Robust Automated Mouse Micro-CT Segmentation Using Swin UNEt TRansformers

Image-guided mouse irradiation is essential to understand interventions involving radiation prior to human studies. Our objective is to employ Swin UNEt TRansformers (Swin UNETR) to segment native micro-CT and contrast-enhanced micro-CT scans and benchmark the results against 3D no-new-Net (nnU-Net). Swin UNETR reformulates mouse organ segmentation as a sequence-to-sequence prediction task using a hierarchical Swin Transformer encoder to extract features at five resolution levels, and it connects to a Fully Convolutional Neural Network (FCNN)-based decoder via skip connections. The models were trained and evaluated on open datasets, with data separation based on individual mice. Further evaluation on an external mouse dataset acquired on a different micro-CT with lower kVp and higher imaging noise was also employed to assess model robustness and generalizability. The results indicate that Swin UNETR consistently outperforms nnU-Net and AIMOS in terms of the average dice similarity coefficient (DSC) and the Hausdorff distance (HD95p), except in two mice for intestine contouring. This superior performance is especially evident in the external dataset, confirming the model’s robustness to variations in imaging conditions, including noise and quality, and thereby positioning Swin UNETR as a highly generalizable and efficient tool for automated contouring in pre-clinical workflows.