An apparatus for conducting luminescence assays in multi-well plates, the apparatus comprising: a light detection subsystem; a liquid handling subsystem; and a plate handling subsystem, wherein said plate handling subsystem comprises: (a) a light-tight enclosure comprising: (i) one or more plate elevators (625, 740) with a plate lifting platform that can be raised and lowered; (ii) a light-tight enclosure top having one or more plate introduction apertures positioned above said plate elevators and an imaging aperture, wherein said enclosure top comprises a sliding light-tight door for sealing said plate introduction apertures; and (iii) a plate translation stage for translating a plate in one or more horizontal directions, wherein said stage comprises a plate carriage for supporting the plate, said plate carriage has an opening to allow said plate elevators positioned below the plate carriage to access and lift the plate, and said plate translation stage is configured to position plates below said imaging aperture and to position said plates above said plate elevators; (b) one or more plate stackers (120, 122) mounted on said enclosure top, above said plate introduction apertures, wherein said plate stackers are configured to receive or deliver plates to said plate elevators; and (c) a light detector mounted on said enclosure top and coupled to said imaging aperture with a light-tight seal; wherein said apparatus processes assay samples by a continuous interleaved process. a light detection subsystem; a liquid handling subsystem; and a plate handling subsystem, wherein said plate handling subsystem comprises: (a) a light-tight enclosure comprising: (i) one or more plate elevators (625, 740) with a plate lifting platform that can be raised and lowered; (ii) a light-tight enclosure top having one or more plate introduction apertures positioned above said plate elevators and an imaging aperture, wherein said enclosure top comprises a sliding light-tight door for sealing said plate introduction apertures; and (iii) a plate translation stage for translating a plate in one or more horizontal directions, wherein said stage comprises a plate carriage for supporting the plate, said plate carriage has an opening to allow said plate elevators positioned below the plate carriage to access and lift the plate, and said plate translation stage is configured to position plates below said imaging aperture and to position said plates above said plate elevators; (b) one or more plate stackers (120, 122) mounted on said enclosure top, above said plate introduction apertures, wherein said plate stackers are configured to receive or deliver plates to said plate elevators; and (c) a light detector mounted on said enclosure top and coupled to said imaging aperture with a light-tight seal; (a) a light-tight enclosure comprising: (i) one or more plate elevators (625, 740) with a plate lifting platform that can be raised and lowered; (ii) a light-tight enclosure top having one or more plate introduction apertures positioned above said plate elevators and an imaging aperture, wherein said enclosure top comprises a sliding light-tight door for sealing said plate introduction apertures; and (iii) a plate translation stage for translating a plate in one or more horizontal directions, wherein said stage comprises a plate carriage for supporting the plate, said plate carriage has an opening to allow said plate elevators positioned below the plate carriage to access and lift the plate, and said plate translation stage is configured to position plates below said imaging aperture and to position said plates above said plate elevators; (b) one or more plate stackers (120, 122) mounted on said enclosure top, above said plate introduction apertures, wherein said plate stackers are configured to receive or deliver plates to said plate elevators; and (c) a light detector mounted on said enclosure top and coupled to said imaging aperture with a light-tight seal;