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An apparatus and a method of locating a specimen with a microscope, the microscope including two point light sources, a transparent specimen holder, a digital imaging device, a processor, and a display. The method includes sequentially illuminating the two point light sources through the specimen holder, across the specimen, and onto the digital imaging device to create shadows associated with each of the two point light sources. Optical images of the specimen are received on the digital imaging device associated with each shadow from the light sources, and a disparity signal is output containing a horizontal, vertical, and depth position of the specimen relative to the digital imaging device. Location of the specimen is determined based on the disparity signal. The specimen is allowed to move freely throughout the transparent specimen holder.