an apparatus for counting microorganism colonies on at least on disposable microorganism culturing medium having a substantially planar substrate . the apparatus has an imaging system for detecting colonies on the substantially planar substrate , and a holder positioning device for storing and queuing one or more holders , each adapted to support one of the substrates . the positioning device moves the holders sequentially into a predetermined position relative to the imaging system so that images can be obtained . the imaging system cooperates with a counting device for counting the colonies using information from several images provided by the imaging system taken at different times as the positioning device cycles the holders past the predetermined location to be imaged . suitable holders , and a method of queuing and counting colonies on substrates , are also disclosed .