1. A microscope system for providing an improved three-dimensional image of a specimen having properties including a variable index of refraction and a variable absorption and said three-dimensional image being defined by low and high frequency components, the system comprising: a light source for generating light; collimating means for collimating the light into a light beam and transmitting the beam along an optical axis; a specimen holder for holding the specimen on said axis downstream of said collimating means; an objective downstream of said specimen holder for generating and transmitting images of said specimen along said axis; focus stepping means for changing the spacing between the specimen and said objective along the optical axis whereby a plurality of said images are obtained incorporating respective values of said index of refraction and said absorption, said images being indicative of respective positions within the specimen along said axis with each of said images including data corresponding to an in-focus portion and an out-of-focus portion; light-modulating means for modifying the in-focus and out-of-focus portions of said image by attenuating the amplitudes of the low frequency components of the image and enhancing the high frequency components thereof; and, computer means for sensing and receiving data corresponding to each of said images and for suppressing the out-of-focus portion corresponding thereto whereby an improved three-dimensional image data file of the specimen is obtained.