Scatterplots are among the most widely used visualization techniques. Compelling scatterplot visualizations improve understanding of data by leveraging visual perception to boost awareness when performing specific visual analytic tasks. Design choices in scatterplots, such as graphical encodings or data aspects, can directly impact decision-making quality for low-level tasks like clustering. Hence, constructing frameworks that consider both the perceptions of the visual encodings and the task being performed enables optimizing visualizations to maximize efficacy. In this article, we propose an automatic tool to optimize the design factors of scatterplots to reveal the most salient cluster structure. Our approach leverages the merge tree data structure to identify the clusters and optimize the choice of subsampling algorithm, sampling rate, marker size, and marker opacity used to generate a scatterplot image. We validate our approach with user and case studies that show it efficiently provides high-quality scatterplot designs from a large parameter space.