Systems, methods, and media for assessing the quality of a microscope slide image. In an embodiment, a plurality of focus point values are acquired for a sample on a microscope slide. Each focus point value comprises x-y coordinates indicating a location on the sample and a z coordinate indicating a focus height for the location on the sample. A best-fit surface is calculated based on the focus point values, and it is determined whether or not outlying focus point values exist based on the best-fit surface and the z coordinate for one or more of the focus point values. A scanned image of the microscope slide may be displayed which comprises, for each outlying focus point value, an overlay that identifies the location on the sample of the outlying focus point value based on the x-y coordinates for the outlying focus point value.