Scanner variation changes how pathology foundation models represent the same tissue. We introduce SlideRuler, which uses regions within a slide as internal controls to estimate and correct acquisition-induced shifts in other regions.

A transfer map learned from paired rescans enables calibration from a single scan at inference while keeping the foundation model fixed. Across two encoders and five SCORPION scanners, learned transfer reduces mean target-to-source embedding distance by 16.3-38.5% relative to raw embeddings.

Comparisons with unrelated same-scanner controls reveal a positive same-slide contribution across all four evaluation settings, including scanner holdout. A source-anchored variant reduces source-feature displacement by 47.7-83.6% relative to learned transfer while retaining most of its alignment gain.

By drawing calibration information from the slide itself, SlideRuler offers a path toward more consistent use of frozen pathology models across imaging systems.