Measure Image Intensity
measures the total intensity in an image by summing all of the pixel intensities (excluding masked pixels).
This module will sum all pixel values to measure the total image intensity. The user can measure all pixels in the image or can restrict the measurement to pixels within objects. If the image has a mask, only unmasked pixels will be measured.
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.
- TotalIntensity: Sum of all pixel intensity values.
- MeanIntensity, MedianIntensity: Mean and median of pixel intensity values.
- StdIntensity, MADIntensity: Standard deviation and median absolute deviation (MAD) of pixel intensity values. The MAD is defined as the median(|xi - median(x)|).
- MinIntensity, MaxIntensity: Minimum and maximum of pixel intensity values.
- LowerQuartileIntensity: The intensity value of the pixel for which 25% of the pixels in the object have lower values.
- UpperQuartileIntensity: The intensity value of the pixel for which 75% of the pixels in the object have lower values.
- TotalArea: Number of pixels measured, e.g., the area of the image.
See also MeasureObjectIntensity, MaskImage.
Select the image to measure
Choose an image name from the drop-down menu to calculate intensity for that
image. Use the Add another image button below to add additional images which will be
measured. You can add the same image multiple times if you want to measure
the intensity within several different objects.
Measure the intensity only from areas enclosed by objects?
Select Yes to measure only those pixels within an object of choice.
Select the input objects
(Used only when measuring intensity from area enclosed by objects)
Select the objects that the intensity will be aggregated within. The intensity measurement will be
restricted to the pixels within these objects.