# Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

## Documentation for package ‘cellmigRation’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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).