Abstract: The invention provides an automated workstation capable of continuous, non-stop processing of specimens. The workstation includes a storage area that holds multiple cassettes containing specimens compounds or other materials to be analyzed or used in conjunction therewith (collectively, “specimens”) which, preferably, are maintained on slides, microliter plates, or the like (collectively, “plates”). The workstation also includes a robotic arm for processing the specimens, e.g., by grasping the plates, moving them from the cassettes to other apparatus contained within the workstation, and placing the plates back in the cassettes. The invention also provides methods and apparatus for acquiring and processing samples in narrow, thin-walled pipettes without transferring them to wells, vials, or other reaction vessels.