Organizations: State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China · School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China · Yau Mathematical Sciences Center, Tsinghua University, Beijing, China · Department of Mathematical Science, Tsinghua University, Beijing, China · Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China · China State Key Laboratory of Respiratory Disease & National Clinical Research Centre for Respiratory Disease, Guangzhou, China · PET/CT Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China · National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
Abstract
Medical expert annotators are scarce, and blind reliance on artificial intelligence (AI) can be misleading, motivating approaches in which humans, particularly junior medical trainees or even non-medical personnel, collaborate with AI to achieve robust medical segmentation. Although the Segment Anything Model (SAM) shows promise for general-purpose image segmentation, its performance in human-AI collaboration for specialized medical tasks has not been thoroughly evaluated. Here we present Hi-Seg, a human-in-the-loop segmentation framework for pulmonary nodules built on SAM. Humans iteratively refine prompts through trial-and-error learning and semantic reasoning, progressively guiding SAM toward higher-quality masks. Using chest CT scans from 1,179 patients across 12 centers, we conducted the first large-scale external validation of collaborative human-SAM segmentation. Across all annotator groups, Hi-Seg achieved a mean Dice score of almost 85%, outperforming five state-of-the-art deep learning models by 10-22% and 13 SAM variants by 1-29%. Hi-Seg improved segmentation accuracy while reducing annotation time for medical annotators, and briefly trained non-medical annotators achieved performance comparable to that of the junior medical student. These findings suggest that human-in-the-loop segmentation can reduce clinician workload, enable scalable crowdsourced annotation, and transform clinical workflows by facilitating the safe and efficient integration of foundation models into routine clinical practice.
Accurate segmentation of pulmonary lesions is essential for effective clinical diagnosis and treatment strategies. Existing segmentation approaches often lack task-specific semantic guidance, as text-based annotations typically offer coarse localization of lesions, leading to inadequate delineation of lesion boundaries and poor performance on small-scale lesions. To address this, we propose CGSM, a Concept-Guided Segmentation Model that integrates LLM-generated and clinically reviewed concepts into the segmentation process. Specifically, we design a Concept-Visual Alignment Module (CVAM) to activate relevant tokens within the concepts that align with visual features, enhancing the interaction between textual and visual information. In addition, we introduce a Concept Modulated Decoder (CM-Decoder), which uses concepts from CVAM as modulation signals to facilitate the adaptive fusion of image and text features, improving the segmentation accuracy. Extensive experiments on two public datasets show that CGSM achieves state-of-the-art performance, with results of 91.59% Dice and 84.49% mIoU on the QaTa-COV19 dataset, demonstrating its effectiveness in pulmonary lesion segmentation.
Semi-supervised learning (SSL) has become a promising solution to alleviate the annotation burden of deep learning-based medical image segmentation models. While recent advances in foundation model-driven SSL have pushed the boundary to extremely limited annotation scenarios, they fail to maintain robust competitive performance in complex imaging modalities. In this paper, we propose SemiSAM-O1, an annotation-efficient framework using only one annotated template image for segmentation. SemiSAM-O1 extends the specialist-generalist collaborative learning framework to the extreme one-label setting by fully exploiting the foundation model's feature representation capability beyond its prompting interface. SemiSAM-O1 operates in two stages. In the first stage, the foundation model's encoder extracts dense features from all volumes, and class prototypes derived from the single annotated template are propagated to the unlabeled pool via feature similarity to produce coarse initial pseudo-labels. In the second stage, an iterative training-and-refinement loop progressively improves both the segmentation model and the pseudo-labels over multiple rounds, where each round trains the model from scratch on current pseudo-labels and generates updated predictions with voxel-wise uncertainty estimates. An uncertainty-guided refinement step further leverages the foundation model's global feature space to correct high-uncertainty regions by aggregating labels from their most similar confident neighbors, establishing a virtuous cycle of mutual improvement. Extensive experiments on a wide range of segmentation tasks across different modalities and anatomical targets demonstrate that SemiSAM-O1 significantly narrows the performance gap between one-label semi-supervised learning and full supervision, while significantly reducing the computational overhead of online foundation model inference.
Transforming foundation segmentation models from human-prompted tools into auto-promptable annotators is critical for scalable medical data annotation. Current methods commonly depend on external feature matchers or auxiliary networks to automate geometric prompting, but introducing architectural overhead and limiting performance scalability. Although SAM3 natively supports concept segmentation via reusable text prompts, its direct use in medical imaging is hindered by a lack of fine-grained clinical knowledge and the ambiguity of human-written descriptions. In this work, we propose Mask to Concept (M2C), an efficient framework that adapts SAM3 for medical few-shot annotation without external modules, parameter retraining, or manual text engineering. Using only a few labeled images, M2C enables SAM3 to automatically search for transferable visual concepts entirely within its frozen architecture: it initializes a learnable concept embedding, uses it to prompt segmentation, and updates the embedding by gradients of minimizing the concept segmentation error. We further introduce a Hybrid Uncertainty Estimation (HUE) module that calculates the prediction entropy and maps concept predictions back to the box prompts, measuring concept-geometry prompting inconsistency. Highly uncertain samples are flagged actively for human correction, and the corrected masks are then fed back to M2C to continuously search for more precise concept embeddings, forming a self-enhancing annotation loop with minimal expert effort. Experiments on medical segmentation benchmarks show that our method achieves SOTA few-shot segmentation performance and outstanding annotation efficiency, offering a practical and efficient pathway toward scalable medical image labeling. Codes are at https://github.com/Huster-Hq/M2C.