Methods and systems for scanning a cytological specimen carried by a slide. Movement or positioning of a motorized stage of an automated screening system may be controlled manually by a user such that the user controls movement, e.g., controlling speed, position, and/or timing, of the motorized stage along a first scan line to controllably scan a first portion of the specimen along the scan line. The user may then index the motorized stage from the first scan line to the next scan line and manually control movement of the stage along the second scan line to controllably scan another portion of the specimen. Stage indexing may also be automatic such that the user does not control or initiate indexing.