EffiDec3D: An Optimized Decoder for High-Performance and Efficient 3D Medical Image Segmentation

Recent 3D deep networks such as SwinUNETR, Swin-Unetrv2, and 3D UX-Net have shown promising performance by leveraging self-attention and large-kernel convolutions to capture the volumetric context. However, their substantial computational requirements limit their use in real-time and resource-constrained environments. The high #FLOPs and #Params in these networks stem largely from complex decoder designs with high-resolution layers and excessive channel counts. In this paper, we propose EffiDec3D, an optimized 3D decoder that employs a channel reduction strategy across all decoder stages, which sets the number of channels to the minimum needed for accurate feature representation. Additionally, EffiDec3D removes the high-resolution layers when their contribution to segmentation quality is minimal. Our optimized EffiDec3D decoder achieves a 96.4% reduction in #Params and a 93.0% reduction in #FLOPs compared to the decoder of original 3D UX-Net. Similarly, for SwinUNETR and SwinUNETRv2 (which share an identical decoder), we observe reductions of 94.9% in #Params and 86.2% in #FLOPs. Our extensive experiments on 12 different medical imaging tasks confirm that EffiDec3D not only significantly reduces the computational demands, but also maintains a performance level comparable to original models, thus establishing a new standard for efficient 3D medical image segmentation. Our implementation is available at https://github.com/SLDGroup/EffiDec3D.