How Measurements are Named

In CellProfiler, measurements are exported as well as stored internally using the following general nomenclature: MeasurementType_Category_SpecificFeatureName_Parameters

Below is the description for each of the terms:

  • MeasurementType: The type of data contained in the measurement, which can be one of three forms:

    • Per-image: These measurements are image-based (e.g., thresholds, counts) and are specified with the name “Image” or with the measurement (e.g., “Mean”) for per-object measurements aggregated over an image.
    • Per-object: These measurements are per-object and are specified as the name given by the user to the identified objects (e.g., “Nuclei” or “Cells”).
    • Experiment: These measurements are produced for a particular measurement across the entire analysis run (e.g., Z’ factors), and are specified with the name “Experiment”. See CalculateStatistics for an example.
  • Category: Typically, this information is specified in one of two ways:

    • A descriptive name indicative of the type of measurement taken (e.g., “Intensity”)
    • No name if there is no appropriate Category (e.g., if the SpecificFeatureName is “Count”, no Category is specfied).
  • SpecificFeatureName: The specific feature recorded by a module (e.g., “Perimeter”). Usually the module recording the measurement assigns this name, but a few modules allow the user to type in the name of the feature (e.g., the CalculateMath module allows the user to name the arithmetic measurement).

  • Parameters: This specifier is to distinguish measurements obtained from the same objects but in different ways. For example, MeasureObjectIntensity can measure intensities for “Nuclei” in two different images. This specifier is used primarily for data obtained from an individual image channel specified by the Images module or a legacy Load module (e.g., “OrigBlue” and “OrigGreen”) or a particular spatial scale (e.g., under the category “Texture” or “Neighbors”). Multiple parameters are separated by underscores.

    Below are additional details specific to various modules:

    • Measurements from the AreaShape and Math categories do not have a Parameter specifier.
    • Measurements from Intensity, Granularity, Children, RadialDistribution, Parent and AreaOccupied categories will have an associated image as the Parameter.
    • Measurements from the *Neighbors and Texture category will have a spatial scale Parameter.*
    • Measurements from the Texture and RadialDistribution categories will have both a spatial scale and an image Parameter.

As an example, consider a measurement specified as Nuclei_Texture_DifferenceVariance_ER_3:

  • MeasurementType is “Nuclei,” the name given to the detected objects by the user.
  • Category is “Texture,” indicating that the module MeasureTexture produced the measurements.
  • SpecificFeatureName is “DifferenceVariance,” which is one of the many texture measurements made by the MeasureTexture module.
  • There are two Parameters, the first of which is “ER”. “ER” is the user-provided name of the image in which this texture measurement was made.
  • The second Parameter is “3”, which is the spatial scale at which this texture measurement was made, according to the user-provided settings for the module.

See also the Available measurements heading under the main help for many of the modules, as well as ExportToSpreadsheet and ExportToDatabase modules.