

cell_minoraxis¶: Major axis of segmented cell.

cell_nuc_area¶: Nucleus radius of segmented cell

cell_nuc_radius¶: Membrane volume of segmented cell..

cell_orientation¶: Minor axis of segmented cell.

cell_perimeter¶: Volume of segmented cell.

cell_pole1_age¶: Cell pole 2 y component (optionally, for rod shaped object lineage reconstruction)

cell_pole1_x¶: Filtered Z component difference between two subsequent frames of segmented cell.

cell_pole1_y¶: Cell pole 1 x component (optionally, for rod shaped object lineage reconstruction)

cell_pole2_age¶: Cell pole 1 age (optionally, for rod shaped object lineage reconstruction)

cell_pole2_x¶: Cell pole 1 y component (optionally, for rod shaped object lineage reconstruction)

cell_pole2_y¶: Cell pole 2 x component (optionally, for rod shaped object lineage reconstruction)

cell_timepoint¶: Cell pole 2 age (optionally, for rod shaped object lineage reconstruction)

cell_volume¶: Area of segmented cell.

cell_zplane¶: Cell timpoint (3D data)

track_age¶: Track fingerprint distance of segmented cell based on track_fingerprint_real.

track_area_assignment_cost¶: Track positional assignment costs of segmented cell.

track_assignment_fraction¶: Track cell cycle phase

track_budneck_total¶: Track has bud indicates whether a track in a certain frame is budding

track_cell_cycle_phase¶: Track lineage of segmented cell.

track_contained_in_track¶: Track index corrected of segmented cell.

track_end_frame¶: Track start frame number of segmented cell determined by penalty function.

track_fingerprint_real¶: Track index of segmented cell after qc verification

track_fingerprint_real_distance¶: Track real frequency based fingerprint of segmented cell.

track_frame_skipping_cost¶: Track rotation assignment costs of segmented cell determined by penalty function.

track_generation¶: Track parent score of parent assignment.

track_has_bud¶: Track cointained in other track of segmented cell.

track_index_corrected¶: Track end frame number of segmented cell.

track_index_qc¶: Track index of segmented cell.

track_lineage_tree¶: Track generation of segmented cell.

track_parent¶: Track age of segmented cell.

track_parent_frame¶: Track parent of segmented cell.

track_parent_prob¶: Track parent frame of segmented cell.

track_parent_score¶: Track parent probabliity of parent assignment.

track_position_assignment_cost¶: Track total assignment costs of segmented cell.

track_rotation_assignment_cost¶: Track area assignment costs of segmented cell determined by penalty function.

track_start_frame¶: Track frame skipping assignment costs of segmented cell determined by penalty function.

track_total_assignment_cost¶: Track assignment fraction if there is a better alternative assignment.

uuid¶: Primary key

Method Summary

initNewEntry(this, uuid, cell_frame, cell_index, cell_center_x, cell_center_y, cell_majoraxis, cell_minoraxis, cell_orientation, cell_area, cell_volume, cell_perimeter, cell_eccentricity, cell_fractionOfGoodMembranePixels, cell_mem_area, cell_mem_volume, cell_nuc_radius, cell_nuc_area, cell_close_neighbour, cell_dif_x, cell_dif_y, cell_filtered_dif_x, cell_filtered_dif_y, cell_pole1_x, cell_pole1_y, cell_pole2_x, cell_pole2_y, cell_pole1_age, cell_pole2_age, track_index, track_index_qc, track_fingerprint_real, track_fingerprint_real_distance, track_age, track_parent, track_parent_frame, track_parent_prob, track_parent_score, track_generation, track_lineage_tree, track_cell_cycle_phase, track_assignment_fraction, track_total_assignment_cost, track_position_assignment_cost, track_area_assignment_cost, track_rotation_assignment_cost, track_frame_skipping_cost, track_start_frame, track_end_frame, track_index_corrected, track_contained_in_track, track_has_bud, track_budneck_total)¶

INITNEWENTRY Adds new segmentation data to the object. Empty parameters should be a NaN array of the same size as the other parameter data arrays.

Parameters:

this (object) – SegmentationData instance
uuid (int) – Primary key
cell_frame (int) – Image frame number
cell_index (int) – Unique segmentation cell index for each frame
cell_center_x (int) – X coordinate of segmented object
cell_center_y (int) – Y coordinate of segmented object
cell_majoraxis (float) – Major axis
cell_minoraxis (float) – Minor axis
cell_orientation (float) – Orienation
cell_area (float) – Area
cell_volume (float) – Volume
cell_perimeter (float) – Perimeter
cell_eccentricity (float) – Eccentricity
cell_fractionOfGoodMembranePixels (float) – Fraction of good membrane pixels
cell_mem_area (float) – Membrane area
cell_mem_volume (float) – Membrane volume
cell_nuc_radius (float) – Nucleus radius
cell_nuc_area (float) – Nucleus area
cell_close_neighbour (array) – Array of closest cell neighbours
cell_dif_x (float) – Frame to frame difference of X coordinate
cell_dif_y (float) – Frame to frame difference of Y coordinate
cell_filtered_dif_x (float) – Filtered frame to frame difference difference of X coordinate
cell_filtered_dif_y (float) – Filtered frame to frame difference difference of Y coordinate
cell_pole1_x (float) – Cell pole1 x coordinate (rod shaped objects);
cell_pole1_y (float) – Cell pole1 y coordinate (rod shaped objects);
cell_pole2_x (float) – Cell pole2 x coordinate (rod shaped objects);
cell_pole2_y (float) – Cell pole2 y coordinate (rod shaped objects);
cell_pole1_age (int) – Cell pole1 age (rod shaped objects);
cell_pole2_age (int) – Cell pole2 age (rod shaped objects);
track_index (int) – Unique track index
track_index_qc (int) – Unique qc verified track index
track_fingerprint_real (array) – Track fingerprint real
track_fingerprint_real_distance (float) – Track fingerprint real distance
track_age (int) – Track age
track_parent (ont) – Track parent
track_parent_frame (int) – Track parent frame
track_parent_prob (float) – Track parent assignemt probability
track_parent_score (float) – Track parent assignemt score
track_generation (int) – Track generation
track_lineage_tree (int) – Track lineage
track_assigmnent_fraction (float) – Assignment fraction
track_total_assignment_cost (float) – Track total assignment costs
track_position_assignment_cost (float) – Track positional costs
track_area_assignment_cost (float) – Track area costs
track_rotation_assignment_cost (float) – Track orientation costs
track_frame_skipping_cost (float) – Track frame skipping costs
track_start_frame (int) – Track start frame
track_end_frame (int) – Track end frame
track_index_corrected (int) – Track index corrected
track_contained_in_track (int) – Track contained in other track
track_has_bud (int) – Track has bud indicates if a track is budding in a certain cell_frame
track_budneck_total (float) – Total budneck signal

Returns:

SegmentationData instance. updated with new data

Return type:

this void (object)

setUUID(this, value)¶

SETUUID Sets a unique id for each segmented cell per image frame such that the +TracX.QuantificationData is mapped to the +TracX.SegmentationData object via a primary key stored in the uuid property.

Parameters:

this (object) – SegmentationData instance.
value (int) – Sets value for uuid.

TemporaryData ¶

class TracX.@TemporaryData.TemporaryData¶

TEMPORARYDATA acts as temprorary data container for TemporaryTrackingData.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

TemporaryData()¶

TEMPORARYDATA Constructs a TemporaryData object instance to keep teporary frame data during tracking.

Returns:: obj – Returns TemporaryData instance.
Return type:: object
Authors:: Andreas P. Cuny - initial implementation

Property Summary

NewFrame¶: TemporaryTrackingData object holding the current image frame data.

VeryOld¶: TemporaryTrackingData object holding the subsequent image frame data.

Method Summary

initializeOldFrame(this)¶

INITIALIZEOLDFRAME Initailizes the OldFrame property of the Tracker with data from the TemporaryData object for the first image frame (frameNumber == 1).

Parameters:: this (object) – TemporaryData instance
Returns:: this – Initializes the TemporaryData.OldFrame property and returns the TemporaryData instance parametrized.
Return type:: object

TemporaryLineageAssignment ¶

class TracX.@TemporaryLineageAssignment.TemporaryLineageAssignment¶

Bases: handle, matlab.mixin.Copyable

TEMPORARYLINEAGEASSIGNMENT Stores temporary mother daughter lineage assignments until final decision is made which cells to assign.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

TemporaryLineageAssignment()¶

TEMPORARYLINEAGETEMPASSIGNMENT Object constructor.

Returns:: TemporaryLineageAssignment instance
Return type:: obj object
Authors:: Andreas P. Cuny - initial implementation

Property Summary

daughterCell¶: DaughterCell property stores daughter cells’ track indicies.

daughterCellStartFrame¶: Start frame of daughter cell segmentation (can be error prone due to missing segmentation)

frameOfMDPair¶: Frame on which a mother daughter pair was found

hasBudNeckSignal¶: Binary bud neck signal quantification

isManualCorr¶: isManualCorr indicates if assignment has been manually corrected

lineProfile¶: Line profile between daughter cell and mother candidate cell centroid

markerChannelID¶: Image channel of cell division marker segmentation.

markerID¶: ID of cell division marker segmentation.

markerTrack¶: Track index of marker corresponding to MD pair.

markerTrackEndFrame¶: Track index of marker corresponding to MD pair end frame (can be error prone due to low SNR / not detectable signal)

markerTrackStartFrame¶: Track index of marker corresponding to MD pair start frame

maxFrameEvalAfterBirth¶: Number of frames for how long mother-dauther pairs should be evaluated if this assignment is correct after daughter cell birth.

motherAssignmentProb¶: Assignment probability

motherAssignmentScore¶: Assignment score

motherCell¶: MotherCell property stores the detected mother cells (track indicies).

motherCellCandidates¶: MotherCellCandidates stores track indicies that are considered to be potenial mother cells.

motherCellCandidatesStartFrame¶: MotherCellCandidatesStart frame stores frame number where the mother cell was segmented for the first time.

motherSigInNucCandidates¶: MotherSigInNucCandidates (G1 phase) 1 if in nuc 0 otherwise for candidates.

reconstructionIsFinished¶: Flag if reconstruction has been finished sucessfully

Method Summary

deleteEntry(this, delIdx)¶

DELETEENTRY Deletes a mother daughter (MD) pair entry form TemporaryLineageAssignment

Parameters:

this (object) – TemporaryLineageAssignment instance
delIdx (int) – Index for deletion.

Return type:

void (-)

deleteRow(this, daughterArray)¶

DELETEROW Deletes the row of assigned mother - daughter pairs.

Parameters:

this (object) – TemporaryLineageAssignment instance
daughterArray (array kx1) – With daughter track_index to remove from object after sucessfull assignment.

Return type:

void (-)

determineMotherCell(this)¶

DETERMINEMOTHERCELL Determines the mother cells from the mother cell canditates based on most frequence occurence.

Parameters:: this (object) – TemporaryLineageAssignment instance
Return type:: void (-)

getWeightedScore(this, p, occ)¶

GETWEIGHTEDSCORE Computes a weighted score for mother daughter candidate pairs based on a probablity and MD pair occurance.

Parameters:

this (object) – TemporaryLineageAssignment instance
p (array kx1) – Probability of MD (mother daughter pair) assignments.
occ (array, kx1) – MD pair detection occurance.

Returns:

Weighted score for MD assignments.

Return type:

score (float)

replaceOrAddNew(this, data2Modify)¶

REPLACEORADDNEW Replaces or adds new data to TemporaryLineageAssignment

Parameters:

this (object) – TemporaryLineageAssignment instance
data2Modify (array) – Array with data to be modified. The collumns correspond to daughter, new mother, old mother, division frame.

Return type:

void (-)

setMarker(this, markerID, channelID, Daughter)¶

SETMARKER Sets the cell division event marker segmentation index as well as the image channel the marker was recorded with.

Parameters:

this (object) – TemporaryLineageAssignment instance
markerID (int) – Cell division segmentation label index.
channelID (int) – Cell division image channel index.

Return type:

void (-)

setMarkerTracks(this, lineageData)¶

SETMARKERTRACKS Assigns the marker track id of the bud neck marker to a mother daughter (MD) canditate pair.

Parameters:

this (object) – TemporaryLineageAssignment instance
lineageData (object) – Marker lineage data.

Return type:

void (-)

setMotherDaughterPair(this, daughterArray, motherArray, frameNumber, budNeckSig, lineProfileRe, daughterFrameArray, motherFrameArray)¶

SETMOTHERDAUGHTERPAIR Sets a mother - daughter pair in the TemporaryLineageAssignment object.

Parameters:

this (object) – TemporaryLineageAssignment instance
daughterArray (array kx1) – With daughter track_index to add to the object for evaluation.
motherArray (array kx1) – With mother track_index to add to the object for evaluation
frameNumber (int) – Image frame number
budNeckSig (bool) – Flag if budneck signal was detected 1, 0 otherwise.
lineProfileRe (array 1x100) – Resampled line profile between mother daugher centroid

Return type:

void (-)

setSigInNuc(this, sigInNuc, daughter)¶

SETSIGINNUC Sets a flag if a signal in the nucleus of a mother cell has been detected (for cell cycle determination).

Parameters:

this (object) – TemporaryLineageAssignment instance
sigInNuc (int) – Flag if signal in nucleus has been detected.
daughter (int) – Daughter track index.

Return type:

void (-)

TemporaryTrackingData ¶

class TracX.@TemporaryTrackingData.TemporaryTrackingData¶

Bases: handle

TEMPORARYTRACKINGDATA Creates an object of minimal required information needed for frame to frame tracking.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

TemporaryTrackingData()¶

TEMPORARYTRACKINGDATA constructs an object of type TracX.TemporaryTrackingData. This object acts as a temporary data storage for relevant data needed during the frame to frame tracking process for a TracX Project.

Returns:: TemporaryTrackingData instance.
Return type:: this (object)
Authors:: Andreas P. Cuny - initial implementation

Property Summary

cell_area¶: Orientation of segmented cell.

cell_center_x¶: Segmentation cell index of segmented cell.

cell_center_y¶: X component of segmented cell.

cell_center_z¶: Y component of segmented cell.

cell_close_neighbour¶: Area of segmented cell.

cell_del¶: Array of closest cell neighbours of segmented cell.

cell_dif_x¶: Z component of segmented cell.

cell_dif_y¶: X component frame to frame difference of segmented cell.

cell_dif_z¶: Y component frame to frame difference of segmented cell.

cell_filtered_dif_x¶: Z component frame to frame difference of segmented cell.

cell_filtered_dif_y¶: Filtered x component frame to frame difference of segmented cell.

cell_filtered_dif_z¶: Filtered y component frame to frame difference of segmented cell.

cell_index¶: Track age segmented cell.

cell_orientation¶: Filtered z component frame to frame difference of segmented cell.

track_age¶: Track index qc validated of segmented cell.

track_assignment_fraction¶: Track fingerprint distance of segmented cell based on track_fingerprint_real.

track_fingerprint_age¶: Fraction of neighbouring cell with lower track_fingerprint_real_distance

track_fingerprint_real¶: Deletion of segmented cell.

track_fingerprint_real_distance¶: Track real frequency based fingerprint of segmented cell.

track_index_qc¶: Track index of segmented cell.

Method Summary

addData(this, track_index, track_index_qc, track_age, cell_index, cell_center_x, cell_center_y, cell_center_z, cell_dif_x, cell_dif_y, cell_dif_z, cell_filtered_dif_x, cell_filtered_dif_y, cell_filtered_dif_z, cell_orientation, cell_area, cell_close_neighbour, cell_del, track_fingerprint_real, track_fingerprint_real_distance, track_assignment_fraction, track_fingerprint_age)¶

ADDDATA Adds data to TracX.TemporaryTrackingData object.

Parameters:

this (object) – TemporaryTrackingData instance.
track_index (int, kx1) – Unique track index arrau
track_index_qc (int, kx1) – Unique qc verified track index array
track_age (int, kx1) – Track age arrau
cell_index (int, kx1) – Unique segmentation cell index for each frame array
cell_center_x (double, kx1) – X coordinate array
cell_center_y (double, kx1) – Y coordinate array
cell_center_z (double, kx1) – Z coordinate array
cell_dif_x (double, kx1) – Frame to frame difference of X coordinates array
cell_dif_y (double, kx1) – Frame to frame difference of Y coordinates array
cell_dif_z (double, kx1) – Frame to frame difference of Z coordinates array
cell_filtered_dif_x (double, kx1) – Filtered frame to frame differences of X coordinates array
cell_filtered_dif_y (double, kx1) – Filtered frame to frame differences of Y coordinates array
cell_filtered_dif_z (double, kx1) – Filtered frame to frame differences of Z coordinates array
cell_orientation (double, kx1) – Orienation
cell_area (double, kx1) – Area
cell_close_neighbour (bool, kxk) – Matrix of closest cell neighbours
cell_del (int, kx1) – Cell deletion
track_fingerprint_real (double, kx1) – Track fingerprint real
track_fingerprint_real_distance (double, kx1) – Track fingerprint real distance
track_assignment_fraction (double, kx1) – Fraction of neighbouring cell with lower track_fingerprint_real_distance
track_fingerprint_age (int, kx1) – Track fingerprint age

Returns:

Returns TracX.TemporaryTrackingData

Return type:

this (object)

recalculateMotionCorrNeighbourhood(this, neighbourhoodSearchRadius)¶

RECALCULATEMOTIONCORRNEIGHBOURHOOD Recalculates the motion. corrected segmentation neighbourhood.

Parameters:

this (object) – TemporaryTrackingData instance.
neighbourhoodSearchRadius (double) – neighbourhoodSearchRadius

Return type:

void (-)

Tracker ¶

TracX.@Tracker.saveTrackerControlImageFrame(this, frameNumber, varargin)¶

SAVETRACKERCONTROLIMAGES Saves a tracking control images with each tracked cell labeled with its track index for a given image frame.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of SegmentationData.
- highlightFieldNameVal (int): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- fontSize (str): Font size of property to be displayed.
- removeContainedTracks (bool): If contained tracks within tracks should be removed. Defaults to true.
- isMarker (bool): If markers should be displayed. Defaults to false.

Returns:

void – Saves images to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.revertSegmentationImageCrop(this)¶

REVERTSEGMENTATIONIMAGECROP Reverts a potentially applied image crop during segmentation to map the segmentation objects’ centroid coordintates to the raw image.

Parameters:: this (obj) – Tracker object
Returns:: void – Acts on Tracker object directly.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

TracX.@Tracker.deleteSegArtefacts(this, varargin)¶

DELSEGARTEFACTS Deletes potential segmentation artefacts (segmented objects which are no cells based the autofluorescence.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- channel (int): Channel number fluo_id of the fluorescent channel to use for segmentation artefact detection. Defaults to 1.
- stdFactor (float): Factor standard deviation. Defaults to 2.
- neighbourhoodSearchRadius (int): Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on Tracker object directly and deletes selected data below threshold.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.prepareDataFromSegmentationMask(this, imagePath, segmentationPath, segmentationFileNameRegex, imageFileNameRegex, varargin)¶

PREPAREDATAFROMSEGMENTATIONMASK Allows tracking with segmentation results from any software given a un- or labeled segmentation mask per image frame. The mask is then converted into the CellX format which is used internaly for structuring the data during tracking.

Parameters:

this (obj) – Tracker instance.
imagePath (str) – Path to the experiment raw images. imageDir
segmentationPath (str) – Path to segmentation results. segmentationResultDir
segmentationFileNameRegex (str) – Regex for the mask filename identifier i.e. Mask_*.
imageFileNameRegex (str) – Regex for the image filename identifier i.e. BF_*.
varargin (str varchar) –
- pxPerPlane (int): Pixel per image plane. Defaults to 0.
- fluoTags (int): Identifier for potential fluorescent images to quantify i.e. {‘XFP’}
- flatFieldFileNames (int): Names of potential flat fields.
- customRegEx (str): Custom regex to identify the segmetnation masks.

Returns:

void – Writes results to disk directly.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.correctMDMisassignment(this, trackIndexDaughter, newMotherTrackIndex, oldMotherTrackIndex, divisionFrameNumber)¶

CORRECTMDMISASSIGNMENT Allows to manually correct a mother daughter assignment for a given lineage. A given daughter track index will be replaced with a new mother track index. The arrays need to have the same size. Lineage roots or on the first frame should have the value 0 instead of a track index.

Parameters:

this (object) – Tracker instance.
trackIndexDaughter (array) – Array of daughter track indices.
newMotherTrackIndex (array) – Array of mother track indices.
oldMotherTrackIndex (array) – Array of old mother track indices.
divisionFrameNumber (array) – Frame number of division frame.

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveTrackerCellCycleResultsAsTable(this, varargin)¶

SAVETRACKERCELLCYCLERESULTSASTABLE Saves the cell cycle results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- resultFilePath (str): Path to where to save the results. Defaults to segmentationResultDir
- resultFileName (str): Results file name. Defaults to ProjectName_CellCycleResults_Timestamp
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Saves cell cycle results as table to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.generateScriptFromTracker(this, varargin)¶

GENERATESCRIPTFROMTRACKER Generates a Matlab (.m) script file based on the tracker project configuration made with the GUI.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- fileName (str): File name. Defaults to TracX_project_ProjectName.m.

Returns:

void – Writes text file to disk

Return type:

(-)

Authors:

Thomas Kuendig - initial implementation

TracX.@Tracker.runReQuantification(this, fluoTags, varargin)¶

RUNREQUANTIFICATION Runs the re segmentation and quantification of merged tracking masks for buds and mothers prior division. It first runs the CellXMaskInterface to resegment and quanfity the merged labels. Then in loads the data and updates it for the mothers and deletes the bud entries prior division (now merged with mothers) to make sure there is no data duplication.

Parameters:

this (object) – Tracker instance.
fluoTags (array) – Array with fluoTags names. Fluorescent images file identifier.
varargin (str varchar) –
- fileIdentifierSegmentationImages (str): File identifier for segmentation images.

Returns:

Runs re quantification and writes results to disk directly.

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.testBudNeckSegmentation(this, frameNumber, varargin)¶

TESTBUDNECKSEGMENTATION Tests the parameter for budneck segmentation and displays a control image to optimize the parameters if needed.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
varargin (str varchar) –
- divisionMarkerDenoising (int): ROF denoising parameter. divisionMarkerDenoising
- divisionMarkerEdgeSensitivityThresh (int): Edge sensitivity threshold for segmenting the marker outlines. divisionMarkerEdgeSensitivityThresh
- divisionMarkerConvexAreaLowerThresh (int): Lower area limit for detected markers. divisionMarkerConvexAreaLowerThresh
- divisionMarkerConvexAreaUpperThresh (int): Upper area limit for detected markers. divisionMarkerConvexAreaUpperThresh
- contrastLimits (array, 1x2): Image contras limits 0-1.

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.testTrackingParameters(this, testRange, varargin)¶

TESTTRACKINGPARAMETERS Tests the current set of tracker parameters as defined in ParameterConfiguration.

Parameters:

this (obj) – Tracker object
testRange (array, 1x2) – Image frame test range to test Tracking [fromFrame, toFrame].
varargin (str varchar) –
- mode (array 1x2): Allows to test the dCRF tracker instead of the full tracker as well as with or without motion correction i.e [1,0].

Returns:

void – Displays the tracking results in an interactive movie player.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveCurrentTrackerState(this, varargin)¶

SAVECURRENTTRACKERSTATE Saves the current state of the tracker to disk.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- resultFilePath (str): Path to where to save the tracker stat. Defaults to segmentationResultDir
- resultFileName (str): Results file name. Defaults to Timestamp_TracX_State_Project_ProjectName

Returns:

void – Saves the tracker object stat to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.testMarkerTrackingParameters(this, testRange, varargin)¶

TESTTRACKINGPARAMETERS Tests the marker tracking parameters as defined in defined in ParameterConfiguration and displays the results for the given range.

Parameters:

this (obj) – Tracker object
testRange (array, 1x2) – Image frame test range to test Tracking [fromFrame, toFrame].
varargin (str varchar) –
- divisionMarkerMaxTrackFrameSkipping (int): Max marker frame skiping. divisionMarkerMaxTrackFrameSkipping
- divisionMarkerMaxObjCenterDisplacement (int): Max marker displacement. divisionMarkerMaxObjCenterDisplacement
- divisionMarkerMaxObjSizeIncrease (float): Max marker size increase. divisionMarkerMaxObjSizeIncrease
- divisionMarkerMaxObjSizeDecrease (float): Max marker size decrease. divisionMarkerMaxObjSizeDecrease
- divisionMarkerFingerprintHalfWindowSideLength (int): Max marker fingerprint half window side length. divisionMarkerFingerprintHalfWindowSideLength

Returns:

void – Displays the marker tracking results in an interactive movie player.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

class TracX.@Tracker.Tracker¶

Bases: handle

TRACKER Tracker main TracX object

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

Tracker()¶

TRACKER Tracker Constructs an empty Tracker object object to save segmentation data as well as tracking results. for a TracX project.

Returns:: obj – Tracker instance.
Return type:: (obj)
Authors:: Andreas P. Cuny - initial implementation

Property Summary

configuration¶: TracX.@TrackerConfiguration instance with the tracking parameters and project metadata.

data¶: TracX.@TrackData instance which stores all segmentation, quantification and lineage data.

evaluation¶: TracX.@TrackerEvaluation instance implementing tracker performance evaluation methods

fingerprint¶: TracX.@Fingerprint instance implementing cell fingerprinting methods.

imageProcessing¶: TracX.@ImageProcessing instance implementing image processing methods.

imageVisualization¶: TracX.@ImageVisualization instance implementing image visualization methods.

io¶: TracX.@IO instance implementing read/write methods.

isAllInstalled¶: Flag, if all TracX dependencies and toolboxes are installed. Defaults to false.

isCorrectMotion¶: Flag, if motion should be corrected for (1). Defaults to true.

isFFPEval¶: Flag, to evaluate FFP for manuscript. Defaults to false

isFullCosts¶: Flag if full costs should be used during tracking (1) or if a minimalized tracker based on dCRF should be run. Defaults to true.

isReady¶: Flag, if TracX is ready to be used. Defaults to false.

lap¶: TracX.@LAP instance implementing linear assignment methods.

lineage¶: TracX.@Lineage instance implementing lineage reconstruction methods

motion¶: TracX.@Motion instance implementing cell motion methods.

utils¶: TracX.@Utils instance implementing utility methods.

version¶: Current TracX version

Method Summary

copyResultsToTrackerData(this, dataToSave, fieldName, emptyDataLocIdx, oldFrameLocIdx, frameNumber)¶

COPYRESULTSTOTRACKERDATA Copies results of the frame by frame tracking to the data store Tracker.TrackerData.

Parameters:

this (obj) – Tracker instance.
dataToSave (array) – Array with data to be saved to TrackerData
fieldName (str) – Fieldname name
emptyDataLocIdx (array) – Location indicies of empty data.
oldFrameLocIdx (array) – OldFrame location indicies for track_index.
frameNumber (int) – Frame number

Returns:

void – Tracker instance

Return type:

(-)

correctMDMisassignment(this, trackIndexDaughter, newMotherTrackIndex, oldMotherTrackIndex, divisionFrameNumber)¶

Parameters:

this (object) – Tracker instance.
trackIndexDaughter (array) – Array of daughter track indices.
newMotherTrackIndex (array) – Array of mother track indices.
oldMotherTrackIndex (array) – Array of old mother track indices.
divisionFrameNumber (array) – Frame number of division frame.

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

correctTrackMisassignment(this, frameArray, oldTrackIndexArray, newTrackIndexArray)¶

CORRECTTRACKMISASSIGNMENT Allows to manually correct a cell to track assignment on specific frames. A given track index will be replaced with a new track index. The arrays need to have the same size.

Parameters:

this (obj) – Tracker instance.
frameArray (array) – Array of image frames.
oldTrackIndexArray (array) – Array of old track indices to be replaced.
newTrackIndexArray (array) – Array of new track indices to relpace the old ones with.

Returns:

void – Acts on Tracker instance directly

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

createNewTrackingProject(this, projectName, imageDir, segmentationResultDir, fileIdentifierFingerprintImages, fileIdentifierWellPositionFingerprint, fileIdentifierCellLineage, imageCropCoordinateArray, nrOfFramesToImport, cellDivisionType)¶

CREATENEWTRACKINGPROJECT Creates a new TracX project. Sets file paths, and load segmentation data.

Parameters:

this (obj) – Tracker instance
projectName (str) – Name of the tracking project.
imageDir (str) – Image directory to be used in the current project.
segmentationResultDir (str) – the segmentation results for the current project
fileIdentifierFingerprintImages (str) – File name identifier for raw Brightfield images.
fileIdentifierWellPositionFingerprint (str) – File name identifier specifing the well position (of a multi well experiment).
fileIdentifierCellLineage (str) – of the fluorescent channel images to be used to reconstruct the cell lineage (i.e. bud neck marker)
imageCropCoordinateArray (array, 1x4) – Array with crop coordinates used during segmentation.
nrOfFramesToImport (int) – Number of frames to track.
cellDivisionType (str) – Cell division type

Returns:

this – Tracker instance with new project initialized.

Return type:

(obj)

deleteByFeature(this, feature, threshold, varargin)¶

DELETEBYFEATURE Deletes segmentation objects exceeding a threshold for a feature.

Parameters:

this (obj) – Tracker object
feature (str) – Any segmentation feature to use to threshold the data before tracking. SegmentationData
threshold (float) – Threshold. Feature values below the threshold are selected.
varargin (str varchar) –
- neighbourhoodSearchRadius (int): Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on Tracker object directly and deletes selected data below threshold.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

deleteByROI(this, roi, varargin)¶

DELETEBYROI Deletes segmentation objects outside a region of interest (ROI).

Parameters:

this (obj) – Tracker object
roi (array) – Region of interest defined by polygon vertices to keep data for tracking.
varargin (str varchar) –
- neighbourhoodSearchRadius (int): Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on Tracker object directly and deletes selected data outside ROI.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

deleteSegArtefacts(this, varargin)¶

DELSEGARTEFACTS Deletes potential segmentation artefacts (segmented objects which are no cells based the autofluorescence.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- channel (int): Channel number fluo_id of the fluorescent channel to use for segmentation artefact detection. Defaults to 1.
- stdFactor (float): Factor standard deviation. Defaults to 2.
- neighbourhoodSearchRadius (int): Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on Tracker object directly and deletes selected data below threshold.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

deleteSegObjAtBorder(this, borderOffset)¶

DELETESEGOBJATBORDER Delete segmentation objects at the image border within the border offset.

Parameters:

this (obj) – Tracker object
borderOffset (int) – Offset from image border in pixel to exclude from tracking.

Returns:

void – Acts on Tracker object directly and deletes selected data from the image border up to the border offset.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

exportCellCycleResults(this, resultFilePath, resultFileName, varargin)¶

EXPORTCELLCYCLERESULTS Exports the cell cycle results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (obj) – Tracker object
resultFilePath (str) – Path to where to save the results. Defaults to segmentationResultDir
resultFileName (str) – Results file name. Defaults to ProjectName_CellCycleResults_Timestamp
varargin (str varchar) –
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Writes text file to disk

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

exportFinalTrackingMasks(this)¶

EXPORTFINALTRACKINGMASKS Exports tracked masks for cells that divide asymmetrically after lineage reconstruction to merge the individual buds with their respective mother mask prior cell division.

Parameters:: this (obj) – Tracker object
Returns:: void – Writes mask files to disk
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

exportTrackingResults(this, joinedTrackerDataTable, resultFilePath, resultFileName, varargin)¶

EXPORTTRACKINGRESULTS Exports results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (obj) – Tracker object
joinedTrackerDataTable (table) – Table of tracking results.
resultFilePath (str) – Path to where to save the results. Defaults to segmentationResultDir
resultFileName (str) – Results file name. Defaults to ProjectName_CellCycleResults_Timestamp
varargin (str varchar) –
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Writes text file to disk

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

generateScriptFromTracker(this, varargin)¶

GENERATESCRIPTFROMTRACKER Generates a Matlab (.m) script file based on the tracker project configuration made with the GUI.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- fileName (str): File name. Defaults to TracX_project_ProjectName.m.

Returns:

void – Writes text file to disk

Return type:

(-)

Authors:

Thomas Kuendig - initial implementation

getTrackIndexStorageIndicies(this)¶

GETTRACKINDEXSTORAGEINDICIES Returns indicies of track_index where to store them.

Parameters:

this (obj) – Tracker instance

Returns:

oldFrameLocIdx (array) – Array with location indices in the oldFrame.
emptyDataLocIdx (array) – Array with location indices for empty data.

importAlphaShapes(this)¶

IMPORTALPHASHAPES Imports the alpha shapes form the project directory.

Parameters:: this (obj) – Tracker instance.
Returns:: void – Tracker instance
Return type:: (-)

importData(this)¶

IMPORTDATA Imports segmentation and eventual quantification data using the settigs set in the configuration.ProjectConfiguration object.

Parameters:: this (obj) – Tracker instance
Returns:: void – Imports data into the Tracker instance
Return type:: (-)

improveInitialTracking(this, frameNumber)¶

IMPROVEINITIALTRACKING Improves the initial tracking by correcting for motion and by using the CRF as proofreading.

Parameters:

this (obj) – Tracker instance
frameNumber (int) – Image frame number.

Returns:

newTrackIndex – Array with new, potentially corrected tracking indices.

Return type:

(array)

initializeTrackerCore(this)¶

INITIALIZETRACKERCORE Initailizes Tracker core.

Parameters:: this (obj) – Tracker instance
Returns:: void – Tracker instance
Return type:: (-)

loadTrackingProject(this, filePath, fileName)¶

LOADTRACKINGPROJECT load a TracX project. Load from xml file the meta data and parameters used during tracking.

Parameters:

this (obj) – Tracker instance
filePath (str) – File path for loading the TracX project
fileName (str) – Filename of Tracking project to load.

Returns:

void – Loads the project.

Return type:

(-)

moveToVeryOld(this, selectedTrackArray)¶

MOVETOVERYOLD Moves temporary data stored in OldFrame to VeryOld.

Parameters:

this (obj) – Tracker instance
selectedTrackArray (int) – Array with track indices to be moved to veryOld.

Returns:

this (obj) – Tracker instance
trackIdxToChange (array) – Array with tracking indices to move.

prepareDataFromSegmentationMask(this, imagePath, segmentationPath, segmentationFileNameRegex, imageFileNameRegex, varargin)¶

Parameters:

this (obj) – Tracker instance.
imagePath (str) – Path to the experiment raw images. imageDir
segmentationPath (str) – Path to segmentation results. segmentationResultDir
segmentationFileNameRegex (str) – Regex for the mask filename identifier i.e. Mask_*.
imageFileNameRegex (str) – Regex for the image filename identifier i.e. BF_*.
varargin (str varchar) –
- pxPerPlane (int): Pixel per image plane. Defaults to 0.
- fluoTags (int): Identifier for potential fluorescent images to quantify i.e. {‘XFP’}
- flatFieldFileNames (int): Names of potential flat fields.
- customRegEx (str): Custom regex to identify the segmetnation masks.

Returns:

void – Writes results to disk directly.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

revertSegmentationImageCrop(this)¶

REVERTSEGMENTATIONIMAGECROP Reverts a potentially applied image crop during segmentation to map the segmentation objects’ centroid coordintates to the raw image.

Parameters:: this (obj) – Tracker object
Returns:: void – Acts on Tracker object directly.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

runLineageReconstruction(this, varargin)¶

RUNLINEAGERECONSTRUCTION Starts lineage reconstruction based on tracking results for symmetrically and asymmetrically dividing cells. Wrapper for lineage instance.

Parameters:

this (object) – Tracker instance
varargin (str varchar) –
- symmetricalDivision (str): Flag if lineage reconstruction should be run for symmetrical division. Defaults to false.
- writeControlImages (bool): Flag if control images should be written. Deftaults to false.
- nuclearMarkerChannel (int): Channel that depicts a nuclear marker (such as i.e. Whi5)

Returns:

Acts on:class:Tracker directly

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

runReQuantification(this, fluoTags, varargin)¶

Parameters:

this (object) – Tracker instance.
fluoTags (array) – Array with fluoTags names. Fluorescent images file identifier.
varargin (str varchar) –
- fileIdentifierSegmentationImages (str): File identifier for segmentation images.

Returns:

Runs re quantification and writes results to disk directly.

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

runTracker(this, varargin)¶

RUNTRACKER Runs the tracker.

Parameters:

this (obj) – Tracker instance
varargin (str varchar) –
- flag (array, 1x2): Flag if full cost (tracker) should be used (1) or not (0) as well if motion should be corrected (1) or not (0). Defaults to [1,1].

Returns:

void – Tracker instance

Return type:

(-)

saveCurrentTrackerState(this, varargin)¶

SAVECURRENTTRACKERSTATE Saves the current state of the tracker to disk.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- resultFilePath (str): Path to where to save the tracker stat. Defaults to segmentationResultDir
- resultFileName (str): Results file name. Defaults to Timestamp_TracX_State_Project_ProjectName

Returns:

void – Saves the tracker object stat to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackerCellCycleResultsAsTable(this, varargin)¶

SAVETRACKERCELLCYCLERESULTSASTABLE Saves the cell cycle results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- resultFilePath (str): Path to where to save the results. Defaults to segmentationResultDir
- resultFileName (str): Results file name. Defaults to ProjectName_CellCycleResults_Timestamp
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Saves cell cycle results as table to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackerControlImageFrame(this, frameNumber, varargin)¶

SAVETRACKERCONTROLIMAGES Saves a tracking control images with each tracked cell labeled with its track index for a given image frame.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
varargin (str varchar) –
- fieldName (str): Property to be displayed on the image. Defaults to ‘track_index’ can be any propery of SegmentationData.
- highlightFieldNameVal (int): Pixel to unit conversion factor. I.e. for a 40X objective with 6.5 micron pixel size would result to 6.5/40.
- fontSize (str): Font size of property to be displayed.
- removeContainedTracks (bool): If contained tracks within tracks should be removed. Defaults to true.
- isMarker (bool): If markers should be displayed. Defaults to false.

Returns:

void – Saves images to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackerControlMaskImageFrame(this, frameNumber, varargin)¶

SAVETRACKERCONTROLMASKIMAGEFRAME Saves a tracker control image for a particular frame where the labeled tracker mask are overlayed onto the raw image. Optionaly the label color can be set using a cmap.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
varargin (str varchar) –
- useTrackIndices (bool): If track indices should be used. Defaults to true. Othewise cell indices are used.
- customCMap (array kx3): Use custom colormat to color the cell segmentation masks. Otherwise auto generates one.

Returns:

void – Saves masks to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackerMarkerControlImages(this)¶

SAVEMARKERCONTROLIMAGES Saves marker tracking control images to disk.

Parameters:: this (obj) – Tracker object
Returns:: void – Saves images to disk.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

saveTrackerMaskFrame(this, frameNumber)¶

SAVETRACKERMASKFRAME Saves a labeled mask file. It is a matrix where the elements correspond to a segmented cell are labeled with their track indices.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.

Returns:

void – Saves masks to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackerProjectControlImages(this, varargin)¶

SAVETRACKERPROJECTCONTROLIMAGES Saves control images for the current experiment for all tracked image frames.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- isParallel (bool): Flag if should be run in parallel. Defaults to false.
- maxWorkers (int): Number of workers to us when running in parallel. Defaults to 4. Limited by CPU.

Returns:

void – Saves images to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackerResultsAsTable(this, varargin)¶

SAVETRACKERRESULTSASTABLE Save the tracking results along with the segmentation data in one table to a file.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- resultFilePath (str): Path to where to save the results. Defaults to segmentationResultDir
- resultFileName (str): Results file name. Defaults to ProjectName_TrackingResults_Timestamp
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Saves data as table to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

saveTrackingProject(this, varargin)¶

SAVETRACKINGPROJECT Save a TracX project. Includes the meta data and parameters used during tracking.

Parameters:

this (obj) – Tracker instance
varargin (str varchar) –
- filePath (str): File path for saving the TracX project.
- fileName (str): Filename for the Tracking project.

Returns:

fullpath (:obj:`str`)

Return type:

Full path with filename and .xml extension

setupDependencies(this)¶

SETUPDEPENDENCIES Checks the presence of the external dependencies. If some are missing they are automatically downloaded. Required for manual installation (zip download) of tracx in the absence of git.

Parameters:

this (obj) – Tracker object

Returns:

status – Status, 1 successful 0 otherwise.

Return type:

(int)

Authors:

Andreas P. Cuny - Initial implementation

testBudNeckSegmentation(this, frameNumber, varargin)¶

TESTBUDNECKSEGMENTATION Tests the parameter for budneck segmentation and displays a control image to optimize the parameters if needed.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
varargin (str varchar) –
- divisionMarkerDenoising (int): ROF denoising parameter. divisionMarkerDenoising
- divisionMarkerEdgeSensitivityThresh (int): Edge sensitivity threshold for segmenting the marker outlines. divisionMarkerEdgeSensitivityThresh
- divisionMarkerConvexAreaLowerThresh (int): Lower area limit for detected markers. divisionMarkerConvexAreaLowerThresh
- divisionMarkerConvexAreaUpperThresh (int): Upper area limit for detected markers. divisionMarkerConvexAreaUpperThresh
- contrastLimits (array, 1x2): Image contras limits 0-1.

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

testFeatureDataRemoval(this, frameNumber, feature, threshold)¶

TESTFEATUREDATAREMOVAL Tests the data removal for cells above a feature (SegmentationData) value threshold.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
feature (str) – Any segmentation feature to use to threshold the data before tracking. SegmentationData
threshold (float) – Threshold. Feature values below the threshold are selected.

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

testImageBorderDataRemoval(this, frameNumber, borderOffset)¶

TESTIMAGEBORDERDATAREMOVAL Tests the data removal for cells touching the image border within borderOffset distance.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
borderOffset (int) – Offset from image border in pixel to exclude from tracking.

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

testMarkerTrackingParameters(this, testRange, varargin)¶

TESTTRACKINGPARAMETERS Tests the marker tracking parameters as defined in defined in ParameterConfiguration and displays the results for the given range.

Parameters:

this (obj) – Tracker object
testRange (array, 1x2) – Image frame test range to test Tracking [fromFrame, toFrame].
varargin (str varchar) –
- divisionMarkerMaxTrackFrameSkipping (int): Max marker frame skiping. divisionMarkerMaxTrackFrameSkipping
- divisionMarkerMaxObjCenterDisplacement (int): Max marker displacement. divisionMarkerMaxObjCenterDisplacement
- divisionMarkerMaxObjSizeIncrease (float): Max marker size increase. divisionMarkerMaxObjSizeIncrease
- divisionMarkerMaxObjSizeDecrease (float): Max marker size decrease. divisionMarkerMaxObjSizeDecrease
- divisionMarkerFingerprintHalfWindowSideLength (int): Max marker fingerprint half window side length. divisionMarkerFingerprintHalfWindowSideLength

Returns:

void – Displays the marker tracking results in an interactive movie player.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

testROIDataRemoval(this, frameNumber)¶

TESTROIDATAREMOVAL Tests the data removal for cells outside a ROI.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame number.

Returns:

roi – Returns the region of interest polygon vertices.

Return type:

(array)

Authors:

Andreas P. Cuny - initial implementation

testSegmentationArtefactRemoval(this, frame, channel, stdFactor, varargin)¶

TESTSEGMENTATIONARTEFACTREMOVAL Test of potential segmentation artefacts removal using the cell autofluorescence. Outcome is visualized as image and detected cell indices printed to the console. Assumption is that false positive segmentations have no autofluorecence or comparable to the cell surounding. Useage Tracker.data.getPotSegArtefacts(fluoChannelId, stdFactor) fluoChannelId: Id number of the fluo channel as found in unique(fluo_id) or its corresponding name unique(fluo_name) stdFactor: factor by which the std of the fluo background is multiplied to define a threshold below a cell intensity would be classified as artefact

Parameters:

this (obj) – Tracker object
frame (int) – Image frame to test.
channel (int) – Channel number fluo_id of the fluorescent channel to use for segmentation artefact detection. Defaults to 1.
stdFactor (float) – Factor standard deviation. Defaults to 2.
varargin (str varchar) –
- figure (object): Figure handle. Defaults [];

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

testTrackingParameters(this, testRange, varargin)¶

TESTTRACKINGPARAMETERS Tests the current set of tracker parameters as defined in ParameterConfiguration.

Parameters:

this (obj) – Tracker object
testRange (array, 1x2) – Image frame test range to test Tracking [fromFrame, toFrame].
varargin (str varchar) –
- mode (array 1x2): Allows to test the dCRF tracker instead of the full tracker as well as with or without motion correction i.e [1,0].

Returns:

void – Displays the tracking results in an interactive movie player.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.exportFinalTrackingMasks(this)¶

EXPORTFINALTRACKINGMASKS Exports tracked masks for cells that divide asymmetrically after lineage reconstruction to merge the individual buds with their respective mother mask prior cell division.

Parameters:: this (obj) – Tracker object
Returns:: void – Writes mask files to disk
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

TracX.@Tracker.testFeatureDataRemoval(this, frameNumber, feature, threshold)¶

TESTFEATUREDATAREMOVAL Tests the data removal for cells above a feature (SegmentationData) value threshold.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
feature (str) – Any segmentation feature to use to threshold the data before tracking. SegmentationData
threshold (float) – Threshold. Feature values below the threshold are selected.

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.exportTrackingResults(this, joinedTrackerDataTable, resultFilePath, resultFileName, varargin)¶

EXPORTTRACKINGRESULTS Exports results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (obj) – Tracker object
joinedTrackerDataTable (table) – Table of tracking results.
resultFilePath (str) – Path to where to save the results. Defaults to segmentationResultDir
resultFileName (str) – Results file name. Defaults to ProjectName_CellCycleResults_Timestamp
varargin (str varchar) –
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Writes text file to disk

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.testSegmentationArtefactRemoval(this, frame, channel, stdFactor, varargin)¶

Parameters:

this (obj) – Tracker object
frame (int) – Image frame to test.
channel (int) – Channel number fluo_id of the fluorescent channel to use for segmentation artefact detection. Defaults to 1.
stdFactor (float) – Factor standard deviation. Defaults to 2.
varargin (str varchar) –
- figure (object): Figure handle. Defaults [];

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.deleteByFeature(this, feature, threshold, varargin)¶

DELETEBYFEATURE Deletes segmentation objects exceeding a threshold for a feature.

Parameters:

this (obj) – Tracker object
feature (str) – Any segmentation feature to use to threshold the data before tracking. SegmentationData
threshold (float) – Threshold. Feature values below the threshold are selected.
varargin (str varchar) –
- neighbourhoodSearchRadius (int): Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on Tracker object directly and deletes selected data below threshold.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveTrackerResultsAsTable(this, varargin)¶

SAVETRACKERRESULTSASTABLE Save the tracking results along with the segmentation data in one table to a file.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- resultFilePath (str): Path to where to save the results. Defaults to segmentationResultDir
- resultFileName (str): Results file name. Defaults to ProjectName_TrackingResults_Timestamp
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Saves data as table to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveTrackerProjectControlImages(this, varargin)¶

SAVETRACKERPROJECTCONTROLIMAGES Saves control images for the current experiment for all tracked image frames.

Parameters:

this (obj) – Tracker object
varargin (str varchar) –
- isParallel (bool): Flag if should be run in parallel. Defaults to false.
- maxWorkers (int): Number of workers to us when running in parallel. Defaults to 4. Limited by CPU.

Returns:

void – Saves images to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.exportCellCycleResults(this, resultFilePath, resultFileName, varargin)¶

EXPORTCELLCYCLERESULTS Exports the cell cycle results to disk as text, csv or mat file format delimited by your choice. Default is as text file and tab delimited.

Parameters:

this (obj) – Tracker object
resultFilePath (str) – Path to where to save the results. Defaults to segmentationResultDir
resultFileName (str) – Results file name. Defaults to ProjectName_CellCycleResults_Timestamp
varargin (str varchar) –
- fileType (str): File type. Defaults to txt. Valid options are ‘txt’, ‘csv’, ‘mat’.
- dataDelimiter (str): Data delimiter. Defaults to tab. Valid options are ‘,’, ‘comma’, ‘ ‘, ‘space’, ‘t’, ‘tab’, ‘;’, ‘semi’, ‘|’, ‘bar’.

Returns:

void – Writes text file to disk

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveTrackerMarkerControlImages(this)¶

SAVEMARKERCONTROLIMAGES Saves marker tracking control images to disk.

Parameters:: this (obj) – Tracker object
Returns:: void – Saves images to disk.
Return type:: (-)
Authors:: Andreas P. Cuny - initial implementation

TracX.@Tracker.setupDependencies(this)¶

Parameters:

this (obj) – Tracker object

Returns:

status – Status, 1 successful 0 otherwise.

Return type:

(int)

Authors:

Andreas P. Cuny - Initial implementation

TracX.@Tracker.testROIDataRemoval(this, frameNumber)¶

TESTROIDATAREMOVAL Tests the data removal for cells outside a ROI.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame number.

Returns:

roi – Returns the region of interest polygon vertices.

Return type:

(array)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.correctTrackMisassignment(this, frameArray, oldTrackIndexArray, newTrackIndexArray)¶

CORRECTTRACKMISASSIGNMENT Allows to manually correct a cell to track assignment on specific frames. A given track index will be replaced with a new track index. The arrays need to have the same size.

Parameters:

this (obj) – Tracker instance.
frameArray (array) – Array of image frames.
oldTrackIndexArray (array) – Array of old track indices to be replaced.
newTrackIndexArray (array) – Array of new track indices to relpace the old ones with.

Returns:

void – Acts on Tracker instance directly

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveTrackerControlMaskImageFrame(this, frameNumber, varargin)¶

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
varargin (str varchar) –
- useTrackIndices (bool): If track indices should be used. Defaults to true. Othewise cell indices are used.
- customCMap (array kx3): Use custom colormat to color the cell segmentation masks. Otherwise auto generates one.

Returns:

void – Saves masks to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.testImageBorderDataRemoval(this, frameNumber, borderOffset)¶

TESTIMAGEBORDERDATAREMOVAL Tests the data removal for cells touching the image border within borderOffset distance.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.
borderOffset (int) – Offset from image border in pixel to exclude from tracking.

Returns:

void – Displays the detected segmentation artifacts in an image.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.saveTrackerMaskFrame(this, frameNumber)¶

SAVETRACKERMASKFRAME Saves a labeled mask file. It is a matrix where the elements correspond to a segmented cell are labeled with their track indices.

Parameters:

this (obj) – Tracker object
frameNumber (int) – Image frame to test.

Returns:

void – Saves masks to disk.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.deleteSegObjAtBorder(this, borderOffset)¶

DELETESEGOBJATBORDER Delete segmentation objects at the image border within the border offset.

Parameters:

this (obj) – Tracker object
borderOffset (int) – Offset from image border in pixel to exclude from tracking.

Returns:

void – Acts on Tracker object directly and deletes selected data from the image border up to the border offset.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.deleteByROI(this, roi, varargin)¶

DELETEBYROI Deletes segmentation objects outside a region of interest (ROI).

Parameters:

this (obj) – Tracker object
roi (array) – Region of interest defined by polygon vertices to keep data for tracking.
varargin (str varchar) –
- neighbourhoodSearchRadius (int): Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on Tracker object directly and deletes selected data outside ROI.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Tracker.runLineageReconstruction(this, varargin)¶

RUNLINEAGERECONSTRUCTION Starts lineage reconstruction based on tracking results for symmetrically and asymmetrically dividing cells. Wrapper for lineage instance.

Parameters:

this (object) – Tracker instance
varargin (str varchar) –
- symmetricalDivision (str): Flag if lineage reconstruction should be run for symmetrical division. Defaults to false.
- writeControlImages (bool): Flag if control images should be written. Deftaults to false.
- nuclearMarkerChannel (int): Channel that depicts a nuclear marker (such as i.e. Whi5)

Returns:

Acts on:class:Tracker directly

Return type:

void -

Authors:

Andreas P. Cuny - initial implementation

TrackerConfiguration ¶

class TracX.@TrackerConfiguration.TrackerConfiguration¶

Bases: handle

TRACKERCONFIGRURATION Creates an object to store and manipulate metadata used and defining a Tracker project. The metadata itself is stored in TracX.@ParameterConfiguration and TracX.@ProjectConfiguration.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

TrackerConfiguration()¶

TrackerConfiguration Constructs a TrackerConfiguration object to manipulate and store tracking TracX.@ParameterConfiguration and TracX.@ProjectConfiguration data.

Parameters:: -
Returns:: Returns a TrackerConfiguration instance. object instance with initialized TracX.@ParameterConfiguration (default values) and TracX.@ProjectConfiguration (empty) objects
Return type:: this object
Authors:: Andreas P. Cuny - initial implementation

Property Summary

ParameterConfiguration¶: TracX.@ParameterConfiguration instance stores all the parameters needed for tracking.

ProjectConfiguration¶: TracX.@ProjectConfiguration instance stores all information needed for a tracking project.

io¶: TracX.@IO instance implementing read/write methods

Method Summary

exportTrackerConfiguration(this, file)¶

EXPORTTRACKERCONFIGURATION Writes a TracX configuration xml file with all the parameters stored in the ParameterConfiguration and ProjectConfiguration object.

Parameters:

this (object) – TrackerConfiguration instance.
file (str) – Path to TracX configuration xml file and its name.

Returns:

Writes to disk directly.

Return type:

void (-)

importTrackerConfiguration(this, file)¶

IMPORTTRACKERCONFIGURATION Reads a TracX configuration xml file and stores the parameters in the ParameterConfiguration object.

Parameters:

this (object) – TrackerConfiguration instance.
file (str) – Path to parameter xml file

Returns:

this – Acts on TrackerConfiguration object directly and returns TracX configured.

Return type:

object

TrackerData ¶

TracX.@TrackerData.getFieldArrayColorMap(this, varargin)¶

GETFIELDARRAYCOLORMAP Returns a colormap for the properties/ field arrays. Special colormaps are returned for ‘track_index’, ‘track_parent’. If currTrack is given, all other tracks will be colored in grey.

Parameters:

this (obj) – TrackerData instance.
varargin (str varchar) –
- property (str): Property of SegmentationData for which colormap shold be returned. Defaults to track_index.
- currTrack (int): Current track index if single track should be highlighted. Defaults to 0.

Returns:

colormap – Returns the colormap

Return type:

(array) kx3

Authors:

Thomas Kuendig - initial implementation in GUI
Andreas P. Cuny - implementation in TracX core.

TracX.@TrackerData.fillTrackHoles(this, imageFrameNumberArray, fingerprintHalfWindowSideLength, fingerprintMaxConsideredFrequencies, imageDir, imageFingerprintFileArray, imageCropCoordinateArray, neighbourhoodSearchRadius)¶

FILLTRACKHOLES is supposed to create a virtual segmentation object for image frames where a certain track index is missing but the image frame before and after still contain the object (cell). This holes (in time) exist when a cell was not segmented (detected) on a particular image frame but does exist.

Parameters:

this (obj) – TrackerData instance.
imageFrameNumberArray (array, kx1) – Array of all existing image frames for the given experiment.
fingerprintHalfWindowSideLength (int) – fingerprintHalfWindowSideLength
fingerprintMaxConsideredFrequencies (int) – fingerprintMaxConsideredFrequencies
imageDir (str) – imageDir
imageFingerprintFileArray (array) – imageFingerprintFileArray
imageCropCoordinateArray (array, 1x4) – imageCropCoordinateArray
neighbourhoodSearchRadius (int) – Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on TrackerData.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@TrackerData.delByROI(this, roi, neighbourhoodSearchRadius)¶

DELETEBYROI Deletes segmentation objects outside a region of interest (ROI).

Parameters:

this (obj) – TrackerData instance.
roi (array) – Region of interest defined by polygon vertices to keep data for tracking.
neighbourhoodSearchRadius (int) – Neighbourhood radius. Defaults to neighbourhoodSearchRadius

Returns:

void – Acts on TrackerData object directly and deletes selected data outside ROI.

Return type:

(-)

Authors:

Andreas P. Cuny - initial implementation

TracX.@TrackerData.propagatePendingDaughters(this, newFrameData, frameNumber, pendingDaughters, oldFrameData)¶

PROPAGATEPENDINGDAUGHTERS Resolve pending mother-daughter assignments on non-last frames.

Called on every frame except the last. Processes only entries that are expected at this frame (flagFrame + 1). If the expected daughter has not yet appeared, the entry is kept for the next iteration. Stale entries (daughter never appeared within a one-frame window) are purged.

Parameters:

this (object) – TrackerData instance.
newFrameData (object) – @TemporaryTrackingData for the current frame
frameNumber (array, 1x1) – Current image frame number
pendingDaughters (struct) – containers.Map of pending assignments.
oldFrameData (object) – @TemporaryTrackingData for the previous frame Used to inherit pole ages when stored ages are absent.

Return type:

void -

See also: propagatePendingDaughtersFinalFrame

Authors:: Andreas P. Cuny - initial implementation

TracX.@TrackerData.assignMammalianTrackparent(this, newFrameData, assignment, parentCandidateArray, parentCandidateType, daughterPairs, frame, printOutput)¶

ASSIGNMAMMALIANTRACKPARENT Assignes the track parent for symmetrical cell division of convex shapes such as for mammalian cells.

Parameters:

this (object) – TrackerData instance.
newFrameData (object) – newFrame data
assignment (object) – Assignment result
parentCandidateArray (array) – Array with parent candidates
parentCandidateType (int) – Type of parents (0 or 1).
daughterPairs (array) – Array with daughter pairs
frame (int) – Image frame to be evaluated
printOutput (bool) – Flag, if text output should be displayed in the console.

Returns:

newFrameData object – Parent set for daughter pair.
splits object – Array with potential splits for continous track.

Authors:

Thomas Kuendig - initial implementation

TracX.@TrackerData.getCloseCellNeighbourIdx(xCoordinateArray, yCoordinateArray, neighbourhoodSearchRadius, varargin)¶

GETCLOSECELLNEIGHBOURIDX Returns a square logical matrix of size length(x) where as 1 corresponds to a neighbour within the neighbourhoodSearchRadius.

Parameters:

ignoredArg (obj) – TrackerData instance.
xCoordinateArray (array, kx1) – Array with x coordinates
yCoordinateArray (array, kx1) – Array with y coordinates
neighbourhoodSearchRadius – [Int] Radius in pixel within an other point defined by the coordinate arrays x and y is considered to be a neighbour of (x_i,y_i). neighbourhoodSearchRadius

Returns:

closeNeighboursIdx – Square logical matrix selecting the neighbours within neighbourhoodSearchRadius.

Return type:

array kxk

Authors:

Andreas P. Cuny - initial implementation

TracX.@TrackerData.getConsecutiveCloseCellNeighbourIdx(xO, xOF, yO, yOF, trO, xN, yN, trN, neighbourhoodSearchRadius)¶

GETCONSECUTIVECLOSECELLNEIGHBOURIDX Returns the neighbourhood indices for consecutive image frames. It returns the joined neighbourhood for segmentation objects existing on both image frames, for segmentation objects only on the first and second frame respectively. The shape of the matrix is first times second frame in the order of the track index of the segmentation objects on the respective frames.

Parameters:

xO (array, 1xN) – Array with x coordinates from oldFrame.
xOF (array, 1xN) – Array with filtered x coordinates from oldFrame.
yO (array, 1xN) – Array with y coordinates from oldFrame.
yOF (array, 1xN) – Array with filtered y coordinates from oldFrame.
trO (array, 1xN) – Array with track indices from oldFrame.
xN (array, 1xN) – Array with x coordinates from newFrame.
yN (array, 1xN) – Array with y coordinates from newFrame.
trN (array, 1xN) – Array with track indices from newFrame.
neighbourhoodSearchRadius (int) – neighbourhoodSearchRadius

Returns:

joinedNeighbours array – Array with joined neighbourhood between old and new frame.
joinedNeighboursWMotion array – Array with joined neighbourhood including motion between old and new frame.
oldNeighbours array – Array with neighbourhood of oldFrame.
newNeighbours array – Array with neighbourhood of newFrame.

Authors:

Andreas P. Cuny - initial implementation

TracX.@TrackerData.decompressOrientationData(this)¶

DECOMPRESSORIENTATIONDATA Decompresses the orientation vector into from a single number.

Parameters:: this (object) – TrackerData instance.
Return type:: void -
Authors:: Thomas Kuendig - initial implementation

TracX.@TrackerData.propagatePendingDaughtersFinalFrame(this, newFrameData, frameNumber, pendingDaughters)¶

PROPAGATEPENDINGDAUGHTERSFINALFRAME Resolve all remaining pending mother-daughter assignments at the last frame of the tracked range.

Called exactly once, on the final frame. Unlike propagatePendingDaughters, this function processes every entry in pendingDaughters regardless of when it was flagged, because no future frames exist to confirm or carry forward any unresolved assignments.

Behaviour per entry:

Daughter present and unassigned assign using stored pole ages,
propagate to master data, remove key.
Daughter present but already set remove key (no action needed).
Daughter absent at final frame log a warning, remove key.
The experiment ended before this daughter appeared; the parent is recorded as having divided but the daughter track is unresolvable.

Pole ages are taken from the values stored in the pendingDaughters map at flagging time (parentPole1Age / parentPole2Age). These are always available because setParentSymDivCells stores them when creating the pending entry. No lookback into historical frame data is needed.

Parameters:

this (object) – TrackerData instance.
newFrameData (object) – @TemporaryTrackingData for the current frame
frameNumber (array, 1x1) – Current image frame number
pendingDaughters (struct) – containers.Map of pending assignments.

Return type:

void -

Utils ¶

TracX.@Utils.getSegAreaBoundingBox(xc, yc, offset)¶

GETSEGAREABOUNDINGBOX Returns the bounding box of an image area that has been segmented to focus/zoom on this particular area for image visualization purpose.

Parameters:

xc (array Nx1) – Array of x components of segmented objects.
yc (array Nx1) – Array of y components of segmented objects.
offset (int) – Offset from true corner points of segmented area.

Returns:

bx (int, 1x1) – X component of bounding box.
by (int, 1x1) – Y component of bounding box.
bw (int, 1x1) – Width component of bounding box.
bh (int, 1x1) – Height component of bounding box.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.getBWLabelColor(colorMap)¶

GETBWLABELCOLOR Returns either a black or white colormap that should be well readable on an given input colorMap.

Parameters:: colorMap (array Nx3) – Colormap
Returns:: color – BW colormap
Return type:: (array Nx3)
Authors:: Thomas Kuendig - initial implementation

TracX.@Utils.natSortNames(X, varargin)¶

NATSORT Wrapper to alphanumeric / Natural-Order sort of a cell array of filenames/filepaths. See TracX.ExternalDependencies.natsortfiles for detailed information.

Parameters:

X (double 1xN) – Array to be sorted
varargin (str) – Additional input arguments. See TracX.ExternalDependencies.natsortfiles for detailed information.

Returns:

X (array 1xN) – Cell of Strings, <X> with all strings sorted into natural-order.
ndx (arrax 1xN) – Numeric Array, such that Y = X(ndx). The same size as <X>.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.insertValueAtIdx(arrIn, val, idx)¶

INSERTVALUEATIDX Inserts an array of values a at a certain position within array b.

Parameters:

arrIn (array 1xM) – Array where values have to be inserted.
val (array 1xN) – Array with values to insert.
idx (int 1x1) – Index withing arrIn where.

Returns:

arrOut – Final array with inserts

Return type:

(array 1x(M+N))

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.padImageCrop(image, imageCropCoordinateArray)¶

PADIMAGECROP creates an image crop of the 2D input image (NxM) applying the crop coordinates. It fills crops at the image border with zeros to always keep the same imgOut image size (image padding).

Parameters:

image (uint16 NxN) – Image matrix
imageCropCoordinateArray (int 1x4) – Array with coordinates to crop an image. imageCropCoordinateArray

Returns:

paddedImage – Image matrix with exact size indicated by imageCropCoordinateArray where as regions outside the input images are set to 0 but the size given by imageCropCoordinateArray is maintained.

Return type:

(uint16, NxM)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.progressBar(total, varargin)¶

PROGRESSBAR Wrapper around a class to provide a convenient and useful progress bar

Parameters:

total (int) – The total number of iterations [default: []] matrix
varargin (array) – Title - the progress bar’s title shown in front [default: ‘Processing’] Unit - the unit of the update process. Can either be ‘Iterations’ or ‘Bytes’ [default: ‘Iterations’] UpdateRate - the progress bar’s update rate in Hz. Defines the printing update interval [default: 5 Hz]

Returns:

retBin – Returns a progressBar instance.

Return type:

(object)

Authors:

J.-A. Adrian (JA) [jensalrik.adrian AT gmail.com] - initial implementation 28-Jun-2016 16:52
Andreas P. Cuny - Wrapper around ProgressBar for TracX

TracX.@Utils.progressUpdateParallel(stepSize, workerDirName)¶

UPDATEPARALLEL Wrapper around update function when ProgressBar is used in parallel setup. For details see TracX.ExternalDependencies.matlabProgressBar

Parameters:

stepSize (int) – The size of the progress step when the function is called. This can be used to pass the number of processed bytes when using ‘Bytes’ as units. If bytes are used be sure to pass only integer values. [default: stepSize = 1]
workerDirName (str) – Directory where the worker aux. files will be saved. This can be specified for debug purposes or if multiple progress bars in a parallel setup would get in each other’s way since all have the same file pattern and would distract each progress bar’s progress state. [default: workerDirName = tempdir()]

Returns:

filePattern – The common beginning of every file name before the unique part begins. This is an auxiliary function output which is used by the ProgressBar() class. Typically not be of interest for the user. The variable is only returned if no input arguments were passed!

Return type:

(str)

Example:

>>> [pattern] = updateParallel(1, pwd)

Authors:

J.-A. Adrian (JA) [jensalrik.adrian AT gmail.com] - initial implementation 28-Jun-2016 16:52
Andreas P. Cuny - Wrapper around updateParallel for TracX

TracX.@Utils.rgb2java(rgb)¶

RGB2JAVA Convert uint8 rgb Matlab image to Java BufferedImage.

Parameters:: rgb (array, NxM) – RGB Matlab image
Returns:: image – Java BufferedImage
Return type:: (array NxM)

Note

Adopted from original im2java2d.m (Matlab) that fails to run with parfor / parpool due to inexistent ‘swing’ check.

Authors:: Andreas P. Cuny - initial implementation Aaron Ponti - initial implementation

TracX.@Utils.imcrop3C(s, cuboidWindow)¶

IMCROP3C Custom fast implementation on Matlabs imcrop3 to crop a 3D image.

Parameters:

s (double NxNx3) – 3D image stack
cuboidWindow (array 1x6) – Crop coordinates in the form of [x, y, z, w, h, l]

Returns:

ret – Croped 3D image stack.

Return type:

(double NxNx3)

Authors:

Thomas Kuendig - initial implementation

TracX.@Utils.getLeadingZeros(str)¶

GETLEADINGZEROS Get the number of leading zeros of a string.

Parameters:: str (str) – String.
Returns:: nLeadingZeros
Return type:: int The number of leading zeros.
Authors:: Andreas P. Cuny - initial implementation

TracX.@Utils.isPointInsideEllipse(x, y, x0, y0, theta, minorAxis, majorAxis)¶

ISPOINTINSIDEELLIPSE Determines if a point P(x,y) lays inside or on the ellipse boundaries given by E(x0,y0, theta, minorAxis, majorAxis).

Parameters:

x (float, Nx1) – x coordinate of query point.
y (float, Nx1) – y coordinate of query point.
x0 (float, 1x1) – x coordinate of ellipse center.
y0 (float, 1x1) – y coordinate of ellipse center.
theta (float, 1x1) – angle of ellipse rotaion in degrees.
minorAxis (float, 1x1) – minorAxis length of ellipse.
majorAxis (float, 1x1) – majorAxis length of ellipse.

Returns:

Result array. If ret < 1 := inside ellipse else if ret == 1 := on ellpise else ret > 1 := outside ellipse.

Return type:

ret (Nx1, float)

Example:

>>> printToConsole('My message')
06-Jun-2017 11:30:30:  My message

Authors:: Andreas P. Cuny - initial implementation

TracX.@Utils.checkToolboxStatus(this)¶

CHECKTOOLBOXSTATUS Checks if all required Matlab toolboxes are installed. Returns 1 if all installed, 0 otherwise.

Parameters:: this (obj) – Tracker object
Returns:: status – Returns 1 if all installed, 0 otherwise.
Return type:: (array Nx3)
Authors:: Andreas P. Cuny - initial implementation

TracX.@Utils.getCommonLogical(logicalA, logicalB)¶

GETCOMMONLOGICAL Get common logical of the subset of the logical array A and a logical array B of the size of the subset of logical A.

Parameters:

logicalA (array, Nx1) – Logical array A.
logicalB (array, Mx1) – Logical array B.

Returns:

logicalA (array Nx1) – Logical array including logicalB but of size logicalA.
logicalAOnlyB (array Nx1) – Logical array of size logicalA but only containing logicalB.

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.getRecursiveTrackParentColoring(this, root, color, colormap, trackIndex, trackParent)¶

GETRECURSIVETRACKPARENTCOLORING Modifies an existing colormap such that track parents are colored at a distance to the input color proportional to the length of the track.

Parameters:

this (object) – Utils instance.
root (int) – Root track index
color (int) – Color
colormap (int, Nx3) – Color map
trackIndex (array, Nx1) – Track index array
trackParent (array, Nx1) – Track parent array

Returns:

colormap – Color map

Return type:

array Nx3

Authors:

Thomas Kuending - initial implementation

TracX.@Utils.downloadFile(this, url, fileName)¶

DOWNLOADFILE Downloads a file and returns the path.

Parameters:

this (obj) – Tracker object
url (str) – URL to the file to be downloaded
fileName (str) – Name of the downloaded file.

Returns:

dest – Returns the file url/location on the system.

Return type:

(str)

Authors:

Andreas P. Cuny - Initial implementation

class TracX.@Utils.Utils¶

UTILS Defines general utility functions used for TracX.

Authors:: Andreas P. Cuny - initial implementation

Constructor Summary

Utils()¶

UTILS Constructor of TracX.Utils class.

Returns:: obj – Returns a Utils instance.
Return type:: object
Authors:: Andreas P. Cuny - initial implementation

Method Summary

checkToolboxStatus(this)¶

CHECKTOOLBOXSTATUS Checks if all required Matlab toolboxes are installed. Returns 1 if all installed, 0 otherwise.

Parameters:: this (obj) – Tracker object
Returns:: status – Returns 1 if all installed, 0 otherwise.
Return type:: (array Nx3)
Authors:: Andreas P. Cuny - initial implementation

downloadFile(this, url, fileName)¶

DOWNLOADFILE Downloads a file and returns the path.

Parameters:

this (obj) – Tracker object
url (str) – URL to the file to be downloaded
fileName (str) – Name of the downloaded file.

Returns:

dest – Returns the file url/location on the system.

Return type:

(str)

Authors:

Andreas P. Cuny - Initial implementation

getBWLabelColor(colorMap)¶

GETBWLABELCOLOR Returns either a black or white colormap that should be well readable on an given input colorMap.

Parameters:: colorMap (array Nx3) – Colormap
Returns:: color – BW colormap
Return type:: (array Nx3)
Authors:: Thomas Kuendig - initial implementation

getColorMap(intendedSize, varargin)¶

GETCOLORMAP Returns a colormap of a user defined size with well distingushable colors.

Parameters:

intendedSize (int, 1x1) – Size of final colormap
varargin (array, Nx3) – [Optional] customColorMap which will be resized to intended size (color pattern will be repeated until final size is reached).

Returns:

cmap – Color map with user defined size based on colors defined in colorScheme1 (repetitions).

Return type:

(array Nx3)

Authors:

Andreas P. Cuny - initial implementation

getCommonLogical(logicalA, logicalB)¶

GETCOMMONLOGICAL Get common logical of the subset of the logical array A and a logical array B of the size of the subset of logical A.

Parameters:

logicalA (array, Nx1) – Logical array A.
logicalB (array, Mx1) – Logical array B.

Returns:

logicalA (array Nx1) – Logical array including logicalB but of size logicalA.
logicalAOnlyB (array Nx1) – Logical array of size logicalA but only containing logicalB.

Authors:

Andreas P. Cuny - initial implementation

getLeadingZeros(str)¶

GETLEADINGZEROS Get the number of leading zeros of a string.

Parameters:: str (str) – String.
Returns:: nLeadingZeros
Return type:: int The number of leading zeros.
Authors:: Andreas P. Cuny - initial implementation

getMaxNumCompThreads()¶

GETMAXNUMCOMPTHREADS Returns the maximal number of compute threads.

Parameters:: ignoredArg (obj) – TracX.@Utils
Returns:: ret – Color map with user defined size based on colors defined in colorScheme1 (repetitions).
Return type:: (int)
Authors:: Andreas P. Cuny - initial implementation

getRecursiveTrackParentColoring(this, root, color, colormap, trackIndex, trackParent)¶

GETRECURSIVETRACKPARENTCOLORING Modifies an existing colormap such that track parents are colored at a distance to the input color proportional to the length of the track.

Parameters:

this (object) – Utils instance.
root (int) – Root track index
color (int) – Color
colormap (int, Nx3) – Color map
trackIndex (array, Nx1) – Track index array
trackParent (array, Nx1) – Track parent array

Returns:

colormap – Color map

Return type:

array Nx3

Authors:

Thomas Kuending - initial implementation

getSegAreaBoundingBox(xc, yc, offset)¶

GETSEGAREABOUNDINGBOX Returns the bounding box of an image area that has been segmented to focus/zoom on this particular area for image visualization purpose.

Parameters:

xc (array Nx1) – Array of x components of segmented objects.
yc (array Nx1) – Array of y components of segmented objects.
offset (int) – Offset from true corner points of segmented area.

Returns:

bx (int, 1x1) – X component of bounding box.
by (int, 1x1) – Y component of bounding box.
bw (int, 1x1) – Width component of bounding box.
bh (int, 1x1) – Height component of bounding box.

Authors:

Andreas P. Cuny - initial implementation

imcrop3C(s, cuboidWindow)¶

IMCROP3C Custom fast implementation on Matlabs imcrop3 to crop a 3D image.

Parameters:

s (double NxNx3) – 3D image stack
cuboidWindow (array 1x6) – Crop coordinates in the form of [x, y, z, w, h, l]

Returns:

ret – Croped 3D image stack.

Return type:

(double NxNx3)

Authors:

Thomas Kuendig - initial implementation

imcropC(image, imageCropCoordinateArray)¶

IMCROPC Crop image. Custom imcrop function. Faster (~3.5-6x) than native MATLAB interactive imcrop function.

Parameters:

image (double, NxM) – Image matrix
imageCropCoordinateArray (int, 1x4) – Array with coordinates to crop an image. imageCropCoordinateArray

Returns:

crop – Croped image matrix.

Return type:

(double NxM)

Authors:

Andreas P. Cuny - initial implementation

insertValueAtIdx(arrIn, val, idx)¶

INSERTVALUEATIDX Inserts an array of values a at a certain position within array b.

Parameters:

arrIn (array 1xM) – Array where values have to be inserted.
val (array 1xN) – Array with values to insert.
idx (int 1x1) – Index withing arrIn where.

Returns:

arrOut – Final array with inserts

Return type:

(array 1x(M+N))

Authors:

Andreas P. Cuny - initial implementation

isPointInsideEllipse(x, y, x0, y0, theta, minorAxis, majorAxis)¶

ISPOINTINSIDEELLIPSE Determines if a point P(x,y) lays inside or on the ellipse boundaries given by E(x0,y0, theta, minorAxis, majorAxis).

Parameters:

x (float, Nx1) – x coordinate of query point.
y (float, Nx1) – y coordinate of query point.
x0 (float, 1x1) – x coordinate of ellipse center.
y0 (float, 1x1) – y coordinate of ellipse center.
theta (float, 1x1) – angle of ellipse rotaion in degrees.
minorAxis (float, 1x1) – minorAxis length of ellipse.
majorAxis (float, 1x1) – majorAxis length of ellipse.

Returns:

Result array. If ret < 1 := inside ellipse else if ret == 1 := on ellpise else ret > 1 := outside ellipse.

Return type:

ret (Nx1, float)

Example:

>>> printToConsole('My message')
06-Jun-2017 11:30:30:  My message

Authors:: Andreas P. Cuny - initial implementation

natSortNames(X, varargin)¶

NATSORT Wrapper to alphanumeric / Natural-Order sort of a cell array of filenames/filepaths. See TracX.ExternalDependencies.natsortfiles for detailed information.

Parameters:

X (double 1xN) – Array to be sorted
varargin (str) – Additional input arguments. See TracX.ExternalDependencies.natsortfiles for detailed information.

Returns:

X (array 1xN) – Cell of Strings, <X> with all strings sorted into natural-order.
ndx (arrax 1xN) – Numeric Array, such that Y = X(ndx). The same size as <X>.

Authors:

Andreas P. Cuny - initial implementation

padImageCrop(image, imageCropCoordinateArray)¶

PADIMAGECROP creates an image crop of the 2D input image (NxM) applying the crop coordinates. It fills crops at the image border with zeros to always keep the same imgOut image size (image padding).

Parameters:

image (uint16 NxN) – Image matrix
imageCropCoordinateArray (int 1x4) – Array with coordinates to crop an image. imageCropCoordinateArray

Returns:

Return type:

(uint16, NxM)

Authors:

Andreas P. Cuny - initial implementation

printTimeLeft(taskName, actStep, totStep)¶

PRINTTIMELEFT printTimeLeft(taskName, actStep, totStep) prints the remaining time in a computation when actStep steps out of totSteps have been made. taskName is a String describing what will be computed A “tic” must have been called at the beginnig of the computation. This code must be called at the end of the step act_step (and not at the beginning). To reduce the computaton overhead, the code will only be active if floor(percentage) has changed in the last step (this can easy be removed by deleting the first ‘if’ condition).

Note

Adopted from inital implementation from Nicolas Le Roux. https://ch.mathworks.com/matlabcentral/fileexchange/8076-ascii-progress-bar?s_tid=prof_contriblnk

Parameters:

taskName (str, 1x1) – Name of the task.
actStep (int, 1x1) – Current step of the evaluation totStep (int, 1x1): Total number of steps in this task/loop.

Returns:

Prints to console directly

Return type:

void (str)

Example:

>>> tic
>>> for i = 1:10
>>>    printTimeLeft('MyTask', i, 10)
>>> end

Authors:

Nicolas Le Roux [lerouxni@iro.umontreal.ca] - initial implementation July, 20th, 2005
Andreas P. Cuny - Restructured code and modified design of waitbar for TracX

printToConsole(message)¶

PRINTTOCONSOLE Outputs logging/status information to the console with a time stamp. A static function in Utils.

Parameters:: message (str) – Message to be printed to the console.
Returns:: Prints message to console directly.
Return type:: void (str)

Example:

>>> printToConsole('My message')
06-Jun-2017 11:30:30:  My message

Authors:: Andreas P. Cuny - initial implementation

progressBar(total, varargin)¶

PROGRESSBAR Wrapper around a class to provide a convenient and useful progress bar

Parameters:

total (int) – The total number of iterations [default: []] matrix
varargin (array) – Title - the progress bar’s title shown in front [default: ‘Processing’] Unit - the unit of the update process. Can either be ‘Iterations’ or ‘Bytes’ [default: ‘Iterations’] UpdateRate - the progress bar’s update rate in Hz. Defines the printing update interval [default: 5 Hz]

Returns:

retBin – Returns a progressBar instance.

Return type:

(object)

Authors:

J.-A. Adrian (JA) [jensalrik.adrian AT gmail.com] - initial implementation 28-Jun-2016 16:52
Andreas P. Cuny - Wrapper around ProgressBar for TracX

progressUpdateParallel(stepSize, workerDirName)¶

UPDATEPARALLEL Wrapper around update function when ProgressBar is used in parallel setup. For details see TracX.ExternalDependencies.matlabProgressBar

Parameters:

stepSize (int) – The size of the progress step when the function is called. This can be used to pass the number of processed bytes when using ‘Bytes’ as units. If bytes are used be sure to pass only integer values. [default: stepSize = 1]
workerDirName (str) – Directory where the worker aux. files will be saved. This can be specified for debug purposes or if multiple progress bars in a parallel setup would get in each other’s way since all have the same file pattern and would distract each progress bar’s progress state. [default: workerDirName = tempdir()]

Returns:

Return type:

(str)

Example:

>>> [pattern] = updateParallel(1, pwd)

Authors:

J.-A. Adrian (JA) [jensalrik.adrian AT gmail.com] - initial implementation 28-Jun-2016 16:52
Andreas P. Cuny - Wrapper around updateParallel for TracX

rgb2java(rgb)¶

RGB2JAVA Convert uint8 rgb Matlab image to Java BufferedImage.

Parameters:: rgb (array, NxM) – RGB Matlab image
Returns:: image – Java BufferedImage
Return type:: (array NxM)

Note

Adopted from original im2java2d.m (Matlab) that fails to run with parfor / parpool due to inexistent ‘swing’ check.

Authors:: Andreas P. Cuny - initial implementation Aaron Ponti - initial implementation

TracX.@Utils.getColorMap(intendedSize, varargin)¶

GETCOLORMAP Returns a colormap of a user defined size with well distingushable colors.

Parameters:

intendedSize (int, 1x1) – Size of final colormap
varargin (array, Nx3) – [Optional] customColorMap which will be resized to intended size (color pattern will be repeated until final size is reached).

Returns:

cmap – Color map with user defined size based on colors defined in colorScheme1 (repetitions).

Return type:

(array Nx3)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.printTimeLeft(taskName, actStep, totStep)¶

Note

Adopted from inital implementation from Nicolas Le Roux. https://ch.mathworks.com/matlabcentral/fileexchange/8076-ascii-progress-bar?s_tid=prof_contriblnk

Parameters:

taskName (str, 1x1) – Name of the task.
actStep (int, 1x1) – Current step of the evaluation totStep (int, 1x1): Total number of steps in this task/loop.

Returns:

Prints to console directly

Return type:

void (str)

Example:

>>> tic
>>> for i = 1:10
>>>    printTimeLeft('MyTask', i, 10)
>>> end

Authors:

Nicolas Le Roux [lerouxni@iro.umontreal.ca] - initial implementation July, 20th, 2005
Andreas P. Cuny - Restructured code and modified design of waitbar for TracX

TracX.@Utils.printToConsole(message)¶

PRINTTOCONSOLE Outputs logging/status information to the console with a time stamp. A static function in Utils.

Parameters:: message (str) – Message to be printed to the console.
Returns:: Prints message to console directly.
Return type:: void (str)

Example:

>>> printToConsole('My message')
06-Jun-2017 11:30:30:  My message

Authors:: Andreas P. Cuny - initial implementation

TracX.@Utils.imcropC(image, imageCropCoordinateArray)¶

IMCROPC Crop image. Custom imcrop function. Faster (~3.5-6x) than native MATLAB interactive imcrop function.

Parameters:

image (double, NxM) – Image matrix
imageCropCoordinateArray (int, 1x4) – Array with coordinates to crop an image. imageCropCoordinateArray

Returns:

crop – Croped image matrix.

Return type:

(double NxM)

Authors:

Andreas P. Cuny - initial implementation

TracX.@Utils.getMaxNumCompThreads()¶

GETMAXNUMCOMPTHREADS Returns the maximal number of compute threads.

Parameters:: ignoredArg (obj) – TracX.@Utils
Returns:: ret – Color map with user defined size based on colors defined in colorScheme1 (repetitions).
Return type:: (int)
Authors:: Andreas P. Cuny - initial implementation