GKE-TUNet: Geometry-Knowledge Embedded TransUNet Model for Retinal Vessel Segmentation Considering Anatomical Topology

Automated retinal vessel segmentation is crucial for computer-aided clinical diagnosis and retinopathy screening. However, deep learning faces challenges in extracting complex intertwined structures and subtle small vessels from densely vascularized regions. To address these issues, we propose a novel segmentation model, called Geometry-Knowledge Embedded TransUNet (GKE-TUNet), which incorporates explicit embedding of topological features of retinal vessel anatomy. In the proposed GKE-TUNet model, a skeleton extraction network is pre-trained to extract the anatomical topology of retinal vessels from refined segmentation labels. During vessel segmentation, the dense skeleton graph is sampled as a graph of key-points and connections and is incorporated into the skip connection layer of TransUNet. The graph vertices are used as node features and correspond to positions in the low-level feature maps. The graph attention network (GAT) is used as the graph convolution backbone network to capture the shape semantics of vessels and the interaction of key locations along the topological direction. Finally, the node features obtained by graph convolution are read out as a sparse feature map based on their corresponding spatial coordinates. To address the problem of sparse feature maps, we employ convolution operators to fuse sparse feature maps with low-level dense feature maps. This fusion is weighted and connected to deep feature maps. Experimental results on the DRIVE, CHASE-DB1, and STARE datasets demonstrate the competitiveness of our proposed method compared to existing ones.