SLIP: Segmentation with Low-latency Interactive Prompting for 3D Medical Images
Authors: Baptiste Podvin, Alexandre Ancel, Flavio Milana, Chiara Innocenzi, Davide Arrigo, Federico Espinola Schulze, Guido Torzilli, Jacques Marescaux, +3 more
Organizations: IRCAD France, Strasbourg, France · Division of Hepatobiliary and General Surgery, Department of Surgery, IRCCS Humanitas Research Hospital, Milan, Italy · Department of Biomedical Sciences, Humanitas University, Milan, Italy · Unità Operativa Complessa Ginecologia Oncologica, Dipartimento di Scienze Della Salute Della Donna e Del Bambino, Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy · Université de Strasbourg, CNRS, ICube, Strasbourg, France
Interactive deep image segmentation enables efficient medical image annotation by iteratively refining predictions from user prompts, such as positive and negative clicks. Recent patch-based methods, including nnInteractive, achieve strong segmentation performance but remain limited in annotation workflows by high interaction latency, limited responsiveness to successive interactions, and the lack of support for reversible prompting. Furthermore, evaluation relies predominantly on simulated rather than controlled real-user interaction studies. We present SLIP, an end-to-end trainable framework for interactive 3D medical image segmentation that decouples image encoding from prompt-guided refinement. Image features are computed once and reused, while a lightweight patch memory bank maintains an interaction-aware segmentation state shared across patches. This representation enables prediction updates by propagating interaction context throughout the image, supports reversible prompting without recomputing image features, and substantially reduces interaction latency. By separating image representation from interactive reasoning, SLIP remains compatible with a wide range of image encoders. We train a single SLIP model for general interactive segmentation across diverse anatomical structures and imaging modalities. Beyond standard simulated evaluation, we conduct a controlled prospective user study comparing manual segmentation, nnInteractive, and SLIP across three clinical annotation tasks, six expert participants, and subjective usability measures, addressing the limited human validation of interactive segmentation methods. SLIP achieves SOTA interactive segmentation performance across 13 public datasets while providing lower interaction latency, greater responsiveness, support for reversible prompting, and higher user preference than existing approaches.
Interactive segmentation allows efficient label generation by leveraging user-provided clicks to progressively refine predictions, which is critical when fully supervised labels are costly or generalization to unseen classes is needed. Existing 3D interactive methods are limited: most operate sequentially, predicting only one object per iteration with binary masks, while several recent approaches depend on 2D foundation models and camera alignment to bridge the 2D-3D gap. To address these limitations, we propose a novel interactive segmentation framework that operates directly on sparse, randomly downsampled 3D points and processes multiple object clicks in a single forward pass. Our framework consists of a point Transformer-based encoder and a hierarchical mask decoder, which integrates multi-level crop-and-merge operations conditioned on learnable semantic embeddings. Unlike prior interactive approaches that require repeated model updates after each manually corrective click, our method jointly reasons over all click queries, modeling inter-instance relationships and refining both spatial masks and semantic predictions through spatial and semantic embeddings. Extensive experiments demonstrate that our model improves the mIoU metric by over 20 percent compared to strong baselines and achieves 8-10 percent gains under cross-dataset evaluation for a one-click per instance setting, often requiring only a single click per object. Our approach provides a generalizable and efficient solution for interactive 3D instance segmentation, particularly suitable for real-time applications such as robotic manipulation, navigation, and rapid 3D semantic annotation.
Annotating large radiology datasets is bottlenecked by the manual effort of delineating structures slice-by-slice in 3D volumes. Interactive methods reduce this effort but stay interaction-inefficient: slice-wise methods (including many foundation models) ignore inter-slice continuity, while 3D and video-based methods propagate a prompt with a \emph{fixed} propagator that never adapts to the target volume, so it drifts on low-contrast or pathological structures and must be re-prompted. We present IMVS, a human-in-the-loop annotation framework that composes three components into a closed loop rather than a new segmentation primitive: a lightweight 2D Slice Mask Adapter (SMA) fine-tuned online from user scribbles, a frozen Volume Mask Tracker (VMT) that propagates corrected masks across adjacent slices, and a soft teacher--student alignment that limits forgetting. The SMA is backbone-agnostic (UNet++, DeepLabV3, TransUNet). Across 8 public CT/MRI datasets, IMVS matches strong interactive baselines in quality while sharply cutting annotation effort: 14.4× faster than a proficient copy-based manual workflow (22.3× over naive manual), 4.6× over slice-wise and 1.9× over 3D interactive methods. MedSAM2 and ScribblePrompt stay competitive or stronger on well-delineated organs; IMVS's advantage is largest on challenging targets and on interaction efficiency. Source code and Demo Video: https://github.com/AbhilakshSinghReen/imvs.
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.