Measure Object Intensity
measures several intensity features for identified objects.
Given an image with objects identified (e.g. nuclei or cells), this module extracts intensity features for each object based on one or more corresponding grayscale images. Measurements are recorded for each object.
Intensity measurements are made for all combinations of the images and objects entered. If you want only specific image/object measurements, you can use multiple MeasureObjectIntensity modules for each group of measurements desired.
Note that for publication purposes, the units of intensity from microscopy images are usually described as "Intensity units" or "Arbitrary intensity units" since microscopes are not calibrated to an absolute scale. Also, it is important to note whether you are reporting either the mean or the integrated intensity, so specify "Mean intensity units" or "Integrated intensity units" accordingly.
Keep in mind that the default behavior in CellProfiler is to rescale the image intensity from 0 to 1 by dividing all pixels in the image by the maximum possible intensity value. This "maxmimum possible" value is defined by the "Set intensity range from" setting in NamesAndTypes; see the help for that setting for more details.
- IntegratedIntensity: The sum of the pixel intensities within an object.
- MeanIntensity: The average pixel intensity within an object.
- StdIntensity: The standard deviation of the pixel intensities within an object.
- MaxIntensity: The maximal pixel intensity within an object.
- MinIntensity: The minimal pixel intensity within an object.
- IntegratedIntensityEdge: The sum of the edge pixel intensities of an object.
- MeanIntensityEdge: The average edge pixel intensity of an object.
- StdIntensityEdge: The standard deviation of the edge pixel intensities of an object.
- MaxIntensityEdge: The maximal edge pixel intensity of an object.
- MinIntensityEdge: The minimal edge pixel intensity of an object.
- MassDisplacement: The distance between the centers of gravity in the gray-level representation of the object and the binary representation of the object.
- LowerQuartileIntensity: The intensity value of the pixel for which 25% of the pixels in the object have lower values.
- MedianIntensity: The median intensity value within the object
- MADIntensity: The median absolute deviation (MAD) value of the intensities within the object. The MAD is defined as the median(|xi - median(x)|).
- UpperQuartileIntensity: The intensity value of the pixel for which 75% of the pixels in the object have lower values.
- Location_CenterMassIntensity_X, Location_CenterMassIntensity_Y: The pixel (X,Y) coordinates of the intensity weighted centroid (= center of mass = first moment) of all pixels within the object.
- Location_MaxIntensity_X, Location_MaxIntensity_Y: The pixel (X,Y) coordinates of the pixel with the maximum intensity within the object.
See also NamesAndTypes, MeasureImageIntensity.
Select an image to measure
Select the grayscale images whose intensity you want to measure.
Select objects to measure
Select the objects whose intensities you want to measure.