A Hybrid Mamba-SAM Architecture for Efficient 3D Medical Image Segmentation

Accurate segmentation of 3D medical images such as MRI and CT is essential for clinical diagnosis and treatment planning. Foundation models like the Segment Anything Model (SAM) provide powerful general-purpose representations but struggle in medical imaging due to domain shift, their inherently 2D design, and the high computational cost of fine-tuning. To address these challenges, we propose Mamba-SAM, a novel and efficient hybrid architecture that combines a frozen SAM encoder with the linear-time efficiency and long-range modeling capabilities of Mamba-based State Space Models (SSMs). We investigate two parameter-efficient adaptation strategies. The first is a dual-branch architecture that explicitly fuses general features from a frozen SAM encoder with domain-specific representations learned by a trainable VMamba encoder using cross-attention. The second is an adapter-based approach that injects lightweight, 3D-aware Tri-Plane Mamba (TPMamba) modules into the frozen SAM ViT encoder to implicitly model volumetric context. Within this framework, we introduce Multi-Frequency Gated Convolution (MFGC), which enhances feature representation by jointly analyzing spatial and frequency-domain information via 3D discrete cosine transforms and adaptive gating. Extensive experiments on the ACDC cardiac MRI dataset demonstrate the effectiveness of the proposed methods. The dual-branch Mamba-SAM-Base model achieves a mean Dice score of 0.906, comparable to UNet++ (0.907), while outperforming all baselines on Myocardium (0.910) and Left Ventricle (0.971) segmentation. The adapter-based TP MFGC variant offers superior inference speed (4.77 FPS) with strong accuracy (0.880 Dice). These results show that hybridizing foundation models with efficient SSM-based architectures provides a practical and effective solution for 3D medical image segmentation.