Flow cell based motion system calibration and control methods

A patterned flow cell, comprising:

• a substrate;
• a plurality of sample sites in a non-fiducial region of the substrate, wherein the plurality of sample sites is arranged in a periodic pattern;
• and
• a plurality of fiducials provided on the substrate in a first dimension associated with a scan direction of the patterned flow cell, wherein each fiducial comprises a plurality of features that are separated by one or more blank regions, wherein each feature is contiguous across one or more columns of the periodic pattern.

A sequencing instrument, comprising:

• a sample stage configured to support a flow cell;
• an objective lens, a photodetector, and a light source configured to operate in combination to image the flow cell when present on the sample stage;
• and
• a controller configured to perform operations comprising:
• advancing the flow cell when undergoing an imaging operation along a linear scan path;
• imaging a patterned surface of the sample container as it is advanced along the linear scan path, wherein the patterned surface comprises:
• a plurality of sample sites arranged in a periodic pattern, wherein a subset of the sample sites are sample site-based fiducials comprising an arrangement of sample sites and blank regions formed linearly in a first dimension associated with a scan direction of the patterned flow cell;
• determining a current feature pattern of the flow cell based on the sample-site based fiducials;
• comparing the current feature pattern with an expected feature pattern;
• and
• adjusting one or both of a location of the sample stage or a speed at which the sample stage is moved based upon the comparison of the current feature pattern with the expected feature pattern.