Concept-to-Pixel: Prompt-Free Universal Medical Image Segmentation

Medical image segmentation is fundamental for biomedical discovery. Existing methods lack generalizability and demand extensive, time-consuming manual annotation for new clinical application. Here, we propose MedSAM-3, a text promptable medical segmentation model for medical image and video segmentation. By fine-tuning the Segment Anything Model (SAM) 3 architecture on medical images paired with semantic conceptual labels, our MedSAM-3 enables medical Promptable Concept Segmentation (PCS), allowing precise targeting of anatomical structures via open-vocabulary text descriptions rather than solely geometric prompts. We further introduce the MedSAM-3 Agent, a framework that integrates Multimodal Large Language Models (MLLMs) to perform complex reasoning and iterative refinement in an agent-in-the-loop workflow. Comprehensive experiments across diverse medical imaging modalities, including X-ray, MRI, Ultrasound, CT, and video, demonstrate that our approach significantly outperforms existing specialist and foundation models. We will release our code and model at https://github.com/Joey-S-Liu/MedSAM3.

Medical image segmentation remains challenging in practical deployment, as models often struggle to generalize beyond the distributions covered by their training data and high-quality pixel-level annotations are typically unavailable for adaptation. Inspired by the cross-task transferability of large language models, we investigate whether unified multimodal models (UMMs) can transfer their pretrained visual understanding, reasoning, and generation capabilities to medical image segmentation without task-specific post-training. By recasting segmentation as structured visual generation, we find that frontier UMMs (e.g., Nano Banana) already exhibit basic segmentation capabilities across diverse clinical scenarios, but still struggle with challenging tasks requiring specialized anatomical or domain-specific knowledge. We further show that these limitations can be effectively mitigated by incorporating visual anatomical knowledge from in-context exemplars, expanding candidate solutions through repeated sampling, and refining suboptimal predictions via targeted editing.Motivated by these observations, we propose SegBanana, to our knowledge, the first agentic visual generation framework for training-free medical image segmentation. SegBanana builds on a frozen UMM as the core generative model, augmented with Anatomy-Aware Knowledge Retrieval and Comparative Quality Critique to unlock its potential segmentation capability. A State-Aware Multimodal Controller maintains structured state and iteratively orchestrates these tools, repeatedly refining intermediate predictions toward higher-quality masks. Across eight medical segmentation datasets, SegBanana achieves an average mDice of 77.45%, outperforming representative generalist (SAM3 and SegGPT) and medical-specific (BiomedParse and MedSAM3) baselines by at least 14.93 points, while remaining robust to out-of-domain visual supports.

Medical image segmentation foundation models are expected to generalize across diverse clinical scenarios, yet existing universal methods remain fragmented by prompt paradigms and spatial dimensions. Visual in-context learning, interactive segmentation, and language-guided segmentation are typically handled by paradigm-specific models, while 2D and 3D images are also modeled separately. Such isolation prevents heterogeneous annotations and data from being jointly absorbed by a single scalable model and limits cross-paradigm knowledge transfer. To address this bottleneck, we propose UniMedSeg, a Transformer-centric universal segmentation framework that maps visual examples, geometric interactions, language instructions, and 2D/3D images into a shared sequence space, enabling heterogeneous medical supervision to be jointly learned through a unified in-context interface without prompt- or dimension-specific branches. To overcome the long-sequence memory bottleneck caused by visual contexts, we introduce Decoupled Split Attention, which reduces attention complexity to linear while preserving hardware-friendly computation and focused context-target interaction. Extensively trained and evaluated on a large corpus curated from 27 public datasets, UniMedSeg achieves state-of-the-art performance across visual in-context, interactive, and language-guided segmentation without task-specific fine-tuning, demonstrating strong generalization on diverse held-out tasks. The code and model weights are publicly available at https://github.com/Lii1228/UniMedSeg