CellProfiler: image analysis software for identifying and quantifying cell phenotypes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Genome Biology. 2006 Oct 31;7(10):R100 As Published http://dx.doi.org/10.1186/gb-2006-7-10-r100 Publisher BioMed Central Ltd Version Final published version Citable link http://hdl.handle.net/1721.1/58762 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.0 1 2 3 Table of Contents Getting Started: MaskImage . 96 Introduction . 6 Morph . 110 Installation . 7 OverlayOutlines . 111 Getting Started with CellProfiler . 9 PlaceAdjacent . 112 RescaleIntensity . 115 Resize . 116 Help: Rotate . 118 BatchProcessing . 11 Smooth . 122 Colormaps. .16 Subtract . 125 DefaultImageFolder . 17 SubtractBackground . 126 DefaultOutputFolder . 18 Tile.............................................127 DeveloperInfo . 19 FastMode . 28 MatlabCrash . 29 Object Processing modules: OutputFilename . 30 ClassifyObjects . 41 PixelSize . 31 ClassifyObjectsByTwoMeasurements . 42 Preferences. .32 ConvertToImage . 45 SkipErrors . 33 Exclude . 65 TechDiagnosis . 34 ExpandOrShrink . 66 FilterByObjectMeasurement . 71 IdentifyObjectsInGrid . 76 File Processing modules: IdentifyPrimAutomatic . 77 CreateBatchFiles . 51 IdentifyPrimManual . 83 ExportToDatabase . 68 IdentifySecondary . 84 ExportToExcel. .70 IdentifyTertiarySubregion. .88 LoadImages . 90 Relate . 113 LoadSingleImage . 94 LoadText. .95 RenameOrRenumberFiles . 114 Measurement modules: Restart. .117 CalculateMath. .38 SaveImages . 119 CalculateRatios . 39 SplitOrSpliceMovie . 124 CalculateStatistics . 40 MeasureCorrelation . 97 MeasureImageAreaOccupied. .98 Image Processing modules: MeasureImageIntensity. .100 Align.............................................35 MeasureImageSaturationBlur . 101 ApplyThreshold. .36 MeasureImageSlope. .102 Average . 37 MeasureObjectAreaShape . 103 ColorToGray. .43 MeasureObjectIntensity . 105 Combine . 44 MeasureObjectNeighbors. .107 CorrectIlluminationApply . 46 MeasureTexture . 108 CorrectIlluminationCalculate. .47 CorrectIlluminationNew . 50 Crop.............................................55 Other modules: DistinguishPixelLabels . 64 CreateWebPage . 53 FindEdges . 72 DefineGrid . 58 Flip..............................................74 DisplayDataOnImage . 59 GrayToColor. .75 DisplayGridInfo . 60 InvertIntensity . 89 DisplayHistogram . 61 4 DisplayImageHistogram . 62 DisplayMeasurement . 63 SendEmail . 121 SpeedUpCellProfiler . 123 Image tools: ImageToolWindow . 128 InteractiveZoom . 129 OpenNewImageFile . 130 ShowHelpForThisMenu . 131 ShowOrHidePixelData . 132 Data tools: AddData . 133 CalculateRatiosDataTool . 134 ClearData . 135 ConvertBatchFiles . 136 DataLayout . 137 ExportData . 138 ExportDatabase . 139 ExportLocations . 140 GenerateHistogramMovie . 141 Histogram. .142 MeasurementCalculator . 145 MergeOutputFiles . 146 PlotMeasurement. .147 ShowDataOnImage . 148 ViewData . 149 5 Introduction CellProfilerTM cell image analysis software CellProfiler cell image analysis software is designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler Developer’s version allows you to write your own modules and tools for CellProfiler using Matlab. 6 Installation Get the latest code from www.cellprofiler.org ************************************************************************* CellProfiler.