Man pages for ocbe-uio/CellMigRation
Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

AddDimensionAdd Dimension to a Molten Data Frame
aggregateFRAggregating the outcome of several experiments or conditions.
aggregateTrackedCellsAggregate trackedCells Objects
bpassPerform a bandpass by convolving with an appropriate kernel
CellMig-classThe CellMig Class.
CellMigPCAPCA
CellMigPCAclustPCA Clusters
CellMigPCAclustALLPCA Clusters of different conditions
cellmigRation-packageTrack And Analyze Cell Migrations
CellTrackerCompute Cell Tracks
CellTrackerMainLoopCell Tracker Main Loop
CentroidArrayBuild a Centroid Array
CentroidValidationValidate Centroids
circshiftShift Array Circularly
cntrdCalculates Centroids
ComputeTracksStatsCompute Tracks Stats
DetectRadiiDetect Linear Paricle Diameters
DiAutoCorDirection AutoCorrelation
DiRatioDirectionality Table
DiRatioPlotDirectionality Ratio plots
EstimateDiameterRangeDetect Paricle Diameters in a Numeric matrix
FianlizeOptiParamsFinalize Output in Parameter Optimization
FilterTrackedCellsFilter an Aggregated Table of Cell Tracks
FinResFinal Results
fixDADirection AutoCorrelation
fixExpNameHandle non-NULL ExpName
fixFM1Forward Migration First Part
fixFM2Forward Migration Second Part
fixFM3Forward Migration Third Part
fixFM4Forward Migration Fourth Part
fixFM5Forward Migration Fifth Part
fixFM6Forward Migration Sixst Part
fixID1Pre-processing First Part
fixID2Pre-processing Second Part
fixID3Pre-processing Third Part
fixID4Pre-processing Fourth Part
fixID5Pre-processing Fifth Part
fixID6Pre-processing Sixst Part
fixMSDMean Square Displacement
fixPER1Persistence and Speed First Part
fixPER2Persistence and Speed Second Part
fixPER3Persistence and Speed Third Part
FMIForward Migration Index
ForwardMigrationForward Migration
GenAllCombosGenerate All Combinations
getAvailableAggrMetricsGet Available Aggregate Cell Metrics
getCellImagesMethod getCellImages
getCellMigSlotMethod getCellMigSlot
getCellsMetaGet MetaData
getCellsStatsGet Cell migration stats
getCellTrackMetaMethod getCellTrackMeta
getCellTracksMethod getCellTracks
getCellTrackStatsMethod getCellTrackStats
getDACtableGetting the Direction AutoCorrelation
getDiRatioGetting the Directionality Table
getFMItableGetting the Forward Migration Index
getForMigtableGetting the Forward Migration
getImageCentroidsMethod getImageCentroids
getImageStacksGet Image Stacks
getMSDtableGetting the Mean Square Displacement
getOptimizedParametersGet Auto Optimized Parameters
getOptimizedParamsMethod getOptimizedParams
getPerAndSpeedGetting the table of Persistence and Speed.
getPopulationStatsGet Cell population stats
getProcessedImagesMethod getProcessedImages
getProcessingStatusMethod getProcessingStatus
getResultsFinal Results
getTracksGet Track Data
getVACtableGetting the Velocity AutoCorrelation
initializeTrackParamsInitialize Tracking parameters
innerBondRasterInner Bond Raster
internalPermutationInternal Permutation
LinearConv2Linear Convolution of a Numeric Matrix
LoadTiffImport Image from TIFF
MakeHypercubeMake Hypercube
matfixClean And Reformat a Numeric Matrix
MigrationStatsCompute Cell Migration Statistics
MSDMean Square Displacement
NextOddReturn the Next Odd Integer
NonParallel4OptimizeParamsNon Paralle Parameter Optimization
NonParallelTrackLoopSingle Core Tracking Loop
nontrivialBondTrackingNon-Trivial Bond Tracking
OptimizeParamsOptimize Detection Params
OptimizeParamsMainLoopMain Loop to Parameter Optimization
Parallel4OptimizeParamsParalle Parameter Optimization
ParallelTrackLoopMulti Core Tracking Loop
PerAndSpeedPersistence and Speed
pkfndFind Signal Peaks
plot3DAllTracksA 3D rose-plot of all cells
plot3DTracksA 3D rose-plot
plotAllTracksA 2D rose-plot
plotSampleTracksA 2D rose-plot of sample cells
PlotTracksSeparatelyA graphical display of the track of each cell.
PostProcessTrackingPost Processing Tracking Routine
Prep4OptimizeParamsPrepare For Parameter Optimization
preProcCellMigTrajectories of 11 cells
rmPreProcessingData preprocessing for random migration (RM)
runTrackingPermutationRun Tracking Permutation
setAnalyticParamsMethod setAnalyticParams
setCellMigSlotMethod setCellMigSlot
setCellsMetaSet MetaData
setCellTracksMethod setCellTracks
setExpNameMethod setExpName
setOptimizedParamsMethod setOptimizedParams
setProcessedImagesMethod setProcessedImages
setProcessingStatusMethod setProcessingStatus
setTrackedCellsMetaMethod setTrackedCellsMeta
setTrackedCentroidsMethod setTrackedCentroids
setTrackedPositionsMethod setTrackedPositions
setTrackingStatsMethod setTrackingStats
sinkAwaySinking Output as part of Parameter Optimization
subNetworkTrackingSubnetwork Tracking
ThreeConditionsIntermediates and Results from Cell Tracking Analyses
trackTrack cells
TrackCellsDatasetSample Stack of Fluorescent Cells
trackedCells-classThe trackedCells Class.
trackHypercubeBuildTrack Hypercube Build
trackSlideProcessingTracking Slide Processing
trackSlideWrapUpTracking Slide Wrap Up
TrajectoryDatasetTrajectories of 350 cells
trivialBondRasterTrivial Bond Raster
trivialBondTrackingTrivial Bond Tracking
ValidateTrackingArgsValidate Tracking Arguments
VeAutoCorVelocity AutoCorrelation
visualizeCellTracksVisualize Cell Tracks originating at an Image Stack
VisualizeCntrVisualize Centroids
VisualizeImgVisualize a matrix image
VisualizeStackCentroidsVisualize Cells in an Image Stack
visualizeTrcksVisualize Cell Tracks
warnMessagePrint Warning Messages
WSADatasetTrajectories of 147 cells
wsaPreProcessingData preprocessing for wound scratch assay (WSA).
ocbe-uio/CellMigRation documentation built on Dec. 26, 2021, 10:19 p.m.