Retriever Encoder Selection Matters for In-Context Learning-based Medical Segmentation

In-context learning-based medical segmentation (ICLM) enables foundation models to generalize to unseen cases without retraining. To enhance performance on test queries, existing methods typically follow a two-stage process: (1) using a retrieval encoder (RE) to map both queries and training samples into a shared feature space, and (2) retrieving and utilizing the top-k most similar training samples. While current methods fix the RE and focus on optimizing stage (2), we show that the choice of RE in stage (1) alone can account for over 70% of the performance variation, highlighting RE selection as a critical yet often overlooked factor in ICLM. In this paper, we conduct an analysis of the RE selection and make two main findings: (1) dynamically selecting the RE for each query outperforms selecting a fixed RE for the entire task; and (2) feature-space heuristics (e.g., intra-class compactness and inter-class separability) fail to predict RE quality. To this end, we propose the instance-adaptive retrieval encoder selection (IRES) method that can select the optimal RE for each query based on output predictions. IRES is based on the intuition that a good RE retrieves relevant demonstrations, helping the ICL model generate more accurate and stable segmentation masks. Thus, we introduce the shape stability score (S 3 ), which evaluates the morphological stability of predicted masks under iterative erosion. Experiments show S 3 correlates strongly with true RE quality (Pearson > 0.8), serving as a reliable selection proxy. To reduce S 3 's per-query cost, we propose parallel prediction with reciprocal neighbor reuse (P2R), which accelerates inference by parallelizing encoding and reusing encoder selections across reciprocal neighbors, avoiding redundant computation. Built on S 3 and P2R, IRES improves ICLM performance across FUNDUS, Brain MRI, and Chest X-ray datasets, with up to 10.6% gain on fundus segmentation.