1. A method of using a computer-controlled microscope imaging system for acquiring and analyzing areas of interest, said method comprising the steps of: scanning and digitizing a specimen at a low magnification through a microscope; displaying to the observer a low magnification, digitized image of the specimen; selecting a segment of the specimen from the low magnification digitized image for viewing at a higher magnification greater than the low magnification; automatically scanning the selected segment at the higher magnification and digitizing the image of the segment; and making available in real time to the view of the observer the respective, low magnification, digitized image and the high magnification, digitized image of the segment.