EICSeg: Universal Medical Image Segmentation via Explicit In-Context Learning

Deep learning models for medical image segmentation often struggle with task-specific characteristics, limiting their generalization to unseen tasks with new anatomies, labels, or modalities. Retraining or fine-tuning these models requires substantial human effort and computational resources. To address this, in-context learning (ICL) has emerged as a promising paradigm, enabling query image segmentation by conditioning on example image-mask pairs provided as prompts. Unlike previous approaches that rely on implicit modeling or non-end-to-end pipelines, we redefine the core interaction mechanism in ICL as an explicit retrieval process, termed E-ICL, benefiting from the emergence of vision foundation models (VFMs). E-ICL captures dense correspondences between queries and prompts at minimal learning cost and leverages them to dynamically weight multi-class prompt masks. Built upon E-ICL, we propose EICSeg, the first end-to-end ICL framework that integrates complementary VFMs for universal medical image segmentation. Specifically, we introduce a lightweight SD-Adapter to bridge the distinct functionalities of the VFMs, enabling more accurate segmentation predictions. To fully exploit the potential of EICSeg, we further design a scalable self-prompt training strategy and an adaptive token-to-image prompt selection mechanism, facilitating both efficient training and inference. EICSeg is trained on 47 datasets covering diverse modalities and segmentation targets. Experiments on nine unseen datasets demonstrate its strong few-shot generalization ability, achieving an average Dice score of 74.0%, outperforming existing in-context and few-shot methods by 4.5%, and reducing the gap to task-specific models to 10.8%. Even with a single prompt, EICSeg achieves a competitive average Dice score of 60.1%. Notably, it performs automatic segmentation without manual prompt engineering, delivering results comparable to interactive models while requiring minimal labeled data. Source code will be available at https://github.com/ zerone-fg/EICSeg.