1. A method for classifying phenotype from threshold compactness features of cells, said features determined from one or more images of the cells, the method comprising the steps of: (a) obtaining the one or more images of the cells; (b) automatically detecting, by a processor of a computing device, an object depicted in an input image selected from the one or more images, thereby defining a masked portion of the input image corresponding to the object; (c) identifying, by the processor, a plurality of provisional objects within the masked portion of the input image using a threshold intensity; (d) computing, by the processor, a threshold compactness for the object, wherein the threshold compactness is a function of total area S of the plurality of provisional objects and total border length P of the plurality of provisional objects; and (e) identifying, by the processor, a phenotype classification associated with the object based at least in part on the threshold compactness.