Silhouette turns raw microscopy data into cell-specific measurements that are suitable for quantitative analysis. To generate each measurement, Silhouette automatically identifies all cells within an image then quantifies the properties of each identified cell. In addition to morphological properties such as cell size and position, the intensities of fluorescent reporters are quantified by averaging all of the pixels within each identified cell.

Silhouette also provides a graphical user interface that allows users to efficiently annotate each measurement. For instance, users may label identified nuclei with their apparent cell type. In this case, assigned labels are appended to the Silhouette file structure in real time, facilitating label-based querying during later stages of analysis.