An automated method for processing a plurality of slides bearing biological samples is disclosed, comprising: performing a set of slide processing operations on the plurality of slides in one or more workstations while the slides in the plurality are held in substantially horizontal positions in a slide tray, wherein the set of slide processing operations includes at least staining samples on the slides by depositing one or more reagents from at least one reagent container, through a fluidics module, onto tops of slides held in the slide tray using at least one dispense nozzle; transporting the slide tray holding the plurality of slides to an automated coverslipper workstation after performing the set of slide tray processing operations; coverslipping the plurality of slides held in the slide tray with separate respective coverslips using the automated coverslipper workstation while the plurality of slides are held in substantially horizontal positions in the slide tray; and removing the slide tray holding the coverslipped slides from the automated coverslipper workstation.