Man pages for ocbe-uio/CellMigRation
Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
| AddDimension | Add Dimension to a Molten Data Frame |
| aggregateFR | Aggregating the outcome of several experiments or conditions. |
| aggregateTrackedCells | Aggregate trackedCells Objects |
| bpass | Perform a bandpass by convolving with an appropriate kernel |
| CellMig-class | The CellMig Class. |
| CellMigPCA | PCA |
| CellMigPCAclust | PCA Clusters |
| CellMigPCAclustALL | PCA Clusters of different conditions |
| cellmigRation-package | Track And Analyze Cell Migrations |
| CellTracker | Compute Cell Tracks |
| CellTrackerMainLoop | Cell Tracker Main Loop |
| CentroidArray | Build a Centroid Array |
| CentroidValidation | Validate Centroids |
| circshift | Shift Array Circularly |
| cntrd | Calculates Centroids |
| ComputeTracksStats | Compute Tracks Stats |
| DetectRadii | Detect Linear Paricle Diameters |
| DiAutoCor | Direction AutoCorrelation |
| DiRatio | Directionality Table |
| DiRatioPlot | Directionality Ratio plots |
| EstimateDiameterRange | Detect Paricle Diameters in a Numeric matrix |
| FianlizeOptiParams | Finalize Output in Parameter Optimization |
| FilterTrackedCells | Filter an Aggregated Table of Cell Tracks |
| FinRes | Final Results |
| fixDA | Direction AutoCorrelation |
| fixExpName | Handle non-NULL ExpName |
| fixFM1 | Forward Migration First Part |
| fixFM2 | Forward Migration Second Part |
| fixFM3 | Forward Migration Third Part |
| fixFM4 | Forward Migration Fourth Part |
| fixFM5 | Forward Migration Fifth Part |
| fixFM6 | Forward Migration Sixst Part |
| fixID1 | Pre-processing First Part |
| fixID2 | Pre-processing Second Part |
| fixID3 | Pre-processing Third Part |
| fixID4 | Pre-processing Fourth Part |
| fixID5 | Pre-processing Fifth Part |
| fixID6 | Pre-processing Sixst Part |
| fixMSD | Mean Square Displacement |
| fixPER1 | Persistence and Speed First Part |
| fixPER2 | Persistence and Speed Second Part |
| fixPER3 | Persistence and Speed Third Part |
| FMI | Forward Migration Index |
| ForwardMigration | Forward Migration |
| GenAllCombos | Generate All Combinations |
| getAvailableAggrMetrics | Get Available Aggregate Cell Metrics |
| getCellImages | Method getCellImages |
| getCellMigSlot | Method getCellMigSlot |
| getCellsMeta | Get MetaData |
| getCellsStats | Get Cell migration stats |
| getCellTrackMeta | Method getCellTrackMeta |
| getCellTracks | Method getCellTracks |
| getCellTrackStats | 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 |
| getImageStacks | Get Image Stacks |
| getMSDtable | Getting the Mean Square Displacement |
| getOptimizedParameters | Get Auto Optimized Parameters |
| getOptimizedParams | Method getOptimizedParams |
| getPerAndSpeed | Getting the table of Persistence and Speed. |
| getPopulationStats | Get Cell population stats |
| getProcessedImages | Method getProcessedImages |
| getProcessingStatus | Method getProcessingStatus |
| getResults | Final Results |
| getTracks | Get Track Data |
| getVACtable | Getting the Velocity AutoCorrelation |
| initializeTrackParams | Initialize Tracking parameters |
| innerBondRaster | Inner Bond Raster |
| internalPermutation | Internal Permutation |
| LinearConv2 | Linear Convolution of a Numeric Matrix |
| LoadTiff | Import Image from TIFF |
| MakeHypercube | Make Hypercube |
| matfix | Clean And Reformat a Numeric Matrix |
| MigrationStats | Compute Cell Migration Statistics |
| MSD | Mean Square Displacement |
| NextOdd | Return the Next Odd Integer |
| NonParallel4OptimizeParams | Non Paralle Parameter Optimization |
| NonParallelTrackLoop | Single Core Tracking Loop |
| nontrivialBondTracking | Non-Trivial Bond Tracking |
| OptimizeParams | Optimize Detection Params |
| OptimizeParamsMainLoop | Main Loop to Parameter Optimization |
| Parallel4OptimizeParams | Paralle Parameter Optimization |
| ParallelTrackLoop | Multi Core Tracking Loop |
| PerAndSpeed | Persistence and Speed |
| pkfnd | Find Signal Peaks |
| 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. |
| PostProcessTracking | Post Processing Tracking Routine |
| Prep4OptimizeParams | Prepare For Parameter Optimization |
| preProcCellMig | Trajectories of 11 cells |
| rmPreProcessing | Data preprocessing for random migration (RM) |
| runTrackingPermutation | Run Tracking Permutation |
| setAnalyticParams | Method setAnalyticParams |
| setCellMigSlot | Method setCellMigSlot |
| setCellsMeta | Set MetaData |
| setCellTracks | Method setCellTracks |
| setExpName | Method setExpName |
| setOptimizedParams | Method setOptimizedParams |
| setProcessedImages | Method setProcessedImages |
| setProcessingStatus | Method setProcessingStatus |
| setTrackedCellsMeta | Method setTrackedCellsMeta |
| setTrackedCentroids | Method setTrackedCentroids |
| setTrackedPositions | Method setTrackedPositions |
| setTrackingStats | Method setTrackingStats |
| sinkAway | Sinking Output as part of Parameter Optimization |
| subNetworkTracking | Subnetwork Tracking |
| ThreeConditions | Intermediates and Results from Cell Tracking Analyses |
| track | Track cells |
| TrackCellsDataset | Sample Stack of Fluorescent Cells |
| trackedCells-class | The trackedCells Class. |
| trackHypercubeBuild | Track Hypercube Build |
| trackSlideProcessing | Tracking Slide Processing |
| trackSlideWrapUp | Tracking Slide Wrap Up |
| TrajectoryDataset | Trajectories of 350 cells |
| trivialBondRaster | Trivial Bond Raster |
| trivialBondTracking | Trivial Bond Tracking |
| ValidateTrackingArgs | Validate Tracking Arguments |
| VeAutoCor | Velocity AutoCorrelation |
| visualizeCellTracks | Visualize Cell Tracks originating at an Image Stack |
| VisualizeCntr | Visualize Centroids |
| VisualizeImg | Visualize a matrix image |
| VisualizeStackCentroids | Visualize Cells in an Image Stack |
| visualizeTrcks | Visualize Cell Tracks |
| warnMessage | Print Warning Messages |
| WSADataset | Trajectories of 147 cells |
| wsaPreProcessing | Data preprocessing for wound scratch assay (WSA). |
