CellProfiler 2.0 FAQ



1. “What happened to the module/data tool names?” or "I can’t find my module/data tool?"

Some of the modules have changed their names between CellProfiler 1.0 and 2.0. In some cases, the change was made to make the nomenclature more consistent; in others, to reflect new, broader functionality.

A pipeline created in CellProfiler 1.0 and loaded into CellProfiler 2.0 will have the appropriate modules converted to their new names automatically. However, if you are looking for a module in CellProfiler 2.0 and can’t find it using the familiar CellProfiler 1.0 name, consult this list of modules that have changed names (former name in parentheses):

  • ConserveMemory (from SpeedUpCellProfiler)

  • ConvertObjectsToImage (from ConvertToImage)

  • EnhanceEdges (from FindEdges)

  • EnhanceOrSuppressFeatures (from EnhanceOrSuppressSpeckles)

  • ExpandOrShrinkObjects (from ExpandOrShrink)

  • ExportToSpreadsheet (from ExportToExcel)

  • FlagImage (from FlagImageForQC)

  • FilterObjects (from FilterByObjectMeasurement)

  • IdentifyObjectsManually (from IdentifyPrimManual)

  • IdentifyPrimaryObjects (from IdentifyPrimAutomatic)

  • IdentifySecondaryObjects (from IdentifySecondary)

  • IdentifyTertiaryObjects (from IdentifyTertiarySubregion)

  • LoadData (from LoadText)

  • MaskObjects (from Exclude)

  • MeasureObjectSizeShape (from MeasureObjectAreaShape)

  • ReassignObjectNumbers (from RelabelObjects)

  • RelateObjects (from Relate)

  • Smooth (from SmoothOrEnhance)

The functionality of some modules has superseded by others. These original modules are now deprecated, and are no longer present. Below are the deprecated modules and the names of the modules that should be used in their place in parentheses:

  • LoadImageDirectory (use MakeProjection, along with LoadImages with metadata)

  • KeepLargestObject (use FilterObjects)

  • Combine (use ImageMath)

  • PlaceAdjacent (use Tile)

  • FilenameMetadata (use LoadImages with metadata)

  • SubtractBackground (use ApplyThreshold with grayscale setting)

  • CalculateRatios (use CalculateMath with ‘divide’ as the operation)

A new module category Data Tools has been created and some modules have been moved from their original categories. These modules may also be found in the Data Tools menu option. The moved modules are listed below along with the former category in parentheses:

  • CalculateMath (from Measurement)

  • CalculateStatistics (from Measurement)

  • ExportToDatabase(from File Processing)

  • ExportToSpreadsheet (from File Processing)

  • FlagImage (from Image Processing)

Some modules have yet to be implemented in CellProfiler 2.0. Loading these modules will currently produce an error message with the option of skipping the module and loading the rest of the pipeline.

  • DICTransform

  • DifferentiateStains

  • DisplayGridInfo

  • DisplayMeasurement

  • GroupMovieFrames

  • LabelImages

  • Restart

  • SplitOrSpliceMovie

Some Data Tools have yet to be implemented in CellProfiler 2.0 but will be in the future. Where possible, a workaround for the functionality is suggested.

  • ConvertBatchFiles

  • MergeOutputFiles

  • ViewData: Export your data using ExportToSpreadsheet and open the resulting spreadsheet in a spreadsheet program like Excel

  • AddData: Use the LoadData module when running your analysis

  • ShowDataOnImage: Use the DisplayDataOnImage module when running your analysis

  • DataLayout, ShowPlateMapData: Use CellProfiler Analyst’s PlateMapViewer tool

  • PlotMeasurement: Some of the functionality is in the CP 2.0 data tool scatterplot and histogram, with the remaining types of plots to be added in the future.

  • SubmitBatch: Use the BatchProfiler tool

  • CalcRatios and MeasurementCalculator: Use the CalculateMath data tool

Some Menu options have not been implemented in CellProfiler 2.0. Where possible, a workaround for the functionality is suggested.

  • Save pipeline as text: Unnecessary in CellProfiler 2.0; pipelines are now saved in a CellProfiler text format with the extension .cp

  • Run multiple pipelines: Will be implemented in the future.

Some Data Tools will not be implemented or supported in CellProfiler 2.0:

  • ClearData

  • GenerateHistogramMovie

  • ExportLocations