1 2 3 Table of Contents Getting Started: InvertIntensity . ?? Introduction. .?? MaskImage. .?? Installation . ?? Morph........................................... ?? Getting Started with CellProfiler. .?? OverlayOutlines . ?? PlaceAdjacent . ?? RescaleIntensity . ?? Help: Resize . ?? BatchProcessing. .?? Rotate . ?? Colormaps . ?? SmoothKeepingEdges. .?? DefaultImageFolder . ?? SmoothOrEnhance . ?? DefaultOutputFolder. .?? Subtract . ?? DeveloperInfo . ?? SubtractBackground . ?? FastMode . ?? Tile..............................................?? MatlabCrash . ?? OutputFilename . ?? PixelSize . ?? Object Processing modules: Preferences . ?? ClassifyObjects . ?? SkipErrors. .?? ClassifyObjectsByTwoMeasurements. .?? TechDiagnosis. .?? ConvertToImage. .?? Exclude . ?? ExpandOrShrink . ?? File Processing modules: FilterByObjectMeasurement. .?? CreateBatchFiles . ?? IdentifyObjectsInGrid . ?? ExportToDatabase. .?? IdentifyPrimAutomatic. .?? ExportToExcel. .?? IdentifyPrimLoG . .?? GroupMovieFrames . ?? IdentifyPrimManual. .?? LoadImages . ?? IdentifySecondary. .?? LoadSingleImage . ?? IdentifyTertiarySubregion . ?? LoadText . ?? KeepLargestObject . ?? RenameOrRenumberFiles . ?? Relate . ?? Restart . ?? SplitIntoContiguousObjects . ?? RunMultiplePipelines . ?? TrackObjects. ?? SaveImages . ?? UnifyObjects . ?? SplitOrSpliceMovie . ?? Measurement modules: Image Processing modules: CalculateMath . ?? Align . ?? CalculateRatios. .?? ApplyThreshold . ?? CalculateStatistics . ?? Average. .?? MeasureCorrelation . ?? ColorToGray . ?? MeasureImageAreaOccupied. .?? Combine . ?? MeasureImageGranularity . ?? CorrectIlluminationApply . ?? MeasureImageIntensity. .?? CorrectIlluminationCalculate . ?? MeasureImageSaturationBlur . ?? Crop............................................. ?? MeasureObjectAreaShape . ?? FindEdges. .?? MeasureObjectIntensity . ?? Flip.............................................. ?? MeasureObjectNeighbors. .?? GrayToColor . ?? MeasureTexture . ?? InvertForPrinting . ?? 4 Other modules: CreateWebPage . ?? DefineGrid . ?? DisplayDataOnImage . ?? DisplayGridInfo . ?? DisplayHistogram. .?? DisplayImageHistogram . ?? DisplayMeasurement. .?? PauseCellProfiler . ?? SendEmail . ?? SpeedUpCellProfiler . ?? Image tools: ImageToolWindow. .?? InteractiveZoom . ?? OpenNewImageFile . ?? ShowHelpForThisMenu . ?? ShowOrHidePixelData . ?? Data tools: AddData . ?? CalculateRatiosDataTool . ?? CalculateStatisticsDataTool . ?? ClearData . ?? ConvertBatchFiles . ?? DataLayout . ?? ExportData . ?? ExportDatabase . ?? ExportLocations . ?? GenerateHistogramMovie . ?? Histogram . ..