Systems and methods for assessing images

A method for scanning a substrate mounted to a stage and populated with features to be sequenced, comprising:

• (a) preparing said stage to allow movements of said stage to thereby allow imaging of a plurality of panels of features on said substrate, said stage movable along a z-axis that is substantially parallel to an optical axis between said substrate and an objective lens;
• (b) for a given panel in a group of panels:
• obtaining an image and assessing said image based on a comparison of a measured signal distribution of a feature with a reference distribution;
• and
• determining whether said image should be re-acquired based on said assessment;
• and
• (c) if re-acquirable:
• correcting a condition that contributed to degradation of said image;
• and
• re-acquiring a new image after said correction.

A method for scanning a substrate mounted to a stage and populated with features arranged in a plurality of panels, said panels further arranged in a plurality of groups, said method comprising:

• (a) preparing said stage to allow predetermined movements of said stage to thereby allow imaging of said plurality of panels of features on said substrate;
• (b) for a given group:
• for each of a sample N panels in said given group, obtaining an image and assessing said image based on a comparison of a measured signal distribution with a reference distribution, and designating said panel as good or bad based on an assessment of said image;
• estimating a probability that ratio of said good panels to bad panels among said sample N panels is representative of an actual good-to-bad panel ratio among all panels in said given group;
• and
• determining whether to perform image assessment and image re-acquisition based on said assessment for all said panels during a full scan of said given group;
• and
• (c) repeating step (b) for other groups of said panels.

A method for dynamically changing a scanning configuration during a scan of a slide, said slide populated with features arranged in a plurality of sub-units, said plurality of sub-units arranged in one or more units, said method comprising:

• obtaining an image of a sub-unit and assessing said image based on a comparison of a measured signal distribution of a feature with a reference distribution;
• determining whether said sub-unit is a bad sub-unit based at least in part on said assessment;
• and
• aborting scanning of the unit in which said bad sub-unit belongs based at least in part on said sub-unit being a bad sub-unit.

A method for focusing during scanning of a microscope slide mounted on a movable stage, comprising:

• obtaining an image of a portion of said slide;
• assessing said image to determine whether said image is a bad image;
• if said image is determined to be bad, predicting what a new a focusing surface should be;
• and
• inducing movement of said stage based on said updated focusing surface.