Coordinated conveyors in an automated system. A system comprises a plurality of conveyors, which each comprise a plurality of segments, and one or more stations. An instruction is received to perform an operation that requires at least one station to process at least a first item held by a first segment of a first conveyor and a second item held by a second segment of a second conveyor. In response to the instruction, one or both of the first and second conveyors are moved, such that the first segment and the second segment are aligned at the station. After alignment, one or more instruments of the station process the first item and the second item.