1. An instrument for scanning at least a part of a large specimen mounted on a specimen holder, the instrument comprising a light source, at least one lens to focus light from the light source, a detection system that comprises at least one detector, a computer programmed and configured to: a) take a plurality of measurements of each pixel at a plurality of exposure values; b) receive, process and store data received from the at least one detector; c) control a power output of the light source; d) control the movement of the specimen holder during scanning and a gain of the at least one detector to produce a digitized image of the at least one part of the specimen with a larger dynamic range than a dynamic range of the detection system e) an increased dynamic range of the instrument being sufficiently large to display image detail in dark, mid-range and bright areas of the image; f) the computer being programmed to combine scan lines to preserve relative pixel intensities across the entire image, the instrument being set up to scan the specimen in fluorescence; and g) acquire sequences of adjacent scan lines in which each scan line has an increased exposure value compared to an exposure value of the immediately previous scan line, the computer programmed to multiply pixel data from a first scan line by a factor and to combine pixel data from the first scan line and a second scan line to produce a single line of pixels in the final image comprised of pixel data from the first scan line multiplied by the factor whenever a pixel intensity value of any pixel in the second scan line is larger than a pre-determined amount and pixel data from the second scan line is used at or below the pre-determined pixel intensity value.