Super-Resolution Based Patch-Free 3D Medical Image Segmentation with Self-Supervised Guidance

High resolution (HR) 3D medical image segmentation plays an important role in clinical diagnoses. However, HR images are difficult to be directly processed by mainstream graphical cards due to limited video memory. Therefore, most existing 3D medical image segmentation methods use patch-based models, which ignores global context information that is useful in accurate segmentation and has low inference efficiency. To address these problems, we propose a super-resolution (SR) guided patch-free 3D medical image segmentation framework that can realize HR segmentation with global information of low-resolution (LR) input. The framework contains two tasks: semantic segmentation (main task) and super resolution (auxiliary task). To balance the information loss with the LR input, we introduce a Self-Supervised Guidance Module (SGM), which employs a selective search method to crop a HR patch from the original image as restoration guidance. Multi-scale convolutional layers are used to mitigate the scale-inconsistency between the HR guidance features and the LR features. Moreover, we propose a Task-Fusion Module (TFM) to exploit the inter connections between segmentation and SR task. This module can also be used for Test Phase Fine-tuning (TPF), leading to a better model generalization ability. When predicting, only the main segmentation task is needed, while other modules can be removed to accelerate the inference. The experiments results on two different datasets show that our framework outperforms current patch-based and patch-free models. Our model also has a four times higher inference speed compared to traditional patch-based methods. Our codes are available at: https://github.com/Dootmaan/PFSeg-Full.