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Learning-based three-dimensional registration with weak bounding box supervision

Abstract. Purpose: Image registration is the process of aligning images, and it is a fundamental task in medical image analysis. While many tasks in the field of image analysis, such as image segmentation, are handled almost entirely with deep learning and exceed the accuracy of conventional algorithms, currently available deformable image registration methods are often still conventional. Deep learning methods for medical image registration have recently reached the accuracy of conventional algorithms. However, they are often based on a weakly supervised learning scheme using multilabel image segmentations during training. The creation of such detailed annotations is very time-consuming. Approach: We propose a weakly supervised learning scheme for deformable image registration. By calculating the loss function based on only bounding box labels, we are able to train an image registration network for large displacement deformations without using densely labeled images. We evaluate our model on interpatient three-dimensional abdominal CT and MRI images. Results: The results show an improvement of ∼10  %   (for CT images) and 20% (for MRI images) in comparison to the unsupervised method. When taking into account the reduced annotation effort, the performance also exceeds the performance of weakly supervised training using detailed image segmentations. Conclusion: We show that the performance of image registration methods can be enhanced with little annotation effort using our proposed method.