The present invention concerns a method and apparatus for automatic processing a biological sample on a carrier, perhaps robotically, by applying predetermined amounts of reagents in a predetermined sequence according to a processing protocol, the processing including pre-treatment steps, under the control of an adaptive processing control system using a sample process parameter input that may be independent and an independent process parameter memory that does not interrupt process operation when being used, such that samples may be added or removed without interrupting the processing of other samples. Also included is an image capture function for sample and reagent identification and process monitoring, as well as temperature regulation and environmental control functions.