A method for an automatic detection of cell colonies, comprising: acquiring lower magnification digital images of sub-areas of a slide using a low power objective; generating background intensity images by grey value morphologically processing the acquired images by a closing followed by an opening; forming background-subtracted sub-area images by subtracting the minimum of a background intensity image and the original image from the original image; generating shrunk sub-area images by shrinking the background-subtracted sub-area images by a predefined scale factor; stitching the shrunk sub-area images into a composite image representing the entire slide; converting the composite image into a binary edge image by the application of an automatic thresholding technique based on analysis of grey level gradients; passing the binary edge image through a Hough transform to produce a Hough space transformed image; analyzing the Hough space transformed image to identify peaks representing a coverslip edge location; subjecting the Hough space transformed image to an inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image; setting to zero all pixels of the composite image outside of the coverslip area; morphologically processing the composite binary edge image by closing followed by opening; identifying colonies in the composite binary edge image; eliminating unwanted colonies from the composite binary edge image based on their size or morphology; recording the location, size, or binary image masks of the remaining colonies on the slide; generating a map of automatic focusing values over the remaining colonies on the slide using a high power objective (470, 475); acquiring a plurality of higher magnification images over the remaining colonies on the slide using a high power objective and the map of automatic focusing values; performing metaphase detection; and assigning each detected metaphase to a colony. acquiring lower magnification digital images of sub-areas of a slide using a low power objective; generating background intensity images by grey value morphologically processing the acquired images by a closing followed by an opening; forming background-subtracted sub-area images by subtracting the minimum of a background intensity image and the original image from the original image; generating shrunk sub-area images by shrinking the background-subtracted sub-area images by a predefined scale factor; stitching the shrunk sub-area images into a composite image representing the entire slide; converting the composite image into a binary edge image by the application of an automatic thresholding technique based on analysis of grey level gradients; passing the binary edge image through a Hough transform to produce a Hough space transformed image; analyzing the Hough space transformed image to identify peaks representing a coverslip edge location; subjecting the Hough space transformed image to an inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image; setting to zero all pixels of the composite image outside of the coverslip area; morphologically processing the composite binary edge image by closing followed by opening; identifying colonies in the composite binary edge image; eliminating unwanted colonies from the composite binary edge image based on their size or morphology; recording the location, size, or binary image masks of the remaining colonies on the slide; generating a map of automatic focusing values over the remaining colonies on the slide using a high power objective (470, 475); acquiring a plurality of higher magnification images over the remaining colonies on the slide using a high power objective and the map of automatic focusing values; performing metaphase detection; and assigning each detected metaphase to a colony.