2.5D UNet with context-aware feature sequence fusion for accurate esophageal tumor semantic segmentation

Segmenting esophageal tumor from computed tomography (CT) sequence images can assist doctors in diagnosing and treating patients with this malignancy. However, accurately extracting esophageal tumor features from CT images often present challenges due to their small area, variable position, and shape, as well as the low contrast with surrounding tissues. This results in not achieving the level of accuracy required for practical applications in current methods. To address this problem, we propose a 2.5D context-aware feature sequence fusion UNet (2.5D CFSF-UNet) model for esophageal tumor segmentation in CT sequence images. Specifically, we embed intra-slice multiscale attention feature fusion (Intra-slice MAFF) in each skip connection of UNet to improve feature learning capabilities, better expressing the differences between anatomical structures within CT sequence images. Additionally, the inter-slice context fusion block (Inter-slice CFB) is utilized in the center bridge of UNet to enhance the depiction of context features between CT slices, thereby preventing the loss of structural information between slices. Experiments are conducted on a dataset of 430 esophageal tumor patients. The results show an 87.13% dice similarity coefficient, a 79.71% intersection over union and a 2.4758 mm Hausdorff distance, which demonstrates that our approach can improve contouring consistency and can be applied to clinical applications.

2.5D MFFAU-Net: a convolutional neural network for kidney segmentation

BACKGROUND

Kidney tumors have become increasingly prevalent among adults and are now considered one of the most common types of tumors. Accurate segmentation of kidney tumors can help physicians assess tumor complexity and aggressiveness before surgery. However, segmenting kidney tumors manually can be difficult because of their heterogeneity.

METHODS

This paper proposes a 2.5D MFFAU-Net (multi-level Feature Fusion Attention U-Net) to segment kidneys, tumors and cysts. First, we propose a 2.5D model for learning to combine and represent a given slice in 2D slices, thereby introducing 3D information to balance memory consumption and model complexity. Then, we propose a ResConv architecture in MFFAU-Net and use the high-level and low-level feature in the model. Finally, we use multi-level information to analyze the spatial features between slices to segment kidneys and tumors.

RESULTS

The 2.5D MFFAU-Net was evaluated on KiTS19 and KiTS21 kidney datasets and demonstrated an average dice score of 0.924 and 0.875, respectively, and an average Surface dice (SD) score of 0.794 in KiTS21.

CONCLUSION

The 2.5D MFFAU-Net model can effectively segment kidney tumors, and the results are comparable to those obtained with high-performance 3D CNN models, and have the potential to serve as a point of reference in clinical practice.

Segmentation of kidney mass using AgDenseU-Net 2.5D model

The Kidney and Kidney Tumor Segmentation Challenge 2021 (KiTS21) released a kidney CT dataset with 300 patients. Unlike KiTS19, KiTS21 provided a cyst category. Therefore, the segmentation of kidneys, tumors, and cysts will be able to assess the complexity and aggressiveness of kidney mass. Deep learning models can save medical resources, but 3D models still have some disadvantages, such as the high cost of computing resources. This paper proposes a scheme that saves computing resources and achieves the segmentation of kidney mass in two steps. First, we preprocess the kidney volume data using the automatic down-sampling method of 3D images, reducing the volume while preserving the feature information. Second, we finely segment kidneys, tumors, and cysts using the AgDenseU-Net (Attention gate DenseU-Net) 2.5D model. KiTS21 proposed using Hierarchical Evaluation Classes (HECs) to compute a metric for the superset: the HEC of kidney considers kidneys, tumors, and cysts as the foreground to compute segmentation performance; the HEC of kidney mass considers both tumor and cyst as the foreground classes; the HEC of tumor considers tumor as the foreground only. For KiTS21, our model achieved a dice score of 0.971 for the kidney, 0.883 for the mass, and 0.815 for the tumor. In addition, we also tested segmentation results without HECs, and our model achieved a dice score of 0.950 for the kidney, 0.878 for the tumor, and 0.746 for the cyst. The results demonstrate that the method proposed in this paper can be used as a reference for kidney tumor segmentation.