New representational technologies, such as virtual microscopy, create new affordances for medical education. In the article, a study on the following two issues is reported: (a) How does collaborative use of virtual microscopy shape students' engagement with and learning from virtual slides of tissue specimen? (b) How do visual and conceptual cues scaffold students' reasoning? Fifteen pairs of medical students participated in two sessions in which the students used a virtual microscope as a diagnostic tool in the context of learning pathology. The slides provided the students with varying levels of visual and conceptual cueing. The sessions were videotaped, and the students' reasoning while using the microscope was analysed. The students' written answers were analysed in terms of the findings they made and the diagnoses suggested. At a general level, the results show that students engage actively in this kind of virtually-mediated environment. The visual and/or conceptual cues improve students' performance, and guide the students' perception and reasoning in a manner that is productive from the point of view of learning to make clinically relevant observations. Scaffolding students' reasoning process through cues furthermore assists the students in avoiding the most obvious pitfalls such as overlooking critical areas of a specimen. Overall, visual and conceptual cues improve students' reasoning in perceptual and cognitive terms, while still allowing space for the making of "relevant mistakes" that may further the students' diagnostic skills.