Many scientific discoveries have depended on external diagrams or visualizations. Many scientists also report to use an internal mental representation or mental imagery to help them solve problems and reason. How do scientists connect these internal and external representations? We examined working scientists as they worked on external scientific visualizations. We coded the number and type of spatial transformations (mental operations that scientists used on internal or external representations or images) and found that there were a very large number of (...) comparisons, either between different visualizations or between a visualization and the scientists’ internal mental representation. We found that when scientists compared visualization to visualization, the comparisons were based primarily on features. However, when scientists compared a visualization to their mental representation, they were attempting to align the two representations. We suggest that this alignment process is how scientists connect internal and external representations. (shrink)