systems and methods for acquiring images of biological samples and analyzing contrast features are provided . the present invention may determine whether a contrast feature in a image of a biological example qualifies as a grain . the size , intensity of contrast features , or other parameters may be tuned to find contrast features that correspond to features having significance in a given application . in addition , the total number of grains per image , the number of grains per sample , the number of grains per unit area , the area fraction occupied by grains , the ratio of intensity of grains to the intensity of the image , or other suitable characteristics may be determined .