CSWinUNETR: Segmentation of Thin Anatomical Structures in Medical Images

Medical image segmentation plays an important role in computer aided diagnosis, treatment planning, and disease monitoring. U-Net has been widely used for biomedical image segmentation because of its encoder decoder structure and skip connections. However, conventional convolution based U-Net models may have limited ability to capture long range dependencies and global contextual information, which can affect performance in complex segmentation tasks. This paper presents a comparative study of five U-Net based architectures: U-Net 3D, Residual U-Net, Attention U-Net, UNETR, and Swin UNETR. The models are evaluated on two benchmark datasets: BraTS 2023 for brain tumor segmentation and DRIVE for retinal vessel segmentation. Experimental results show that Swin UNETR achieves the best overall performance, with Dice scores of 0.8965 on BraTS 2023 and 0.8078 on DRIVE. The results suggest that transformer based U-Net variants are effective for segmentation tasks requiring global contextual modeling, while residual learning remains useful for fine structure segmentation. This study provides practical insights into model selection for medical image segmentation across volumetric MRI and retinal imaging tasks.

Early detection of vision-threatening conditions such as diabetic retinopathy, glaucoma, and age-related macular degeneration depends on retinal fundus image analysis, but manual assessment is slow and expert-dependent. Automated convolutional neural networks classify fundus images accurately yet act as black boxes, and existing retinal vessel segmentation methods lose discriminative power under pathology and seldom exploit attention or transformer backbones. Using the FIVES and DRIVE fundus datasets, we develop a two-pipeline framework that pairs four-class disease classification with attention- and transformer-based vessel segmentation, organised in three stages: (1) FIVES images are augmented by rotation and horizontal and vertical flips and used to fine-tune eight ImageNet-pretrained CNNs: ResNet101, DenseNet169, Xception, InceptionV3, DenseNet121, InceptionResNetV2, ResNet50, and EfficientNetB0. (2) Five gradient-based explanation methods, Grad-CAM, Grad-CAM++, Score-CAM, Faster Score-CAM, and Layer-CAM, are computed on the final convolutional block of each classifier and compared qualitatively across architectures. (3) Ten U-Net variants are benchmarked for vessel segmentation: TransUNet (hybrid CNN--Transformer encoder) and Attention U-Net (gated skip connections), evaluated with ResNet50V2, ResNet101V2, and ResNet152V2 backbones, along with additional Attention U-Net configurations using DenseNet backbones, and the fully transformer-based Swin-UNet. ResNet101 gives the highest classification accuracy: 94.17% (F1 0.942) $>$ 88.33% for EfficientNetB0. For segmentation, the architecture ranking is consistent on both datasets: Attention U-Net $>$ TransUNet $>$ Swin-UNet. The strongest configuration is Attention U-Net with a ResNet101V2 backbone: FIVES IoU 0.722, Dice 0.838; DRIVE IoU 0.648, Dice 0.787, lifting DRIVE IoU 60.80 $\rightarrow$ 64.83 over a prior custom U-Net.

Accurate pulmonary vessel segmentation remains challenging due to the sparse, tortuous, and multi-scale nature of vascular structures, where small branches are easily lost and topology integrity is difficult to preserve under voxel-wise supervision. Existing deep segmentation models primarily optimize binary masks, lacking explicit geometric constraints, thus struggling to recover continuous tubular morphology and fine vascular connectivity. In this study, we introduce MorVess, a morphology-aware segmentation framework that integrates differentiable geometric priors with large-scale foundation model adaptation to achieve fine-grained vascular parsing. MorVess jointly predicts vessel masks, distance maps, and thickness maps, providing explicit supervision for vascular boundaries, centerline consistency, and smooth diameter transitions. A lightweight 2.5D adapter bridges 3D spatial context and 2D SAM representations, while a global-local fusion block aggregates multi-level semantics and geometric cues for high-fidelity topology reconstruction. Across two challenging pulmonary CT benchmarks, MorVess delivers superior Dice, clDice, and HD95 scores, substantially improving small-vessel recovery and global connectivity. These results demonstrate that embedding geometric intelligence into pretrained vision models offers a principled and scalable pathway toward precise vessel analysis and clinically reliable structural quantification. Our source code is available at https://github.com/MaoFuyou/MorVess.