Methods, carrier assemblies, and systems for imaging samples for biological or chemical analysis

An assay system comprising:

• a system stage having a base surface that extends parallel to an XY plane and a plurality of datums coupled to the base surface, the datums including projections that extend away from the base surface along a Z axis that is perpendicular to the XY plane;
• an optical system including an objective lens, the objective lens configured to move relative to the system stage along the XY plane;
• a fluidic control system configured to control flow of one or more fluids through a flow cell when the flow cell is mounted onto the system stage;
• and
• a system controller configured to control the fluidic control system and the optical system to conduct different first and second assay protocols with first and second samples, respectively, wherein, during the first assay protocol, the system controller commands the fluidic control system to direct one or more fluids through the flow cell on the system stage and commands the optical system to detect optical signals from the first sample on the flow cell, and wherein, during the second assay protocol, the system controller commands the optical system to detect optical signals from the second sample on an open-face substrate on the system stage without flowing fluids through the second sample.