Abstract: The present invention relates to a method and apparatus for counting the number of microorganism colonies present on a disposable microorganism culturing device having a substantially planar substrate. The preferred apparatus of the present invention includes an LED bar illuminating the surface of the substrate and a linear array of SELFOC lenses which focus the light reflected off of the substrate onto a linear CCD sensor array. The CCD sensor array is connected to a microprocessor which analyzes the raster-scanned data using the preferred algorithm. The preferred algorithm uses the sigma-shaped neighborhood for image processing. The preferred algorithm passes the sigma region across the image in a raster-scanned order to detect object starts and merges which yield a colony count for a scanned microorganism culturing device.