Toward an automatic preoperative pipeline for image-guided temporal bone surgery Abstract Purpose Minimally invasive surgery is often built upon a time-consuming preoperative step consisting of segmentation and trajectory planning. At the temporal bone, a complete automation of these two tasks might lead to faster interventions and more reproducible results, benefiting clinical workflow and patient health. Methods We propose an automatic segmentation and trajectory planning pipeline for image-guided interventions at the temporal bone. For segmentation, we use a shape regularized deep learning approach that is capable of automatically detecting even the cluttered tiny structures specific for this anatomy. We then perform trajectory planning for both linear and nonlinear interventions on these automatically segmented risk structures. Results We evaluate the usability of segmentation algorithms for planning access canals to the cochlea and the internal auditory canal on 24 CT data sets of real patients. Our new approach achieves similar results to the existing semiautomatic method in terms of Dice but provides more accurate organ shapes for the subsequent trajectory planning step. The source code of the algorithms is publicly available. Conclusion Automatic segmentation and trajectory planning for various clinical procedures at the temporal bone are feasible. The proposed automatic pipeline leads to an efficient and unbiased workflow for preoperative planning.