Understanding Annotation Error Propagation and Learning an Adaptive Policy for Expert Intervention in Barrett's Video Segmentation

Surgical instrument segmentation is a fundamental task for computer-assisted interventions, yet most existing methods rely on pixel-level annotations or manual spatial prompts, which limit scalability and automation. The recently introduced Segment Anything Model 3 (SAM3) offers a pathway to annotation-free, automatic segmentation via text-based prompting; however, the instrument name as a text prompt could not be directly used due to a large domain gap. To overcome these limitations, we propose a two-stage framework that achieves instance-level segmentation without requiring ground truth masks or manual interaction. In the first stage, we leverage a natural-language-aligned generic prompt - "tool" - to produce binary masks using SAM3's zero-shot capability. In the second stage, these masks are extended to instance-level by integrating a vision-language model (Qwen) that is fine-tuned on SAM3-generated masked regions for instrument classification. We evaluate our approach on the EndoVis 2017 and 2018 datasets. Results show that, while our two-stage approach does not reach the performance of current fully supervised methods, it significantly outperforms the direct use of SAM3 for instance-level instrument segmentation with text prompts. Overall, our findings highlight both the limitations and potential of SAM3, suggesting a promising direction toward annotation-free surgical instrument segmentation.

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.

Precise spatial-temporal annotation of laparoscopic videos is time-consuming and requires expert knowledge. We propose a human-in-the-loop knowledge acquisition framework that combines active learning with dual-loss optimization to significantly reduce the annotation effort needed for automatic localization and segmentation of objects in the surgical field. Our method employs a foundation model to generate temporally consistent class activation maps (CAMs) from video using two complementary training objectives: a weak supervision loss on video-level tool presence labels for weakly annotated data, and an image-level mask loss on human-corrected annotations obtained through active learning. Rather than requiring dense pixel-level annotation upfront, our pipeline iteratively proposes pseudo-masks that guide the expert annotator to refine the knowledge previously captured by the model. We demonstrate that our framework reduces the effort of surgical video annotation by 50% by the end of training in comparison to fully manual annotation. Through eliminating the need for large, fully annotated datasets from the start, this framework enables scalability to the development of surgical tool segmentation models. This iterative human-in-the-loop refinement supports efficient knowledge acquisition with minimal expert input, providing a practical and deployable strategy for expanding tool segmentation to larger, more diverse datasets and real-world clinical settings.