A biological scanner provides automated selection of image processing profiles to scan different types of biological growth plates. The scanner automatically identifies the type of plate to be scanned by the scanner, and then selects one of the image processing profiles appropriate for the identified plate type. For example, the image processing profiles may apply different color, shape, size and proximity criteria in counting different types of bacterial colonies. The scanner may identify the plate type by reference to a variety of machine-readable indicators, such as optically or magnetically readable marks, carried on the plate. Accordingly, biological growth plates carrying particular indicators that permit plate type identification are also contemplated. The plates may be scanned in order to read or count different types of bacterial colonies, or the amount of a particular biological agent on the biological growth plate.