An automated method for processing a plurality of slides (210, 248, 442, 672, 1608) bearing biological samples, comprising: performing a set of slide processing operations on the plurality of slides (210, 248, 442, 672, 1608) in one or more workstations (4, 6, 8, 10, 501, 1500) while the slides (210, 248, 442, 672, 1608) in the plurality are held in substantially horizontal positions in a slide tray (70, 200, 406, 618, 1502), wherein the set of slide processing operations includes at least staining samples on the slides (210, 248, 442, 672, 1608) by depositing one or more reagents onto tops of slides (210, 248, 442, 672, 1608) held in the slide tray (70, 200, 406, 618, 1502) using at least one dispense nozzle (410, 550, 738); transporting the slide tray (70, 200, 406, 618, 1502) holding the plurality of slides (210, 248, 442, 672, 1608) to an automated coverslipper workstation (32, 108, 700) after performing the set of slide tray processing operations; and performing a coverslipping operation at the automated coverslipper workstation (32, 108, 700), wherein coverslips are added to the plurality of slides (210, 248, 442, 672, 1608) held in the tray (70, 200, 406, 618, 1502) in substantially horizontal positions, wherein holding the slides (210, 248, 442, 672, 1608) in the slide tray (70, 200, 406, 618,1502) comprises introducing a slide (210, 248, 442, 672, 1608) into a slide clip of a slide clip pillar, said slide clip including a rigid top portion and a flexible lower portion, and wherein each individual slide (210, 248, 442, 672, 1608) in the plurality of slides (210, 248, 442, 672, 1608) is supported at one end on each side of slide (210, 248, 442, 672, 1608) by two slide clip pillars. performing a set of slide processing operations on the plurality of slides (210, 248, 442, 672, 1608) in one or more workstations (4, 6, 8, 10, 501, 1500) while the slides (210, 248, 442, 672, 1608) in the plurality are held in substantially horizontal positions in a slide tray (70, 200, 406, 618, 1502), wherein the set of slide processing operations includes at least staining samples on the slides (210, 248, 442, 672, 1608) by depositing one or more reagents onto tops of slides (210, 248, 442, 672, 1608) held in the slide tray (70, 200, 406, 618, 1502) using at least one dispense nozzle (410, 550, 738); transporting the slide tray (70, 200, 406, 618, 1502) holding the plurality of slides (210, 248, 442, 672, 1608) to an automated coverslipper workstation (32, 108, 700) after performing the set of slide tray processing operations; and performing a coverslipping operation at the automated coverslipper workstation (32, 108, 700), wherein coverslips are added to the plurality of slides (210, 248, 442, 672, 1608) held in the tray (70, 200, 406, 618, 1502) in substantially horizontal positions, wherein holding the slides (210, 248, 442, 672, 1608) in the slide tray (70, 200, 406, 618,1502) comprises introducing a slide (210, 248, 442, 672, 1608) into a slide clip of a slide clip pillar, said slide clip including a rigid top portion and a flexible lower portion, and wherein each individual slide (210, 248, 442, 672, 1608) in the plurality of slides (210, 248, 442, 672, 1608) is supported at one end on each side of slide (210, 248, 442, 672, 1608) by two slide clip pillars.