Scanning microscope using pulsed illumination and MSIA

An instrument for scanning a specimen, comprising:

• a. a scanning stage for supporting the specimen;
• b. a detector having a plurality of pixels, the scanning stage and the detector movable relative to each other to move the specimen in a scan direction at a constant scan speed during a scan;
• c. a pulsed illumination source synchronized with the motion of the specimen on the scanning stage;
• and
• d. a processor operable to perform Moving Specimen Image Averaging (MSIA) on image data to generate an image of the specimen;
• e. wherein at least some of the pixels of the detector are operable to collect light emitted from or reflected by the specimen during the scan due to the pulsed illumination source;
• and
• f. wherein a color of the pulsed illumination source is changed each time the specimen has moved a distance that causes the image of the specimen projected onto the detector to move, at a constant image speed with respect to the detector, a distance equal to the distance between lines of pixels in the detector.