Abstract: We present an interactive approach for identifying skeletons (i.e. centerlines) in intensity volumes, such as those produced by biomedical imaging. While skeletons are very useful for a range of image analysis tasks, it is extremely difficult to obtain skeletons with correct connectivity and shape from noisy inputs using automatic skeletonization methods. In this paper we explore how easy-to-supply user inputs, such as simple mouse clicking and scribbling, can guide the creation of satisfactory skeletons. Our contributions include formulating the task of drawing 3D centerlines given 2D user inputs as a constrained optimization problem, solving this problem on a discrete graph using a shortest-path algorithm, building a graphical interface for interactive skeletonization and testing it on a range of biomedical data.