Detailed information of substructures of the whole heart is usually vital in the diagnosis of cardiovascular diseases and in 3D modeling of the heart. Deep convolutional neural networks have been demonstrated to achieve state-ofthe-art performance in 3D cardiac structures segmentation. However, when dealing with high-resolution 3D data, current methods employing tiling strategies usually degrade segmentation performances due to GPU memory constraints. This work develops a two-stage multi-modality whole heart segmentation strategy, which adopts an improved Combination of Faster R-CNN and 3D U-Net (CFUN+). More specifically, the bounding box of the heart is first detected by Faster R-CNN, and then the original Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) images of the heart aligned with the bounding box are input into 3D U-Net for segmentation. The proposed CFUN+ method redefines the bounding box loss function by replacing the previous Intersection over Union (IoU) loss with Complete Intersection over Union (CIoU) loss. Meanwhile, the integration of the edge loss makes the segmentation results more accurate, and also improves the convergence speed. The proposed method achieves an average Dice score of 91.1% on the Multi-Modality Whole Heart Segmentation (MM-WHS) 2017 challenge CT dataset, which is 5.2% higher than the baseline CFUN model, and achieves state-of-the-art segmentation results. In addition, the segmentation speed of a single heart has been dramatically improved from a few minutes to less than 6 seconds.

Accurate myocardial segmentation is crucial in the diagnosis and treatment of myocardial infarction (MI), especially in Late Gadolinium Enhancement (LGE) cardiac magnetic resonance (CMR) images, where the infarcted myocardium exhibits a greater brightness. However, segmentation annotations for LGE images are usually not available. Although knowledge gained from CMR images of other modalities with ample annotations, such as balanced-Steady State Free Precession (bSSFP), can be transferred to the LGE images, the difference in image distribution between the two modalities (i.e., domain shift) usually results in a significant degradation in model performance. To alleviate this, an end-to-end Variational autoencoder based feature Alignment Module Combining Explicit and Implicit features (VAMCEI) is proposed. We first re-derive the Kullback-Leibler (KL) divergence between the posterior distributions of the two domains as a measure of the global distribution distance. Second, we calculate the prototype contrastive loss between the two domains, bringing closer the prototypes of the same category across domains and pushing away the prototypes of different categories within or across domains. Finally, a domain discriminator is added to the output space, which indirectly aligns the feature distribution and forces the extracted features to be more favorable for segmentation. In addition, by combining CycleGAN and VAMCEI, we propose a more refined multi-stage unsupervised domain adaptation (UDA) framework for myocardial structure segmentation. We conduct extensive experiments on the MSCMRSeg 2019, MyoPS 2020 and MM-WHS 2017 datasets. The experimental results demonstrate that our framework achieves superior performances than state-of-the-art methods.