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Visual comparison is integral to learning and reasoning in STEM domains. Prior work has found that visual comparison is more efficient and effective when it follows the spatial alignment principle, in which figures are laid out to support proper alignment of corresponding elements. In this study, we test this principle with middle-schoolers comparing life-science images (skeletons). We found, as prior work with adults has found, that visual comparison is facilitated by spatial alignment when figures are hard to make sense of. We conclude that spatial alignment has the potential to improve visual comparison in STEM materials, especially for challenging representations.