In most cases, the reason for identifying image features is to make
measurements on them. CellProfiler has a number of modules dedicated to
calculating measurements of various types, on both images and objects;
these are accessible by clicking the button (located underneath the pipeline
panel)
Below is a list of measurement categories; these is not meant to be comprehensive, but are sufficient for most assays:
Measurement | Description | Relevant modules |
---|---|---|
Count | The number of objects in an image. | All modules which produce a new set of objects, such as IdentifyPrimaryObjects |
Location | The (x,y) coordinates of each object, which can be of interest in time-lapse imaging. | All modules which produce a new set of objects |
Morphology | Quantities defining the geometry of the object, as defined by its external boundary. This includes quantities like area, perimeter, etc. | MeasureImageAreaOccupied,MeasureObjectSizeShape |
Intensity | In fluorescence assays, the intensity of a pixel is related to the substance labeled with a fluorescence marker at that location. The maximal, minimal, mean, and integrated (total) intensity of each marker can be measured as well as correlations in intensity between channels. | MeasureObjectIntensity, MeasureImageIntensity, MeasureObjectRadialDistribution, MeasureColocalization |
Texture | These quantities characterize spatial smoothness and regularity across an object, and are often useful for characterizing the fine patterns of localization. | MeasureTexture |
Clustering | Spatial relationships can be characterized by adjacency descriptors, such as the number of neighboring objects, the percent of the perimeter touching neighbor objects, etc. | MeasureObjectNeighbors |
For more information on these modules and how to configure them for best
performance, please see the detailed help by selecting the module and
clicking the button at the bottom of
the pipeline panel. You can also find details on measurement nomenclature
when exporting under Help > Using Your Output > How Measurements are Named