A scanning confocal microscope scans a sample with an incident beam of radiation, in a raster scan pattern, causing the sample to fluoresce and emit visible radiation in at least two wavelengths. A portion of the fluorescent light retraces a portion of the path optical of incident beam, to a dichroic mirror that separates it from the incident beam for detection by a pair of photomultiplier tubes. A data processor accumulates digital data from the photomultiplier tubes to form a succession of image data frames of the sample being scanned, in the two wavelengths. Image data for a selected number of frames in each wavelength is averaged and then recorded on a single track of a recording system, in an alternating fashion with averaged data for the other wavelength. In addition, a ratio of the averaged data for the two wavelengths is delivered to a video display.