ENSAM: an efficient foundation model for interactive segmentation of 3D medical images

Abstract

We present ENSAM (Equivariant, Normalized, Segment Anything Model), a lightweight and promptable model for universal 3D medical image segmentation. ENSAM combines a SegResNet-based encoder with a prompt encoder and mask decoder in a U-Net-style architecture, using latent cross-attention, relative positional encoding, normalized attention, and the Muon optimizer for training. ENSAM is designed to achieve good performance under limited data and computational budgets, and is trained from scratch on under 5,000 volumes from multiple modalities (CT, MRI, PET, ultrasound, microscopy) on a single 32 GB GPU in 6 hours. As part of the CVPR 2025 Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge, ENSAM was evaluated on hidden test set with multimodal 3D medical images, obtaining a DSC AUC of 2.404, NSD AUC of 2.266, final DSC of 0.627, and final NSD of 0.597, outperforming two previously published baseline models (VISTA3D, SAM-Med3D) and matching the third (SegVol), surpassing its performance in final DSC but trailing behind in the other three metrics. In the coreset track of the challenge, ENSAM ranks 5th of 10 overall and best among the approaches not utilizing pretrained weights. Ablation studies confirm that our use of relative positional encodings and the Muon optimizer each substantially speed up convergence and improve segmentation quality.