Prompt Group-Aware Training for Robust Text-Guided Nuclei Segmentation

Is Segment Anything Model 3 (SAM3) capable in segmenting Any Pathology Images? Digital pathology segmentation spans tissue-level and nuclei-level scales, where traditional methods often suffer from high annotation costs and poor generalization. SAM3 introduces Promptable Concept Segmentation, offering a potential automated interface via text prompts. With this work, we propose a systematic evaluation protocol to explore the capability space of SAM3 in a structured manner. Specifically, we evaluate SAM3 under different supervision settings including zero-shot, few-shot, and supervised with varying prompting strategies. Our extensive evaluation on pathological datasets including NuInsSeg, PanNuke and GlaS, reveals that: (1) text-only prompts poorly activate nuclear concepts; (2) performance is highly sensitive to visual prompt types and budgets; (3) few-shot learning offers gains, but SAM3 lacks robustness against visual prompt noise; and (4) a significant gap persists between prompt-based usage and task-trained adapter-based reference. Our study delineates SAM3's boundaries in pathology image segmentation and provides practical guidance on the necessity of pathology domain adaptation.

Segmentation is central to clinical diagnosis and monitoring, yet the reliability of modern foundation models in medical imaging still depends on the availability of precise prompts. The Segment Anything Model (SAM) offers powerful zero-shot capabilities, although it collapses under the weak, generic, and noisy prompts that dominate real clinical workflows. In practice, annotations such as centerline points are coarse and ambiguous, often drifting across neighboring anatomy and misguiding SAM toward inconsistent or incomplete masks. We introduce SPD, a Saliency-Guided Prompt Distillation framework that converts these unreliable cues into robust guidance. SPD first learns data-driven anatomical priors through a lightweight saliency head to obtain confident localization maps. These priors then drive Contextual Prompt Distillation, which validates and enriches noisy prompts using cues from anatomically adjacent slices, producing a consensus prompt set that matches the behavior of expert reasoning. A Pairwise Slice Consistency objective further enforces local anatomical coherence during segmentation. Experiments on four challenging MRI and CT benchmarks demonstrate that SPD consistently outperforms existing SAM adaptations and supervised baselines, delivering large gains in both region-based and boundary-based metrics. SPD provides a practical and principled path toward reliable foundation model deployment in clinical environments where only imperfect prompts are available.

Specifying segmentation targets with natural language provides flexible semantic conditioning for medical image segmentation. However, existing methods still struggle to reliably ground high-level textual semantics into accurate pixel-level spatial prompts, especially under low-contrast lesions, ambiguous boundaries, and visually similar anatomical contexts. In this paper, we propose RADAR (Residual Aggregation and Dense Alignment Representations), a parameter-efficient framework for text-guided medical image segmentation. RADAR explicitly decouples and synergizes the medical semantic anchoring capability of BiomedCLIP with the prompt-driven mask decoding ability of MedSAM2, while enabling low-cost task adaptation via LoRA. Specifically, Guided Residual Depth Aggregation adaptively aggregates cross-layer features under semantic guidance to alleviate delayed textual injection and deep semantic dilution. Structured Dense Representation Alignment leverages a frozen BiomedCLIP to construct crop-level target, boundary, and context anchors, improving the local discriminability of dense features and the reliability of automatic prompts. Multi-modal Prompt Generation further converts cross-modal semantic responses into composite text, point, and mask prompts for MedSAM2 decoding. Experiments on three public medical image segmentation datasets show that RADAR achieves competitive performance with only 0.74M trainable parameters, demonstrating its effectiveness in parameter-efficient adaptation, semantic grounding, and dense representation enhancement. The source code is available at https://github.com/JGuiidev/RADAR.