Patent ID: 8655037

Claim:
A method for defining a first marker-defined biological compartment relative to a second marker-defined biological compartment present in a biological sample of interest, comprising comparing the intensity in each of the pixel locations in a first image of the first marker defined biological compartment with the intensity in each of the corresponding pixel locations of a second image of the second marker-defined biological compartment, wherein the first image was prepared using a first imaging agent that is specific for the first marker-defined biological compartment, and wherein the second image was prepared using a second imaging agent that is specific for the second marker-defined biological compartment, wherein differences in pixel intensity define the first marker-defined biological compartment relative to the second marker-defined biological compartment, assigning pixels to a cluster characterized by high first imaging agent intensity and low second imaging agent intensity to the first compartment; assigning pixels to a cluster characterized by high second imaging agent intensity and low first imaging agent intensity to the second compartment; and assigning pixels to a cluster characterized by low first imaging agent intensity and low second imaging agent intensity to background and removing such pixels from further analysis, wherein any of the assigning steps are performed using a k means clustering method to determine a cluster membership for each pixel, and wherein the method is automated.