How to select slices for annotation to train best-performing deep learning segmentation models for cross-sectional medical images?

Automated segmentation of medical images highly depends on the availability of accurate manual image annotations. Such annotations are very time-consuming and costly to generate, and often require specialized expertise, particularly for cross-sectional images which contain many slices for each patient. It is crucial to ensure the best use of annotation resources. In this paper, we systematically answer the question of how to select slices of cross-sectional medical images in order to maximize performance of the resulting deep learning segmentation models. We conducted experiments on 4 medical imaging segmentation tasks with varying annotation budgets, numbers of annotated cases, numbers of annotated slices per volume, slice selection techniques, and mask interpolations. We found that: 1) It is almost always preferable to annotate fewer slices per volume and more volumes given an annotation budget. 2) Selecting slices for annotation by unsupervised active learning (UAL) is not superior to selecting slices randomly or at fixed intervals, provided that each volume is allocated the same number of annotated slices. 3) Interpolating masks between annotated slices rarely enhances model performance, with exceptions of some specific configuration for 3D models.