Track Cells, Analyze Cell Trajectories and Compute Migration Statistics


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Documentation for package ‘cellmigRation’ version 1.12.0

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aggregateFR Aggregating the outcome of several experiments or conditions.
aggregateTrackedCells Aggregate trackedCells Objects
CellMig The CellMig Class.
CellMig-class The CellMig Class.
CellMigPCA PCA
CellMigPCAclust PCA Clusters
CellMigPCAclustALL PCA Clusters of different conditions
CellTracker Compute Cell Tracks
ComputeTracksStats Compute Tracks Stats
DiAutoCor Direction AutoCorrelation
DiRatio Directionality Table
DiRatioPlot Directionality Ratio plots
EstimateDiameterRange Detect Paricle Diameters in a Numeric matrix
FilterTrackedCells Filter an Aggregated Table of Cell Tracks
FinRes Final Results
FMI Forward Migration Index
ForwardMigration Forward Migration
getAvailableAggrMetrics Get Available Aggregate Cell Metrics
getCellImages Method getCellImages
getCellImages-method Method getCellImages
getCellMigSlot Method getCellMigSlot
getCellMigSlot-method Method getCellMigSlot
getCellsMeta Get MetaData
getCellsStats Get Cell migration stats
getCellTrackMeta Method getCellTrackMeta
getCellTrackMeta-method Method getCellTrackMeta
getCellTracks Method getCellTracks
getCellTracks-method Method getCellTracks
getCellTrackStats Method getCellTrackStats
getCellTrackStats-method Method getCellTrackStats
getDACtable Getting the Direction AutoCorrelation
getDiRatio Getting the Directionality Table
getFMItable Getting the Forward Migration Index
getForMigtable Getting the Forward Migration
getImageCentroids Method getImageCentroids
getImageCentroids-method Method getImageCentroids
getImageStacks Get Image Stacks
getMSDtable Getting the Mean Square Displacement
getOptimizedParameters Get Auto Optimized Parameters
getOptimizedParams Method getOptimizedParams
getOptimizedParams-method Method getOptimizedParams
getPerAndSpeed Getting the table of Persistence and Speed.
getPopulationStats Get Cell population stats
getProcessedImages Method getProcessedImages
getProcessedImages-method Method getProcessedImages
getProcessingStatus Method getProcessingStatus
getProcessingStatus-method Method getProcessingStatus
getResults Final Results
getTracks Get Track Data
getVACtable Getting the Velocity AutoCorrelation
initialize-method The CellMig Class.
initialize-method The trackedCells Class.
LoadTiff Import Image from TIFF
MSD Mean Square Displacement
OptimizeParams Optimize Detection Params
PerAndSpeed Persistence and Speed
plot3DAllTracks A 3D rose-plot of all cells
plot3DTracks A 3D rose-plot
plotAllTracks A 2D rose-plot
plotSampleTracks A 2D rose-plot of sample cells
PlotTracksSeparately A graphical display of the track of each cell.
rmPreProcessing Data preprocessing for random migration (RM)
setAnalyticParams Method setAnalyticParams
setAnalyticParams-method Method setAnalyticParams
setCellMigSlot Method setCellMigSlot
setCellMigSlot-method Method setCellMigSlot
setCellsMeta Set MetaData
setCellTracks Method setCellTracks
setCellTracks-method Method setCellTracks
setExpName Method setExpName
setExpName-method Method setExpName
setOptimizedParams Method setOptimizedParams
setOptimizedParams-method Method setOptimizedParams
setProcessedImages Method setProcessedImages
setProcessedImages-method Method setProcessedImages
setProcessingStatus Method setProcessingStatus
setProcessingStatus-method Method setProcessingStatus
setTrackedCellsMeta Method setTrackedCellsMeta
setTrackedCellsMeta-method Method setTrackedCellsMeta
setTrackedCentroids Method setTrackedCentroids
setTrackedCentroids-method Method setTrackedCentroids
setTrackedPositions Method setTrackedPositions
setTrackedPositions-method Method setTrackedPositions
setTrackingStats Method setTrackingStats
setTrackingStats-method Method setTrackingStats
trackedCells The trackedCells Class.
trackedCells-class The trackedCells Class.
TrajectoryDataset Trajectories of 350 cells
VeAutoCor Velocity AutoCorrelation
visualizeCellTracks Visualize Cell Tracks originating at an Image Stack
VisualizeStackCentroids Visualize Cells in an Image Stack
wsaPreProcessing Data preprocessing for wound scratch assay (WSA).