Methods and systems are provided that allow scanning of barcode information on sample vessels in situ in a tray. A laboratory instrument includes one or more trays, each having a plurality of recesses, which are configured to hold a plurality of sample vessels, and a plurality of openings between the recesses. The instrument further includes one or more rods that are separate from the trays, each having optical elements configured to read barcode information on the sample vessels. The rods are configured to move through the plurality of openings.