The flow cell compartment houses the flow cell stage and contains four magnetic flow cell positions numbered 1 through 4, left to right. Before the run begins, the instrument software performs a check to ensure that each flow cell is securely positioned on the stage.
Each flow cell position has a light that indicates the status of the position:
Color
Action
Description
White
Solid
Awaiting flow cell.
Note that for a maintenance wash, the light is also white if the flow cell is detected, but no seal check performed.
Green
Solid
Flow cell detected, no seal check performed yet.
Note that for a maintenance wash, there is no green light if a flow cell is detected.
Blue
Flashing
Performing seal check
Blue
Solid
Seal check passed
Red
Solid
Seal check failed
No Light
Flow cell position not used, or all seal check completed successfully for all assigned flow cells.
