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Nicolas Padoy

Publications and source records attributed to Nicolas Padoy.

At least 37 records · Page 2Linked to original sources

S4M: 4-points to Segment Anything

Purpose: The Segment Anything Model (SAM) promises to ease the annotation bottleneck in medical segmentation, but overlapping anatomy and blurred boundaries make its point prompts ambiguous, leading to cycles of manual refinement to achieve precise masks. Better prompting strategies are needed. Methods: We propose a structured prompting strategy using 4 points as a compact instance-level shape description. We study two 4-point variants: extreme points and the proposed major/minor axis endpoints, inspired by ultrasound measurement practice. SAM cannot fully exploit such structured prompts because it treats all points identically and lacks geometry-aware reasoning. To address this, we introduce S4M (4-points to Segment Anything), which augments SAM to interpret 4 points as relational cues rather than isolated clicks. S4M expands the prompt space with role-specific embeddings and adds an auxiliary "Canvas" pretext task that sketches coarse masks directly from prompts, fostering geometry-aware reasoning. Results: Across eight datasets in ultrasound and surgical endoscopy, S4M improves segmentation by +3.42 mIoU over a strong SAM baseline at equal prompt budget. An annotation study with three clinicians further shows that major/minor prompts enable faster annotation. Conclusion: S4M increases performance, reduces annotation effort, and aligns prompting with clinical practice, enabling more scalable dataset development in medical imaging. We release our code and pretrained models at https://github.com/CAMMA-public/S4M.

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CliPPER: Contextual Video-Language Pretraining on Long-form Intraoperative Surgical Procedures for Event Recognition

Video-language foundation models have proven to be highly effective in zero-shot applications across a wide range of tasks. A particularly challenging area is the intraoperative surgical procedure domain, where labeled data is scarce, and precise temporal understanding is often required for complex downstream tasks. To address this challenge, we introduce CliPPER (Contextual Video-Language Pretraining on Long-form Intraoperative Surgical Procedures for Event Recognition), a novel video-language pretraining framework trained on surgical lecture videos. Our method is designed for fine-grained temporal video-text recognition and introduces several novel pretraining strategies to improve multimodal alignment in long-form surgical videos. Specifically, we propose Contextual Video-Text Contrastive Learning (VTC_CTX) and Clip Order Prediction (COP) pretraining objectives, both of which leverage temporal and contextual dependencies to enhance local video understanding. In addition, we incorporate a Cycle-Consistency Alignment over video-text matches within the same surgical video to enforce bidirectional consistency and improve overall representation coherence. Moreover, we introduce a more refined alignment loss, Frame-Text Matching (FTM), to improve the alignment between video frames and text. As a result, our model establishes a new state-of-the-art across multiple public surgical benchmarks, including zero-shot recognition of phases, steps, instruments, and triplets. The source code and pretraining captions can be found at https://github.com/CAMMA-public/CliPPER.

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From Panel to Pixel: Zoom-In Vision-Language Pretraining from Biomedical Scientific Literature

There is a growing interest in developing strong biomedical vision-language models. A popular approach to achieve robust representations is to use web-scale scientific data. However, current biomedical vision-language pretraining typically compresses rich scientific figures and text into coarse figure-level pairs, discarding the fine-grained correspondences that clinicians actually rely on when zooming into local structures. To tackle this issue, we introduce Panel2Patch, a novel data pipeline that mines hierarchical structure from existing biomedical scientific literature, i.e., multi-panel, marker-heavy figures and their surrounding text, and converts them into multi-granular supervision. Given scientific figures and captions, Panel2Patch parses layouts, panels, and visual markers, then constructs hierarchical aligned vision-language pairs at the figure, panel, and patch levels, preserving local semantics instead of treating each figure as a single data sample. Built on this hierarchical corpus, we develop a granularity-aware pretraining strategy that unifies heterogeneous objectives from coarse didactic descriptions to fine region-focused phrases. By applying Panel2Patch to only a small set of the literature figures, we extract far more effective supervision than prior pipelines, enabling substantially better performance with less pretraining data.

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Surg-R1: A Hierarchical Reasoning Foundation Model for Scalable and Interpretable Surgical Decision Support with Multi-Center Clinical Validation

Surgical scene understanding demands not only accurate predictions but also interpretable reasoning that surgeons can verify against clinical expertise. However, existing surgical vision-language models generate predictions without reasoning chains, and general-purpose reasoning models fail on compositional surgical tasks without domain-specific knowledge. We present Surg-R1, a surgical Vision-Language Model that addresses this gap through hierarchical reasoning trained via a four-stage pipeline. Our approach introduces three key contributions: (1) a three-level reasoning hierarchy decomposing surgical interpretation into perceptual grounding, relational understanding, and contextual reasoning; (2) the largest surgical chain-of-thought dataset with 320,000 reasoning pairs; and (3) a four-stage training pipeline progressing from supervised fine-tuning to group relative policy optimization and iterative self-improvement. Evaluation on SurgBench, comprising six public benchmarks and six multi-center external validation datasets from five institutions, demonstrates that Surg-R1 achieves the highest Arena Score (64.9%) on public benchmarks versus Gemini 3.0 Pro (46.1%) and GPT-5.1 (37.9%), outperforming both proprietary reasoning models and specialized surgical VLMs on the majority of tasks spanning instrument localization, triplet recognition, phase recognition, action recognition, and critical view of safety assessment, with a 15.2 percentage point improvement over the strongest surgical baseline on external validation.

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SurgVidLM: Towards Multi-grained Surgical Video Understanding with Large Language Model

Surgical scene understanding is critical for surgical training and robotic decision-making in robot-assisted surgery. Recent advances in Multimodal Large Language Models (MLLMs) have demonstrated great potential for advancing scene perception in the medical domain, facilitating surgeons to understand surgical scenes and procedures. However, these methods are primarily oriented towards image-based analysis or global video understanding, overlooking the fine-grained video reasoning that is crucial for analyzing specific processes and capturing detailed task execution within a surgical procedure. To bridge this gap, we propose SurgVidLM, the first video language model designed to address both full and fine-grained surgical video comprehension. To train our SurgVidLM, we construct the SVU-31K that is a large-scale dataset with over 31K video-instruction pairs, enabling both holistic understanding and detailed analysis of surgical procedures. Building on this resource, SurgVidLM incorporates a two-stage StageFocus mechanism: the first stage extracts global procedural context, while the second stage performs high-frequency local analysis guided by temporal cues. We also develop the Multi-frequency Fusion Attention to effectively integrate low- and high-frequency visual tokens, ensuring the preservation of critical task-specific details. Experimental results demonstrate that SurgVidLM significantly outperforms state-of-the-art Vid-LLMs of comparable parameter scale in both full and fine-grained video understanding tasks, showcasing its superior capability in capturing the context of complex robot-assisted surgeries. Our code and dataset will be publicly accessible soon.

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The SAGES Critical View of Safety Challenge: A Global Benchmark for AI-Assisted Surgical Quality Assessment

Advances in artificial intelligence (AI) for surgical quality assessment promise to democratize access to expertise, with applications in training, guidance, and accreditation. This study presents the SAGES Critical View of Safety (CVS) Challenge, the first AI competition organized by a surgical society, using the CVS in laparoscopic cholecystectomy, a universally recommended yet inconsistently performed safety step, as an exemplar of surgical quality assessment. A global collaboration across 54 institutions in 24 countries engaged hundreds of clinicians and engineers to curate 1,000 videos annotated by 20 surgical experts according to a consensus-validated protocol. The challenge addressed key barriers to real-world deployment in surgery, including achieving high performance, capturing uncertainty in subjective assessment, and ensuring robustness to clinical variability. To enable this scale of effort, we developed EndoGlacier, a framework for managing large, heterogeneous surgical video and multi-annotator workflows. Thirteen international teams participated, achieving up to a 17% relative gain in assessment performance, over 80% reduction in calibration error, and a 17% relative improvement in robustness over the state-of-the-art. Analysis of results highlighted methodological trends linked to model performance, providing guidance for future research toward robust, clinically deployable AI for surgical quality assessment.

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DExTeR: Weakly Semi-Supervised Object Detection with Class and Instance Experts for Medical Imaging

Detecting anatomical landmarks in medical imaging is essential for diagnosis and intervention guidance. However, object detection models rely on costly bounding box annotations, limiting scalability. Weakly Semi-Supervised Object Detection (WSSOD) with point annotations proposes annotating each instance with a single point, minimizing annotation time while preserving localization signals. A Point-to-Box teacher model, trained on a small box-labeled subset, converts these point annotations into pseudo-box labels to train a student detector. Yet, medical imagery presents unique challenges, including overlapping anatomy, variable object sizes, and elusive structures, which hinder accurate bounding box inference. To overcome these challenges, we introduce DExTeR (DETR with Experts), a transformer-based Point-to-Box regressor tailored for medical imaging. Built upon Point-DETR, DExTeR encodes single-point annotations as object queries, refining feature extraction with the proposed class-guided deformable attention, which guides attention sampling using point coordinates and class labels to capture class-specific characteristics. To improve discrimination in complex structures, it introduces CLICK-MoE (CLass, Instance, and Common Knowledge Mixture of Experts), decoupling class and instance representations to reduce confusion among adjacent or overlapping instances. Finally, we implement a multi-point training strategy which promotes prediction consistency across different point placements, improving robustness to annotation variability. DExTeR achieves state-of-the-art performance across three datasets spanning different medical domains (endoscopy, chest X-rays, and endoscopic ultrasound) highlighting its potential to reduce annotation costs while maintaining high detection accuracy.

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Where It Moves, It Matters: Referring Surgical Instrument Segmentation via Motion

Enabling intuitive, language-driven interaction with surgical scenes is a critical step toward intelligent operating rooms and autonomous surgical robotic assistance. However, the task of referring segmentation, localizing surgical instruments based on natural language descriptions, remains underexplored in surgical videos, with existing approaches struggling to generalize due to reliance on static visual cues and predefined instrument names. In this work, we introduce SurgRef, a novel motion-guided framework that grounds free-form language expressions in instrument motion, capturing how tools move and interact across time, rather than what they look like. This allows models to understand and segment instruments even under occlusion, ambiguity, or unfamiliar terminology. To train and evaluate SurgRef, we present Ref-IMotion, a diverse, multi-institutional video dataset with dense spatiotemporal masks and rich motion-centric expressions. SurgRef achieves state-of-the-art accuracy and generalization across surgical procedures, setting a new benchmark for robust, language-driven surgical video segmentation.

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Expert Consensus-based Video-Based Assessment Tool for Workflow Analysis in Minimally Invasive Colorectal Surgery: Development and Validation of ColoWorkflow

Minimally invasive colorectal surgery is characterized by procedural variability, a difficult learning curve, and complications that impact quality and outcomes. Video-based assessment (VBA) offers an opportunity to generate data-driven insights to reduce variability, optimize training, and improve surgical performance. However, existing tools for workflow analysis remain difficult to standardize and implement. This study aims to develop and validate a VBA tool for workflow analysis across minimally invasive colorectal procedures. A Delphi process was conducted to achieve consensus on generalizable workflow descriptors. The resulting framework informed the development of a new VBA tool, ColoWorkflow. Independent raters then applied ColoWorkflow to a multicentre video dataset of laparoscopic and robotic colorectal surgery (CRS). Applicability and inter-rater reliability were evaluated. Consensus was achieved for 10 procedure-agnostic phases and 34 procedure-specific steps describing CRS workflows. ColoWorkflow was developed and applied to 54 colorectal operative videos (left and right hemicolectomies, sigmoid and rectosigmoid resections, and total proctocolectomies) from five centres. The tool demonstrated broad applicability, with all but one label utilized. Inter-rater reliability was moderate, with mean Cohen's K of 0.71 for phases and 0.66 for steps. Most discrepancies arose at phase transitions and step boundary definitions. ColoWorkflow is the first consensus-based, validated VBA tool for comprehensive workflow analysis in minimally invasive CRS. It establishes a reproducible framework for video-based performance assessment, enabling benchmarking across institutions and supporting the development of artificial intelligence-driven workflow recognition. Its adoption may standardize training, accelerate competency acquisition, and advance data-informed surgical quality improvement.

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Artificial Intelligence for the Assessment of Peritoneal Carcinosis during Diagnostic Laparoscopy for Advanced Ovarian Cancer

Advanced Ovarian Cancer (AOC) is often diagnosed at an advanced stage with peritoneal carcinosis (PC). Fagotti score (FS) assessment at diagnostic laparoscopy (DL) guides treatment planning by estimating surgical resectability, but its subjective and operator-dependent nature limits reproducibility and widespread use. Videos of patients undergoing DL with concomitant FS assessments at a referral center were retrospectively collected and divided into a development dataset, for data annotation, AI training and evaluation, and an independent test dataset, for internal validation. In the development dataset, FS-relevant frames were manually annotated for anatomical structures and PC. Deep learning models were trained to automatically identify FS-relevant frames, segment structures and PC, and predict video-level FS and indication to surgery (ItS). AI performance was evaluated using Dice score for segmentation, F1-scores for anatomical stations (AS) and ItS prediction, and root mean square error (RMSE) for final FS estimation. In the development dataset, the segmentation model trained on 7,311 frames, achieved Dice scores of 70$\pm$3% for anatomical structures and 56$\pm$3% for PC. Video-level AS classification achieved F1-scores of 74$\pm$3% and 73$\pm$4%, FS prediction showed normalized RMSE values of 1.39$\pm$0.18 and 1.15$\pm$0.08, and ItS reached F1-scores of 80$\pm$8% and 80$\pm$2% in the development (n=101) and independent test datasets (n=50), respectively. This is the first AI model to predict the feasibility of cytoreductive surgery providing automated FS estimation from DL videos. Its reproducible and reliable performance across datasets suggests that AI can support surgeons through standardized intraoperative tumor burden assessment and clinical decision-making in AOC.

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Endoshare: A Publicly Available, Surgeons-Friendly Solution to De-Identify and Manage Surgical Videos

Video-based assessment and surgical data science can advance surgical training, research, and quality improvement, yet adoption remains limited by heterogeneous recording formats and privacy concerns linked to video sharing. This work develops, evaluates, and publicly releases Endoshare, a surgeon-friendly application that merges, standardizes, and de-identifies endoscopic videos. Development followed an iterative, user-centered software life cycle. In the analysis phase, an internal survey of four clinicians and four computer scientists, based on 10 usability heuristics, identified early requirements and guided a cross-platform, privacy-by-design architecture. Prototype testing reported high usability for clinicians (4.68 +/- 0.40 out of 5) and for computer scientists (4.03 +/- 0.51 out of 5), with the lowest score (4.00 +/- 0.93 out of 5) relating to label clarity, prompting interface refinement to streamline case selection, video merging, automated out-of-body removal, and filename pseudonymization. In the testing phase, ten surgeons completed an external survey combining the same heuristics with Technology Acceptance Model constructs, reporting high perceived usefulness (5.07 +/- 1.75 out of 7), ease of use (5.15 +/- 1.71 out of 7), heuristic usability (4.38 +/- 0.48 out of 5), and strong recommendation likelihood (9.20 +/- 0.79 out of 10). A performance assessment across different hardware and configurations showed that processing time increased proportionally with video duration and was consistently lower in fast mode. Endoshare is a publicly available solution to manage surgical videos, with potential to support training, research, and quality improvement. Compliance certification and broader interoperability validation are needed to establish it as a reliable tool for surgical video management. The software is available at https://camma-public.github.io/Endoshare

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UltraSam: A Foundation Model for Ultrasound using Large Open-Access Segmentation Datasets

Purpose: Automated ultrasound image analysis is challenging due to anatomical complexity and limited annotated data. To tackle this, we take a data-centric approach, assembling the largest public ultrasound segmentation dataset and training a versatile visual foundation model tailored for ultrasound. Methods: We compile US-43d, a large-scale collection of 43 open-access ultrasound datasets with over 280,000 images and segmentation masks for more than 50 anatomical structures. We then introduce UltraSam, an adaptation of the Segment Anything Model (SAM) that is trained on US-43d and supports both point- and box-prompts. Finally, we introduce a new use case for SAM-style models by using UltraSam as a model initialization that can be fine-tuned for various downstream analysis tasks, demonstrating UltraSam's foundational capabilities. Results: UltraSam achieves vastly improved performance over existing SAM-style models for prompt-based segmentation on three diverse public datasets. Moreover, an UltraSam-initialized Vision Transformer surpasses ImageNet-, SAM-, and MedSAM-initialized models in various downstream segmentation and classification tasks, highlighting UltraSam's effectiveness as a foundation model. Conclusion: We compile US-43d, a large-scale unified ultrasound dataset, and introduce UltraSam, a powerful multi-purpose SAM-style model for ultrasound images. We release our code and pretrained models at https://github.com/CAMMA-public/UltraSam and invite the community to further this effort by contributing high-quality datasets.

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End-to-End Learning of Multi-Organ Implicit Surfaces from 3D Medical Imaging Data

The fine-grained surface reconstruction of different organs from 3D medical imaging can provide advanced diagnostic support and improved surgical planning. However, the representation of the organs is often limited by the resolution, with a detailed higher resolution requiring more memory and computing footprint. Implicit representations of objects have been proposed to alleviate this problem in general computer vision by providing compact and differentiable functions to represent the 3D object shapes. However, architectural and data-related differences prevent the direct application of these methods to medical images. This work introduces ImplMORe, an end-to-end deep learning method using implicit surface representations for multi-organ reconstruction from 3D medical images. ImplMORe incorporates local features using a 3D CNN encoder and performs multi-scale interpolation to learn the features in the continuous domain using occupancy functions. We apply our method for single and multiple organ reconstructions using the totalsegmentator dataset. By leveraging the continuous nature of occupancy functions, our approach outperforms the discrete explicit representation based surface reconstruction approaches, providing fine-grained surface details of the organ at a resolution higher than the given input image. The source code will be made publicly available at: https://github.com/CAMMA-public/ImplMORe

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Jumpstarting Surgical Computer Vision

Consensus amongst researchers and industry points to a lack of large, representative annotated datasets as the biggest obstacle to progress in the field of surgical data science. Advances in Self-Supervised Learning (SSL) represent a solution, reducing the dependence on large labeled datasets by providing task-agnostic initializations. However, the robustness of current self-supervised learning methods to domain shifts remains unclear, limiting our understanding of its utility for leveraging diverse sources of surgical data. Shifting the focus from methods to data, we demonstrate that the downstream value of SSL-based initializations is intricately intertwined with the composition of pre-training datasets. These results underscore an important gap that needs to be filled as we scale self-supervised approaches toward building general-purpose "foundation models" that enable diverse use-cases within the surgical domain. Through several stages of controlled experimentation, we develop recommendations for pretraining dataset composition evidenced through over 300 experiments spanning 20 pre-training datasets, 9 surgical procedures, 7 centers (hospitals), 3 labeled-data settings, 3 downstream tasks, and multiple runs. Using the approaches here described, we outperform state-of-the-art pre-trainings on two public benchmarks for phase recognition: up to 2.2% on Cholec80 and 5.1% on AutoLaparo.

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CycleSAM: Few-Shot Surgical Scene Segmentation with Cycle- and Scene-Consistent Feature Matching

Surgical image segmentation is highly challenging, primarily due to scarcity of annotated data. Generalist prompted segmentation models like the Segment-Anything Model (SAM) can help tackle this task, but because they require image-specific visual prompts for effective performance, their use is limited to improving data annotation efficiency. Recent approaches extend SAM to automatic segmentation by using a few labeled reference images to predict point prompts; however, they rely on feature matching pipelines that lack robustness to out-of-domain data like surgical images. To tackle this problem, we introduce CycleSAM, an improved visual prompt learning approach that employs a data-efficient training phase and enforces a series of soft constraints to produce high-quality feature similarity maps. CycleSAM label-efficiently addresses domain gap by leveraging surgery-specific self-supervised feature extractors, then adapts the resulting features through a short parameter-efficient training stage, enabling it to produce informative similarity maps. CycleSAM further filters the similarity maps with a series of consistency constraints before robustly sampling diverse point prompts for each object instance. In our experiments on four diverse surgical datasets, we find that CycleSAM outperforms existing few-shot SAM approaches by a factor of 2-4x in both 1-shot and 5-shot settings, while also achieving strong performance gains over traditional linear probing, parameter-efficient adaptation, and pseudo-labeling methods.

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Recognizing Surgical Phases Anywhere: Few-Shot Test-time Adaptation and Task-graph Guided Refinement

The complexity and diversity of surgical workflows, driven by heterogeneous operating room settings, institutional protocols, and anatomical variability, present a significant challenge in developing generalizable models for cross-institutional and cross-procedural surgical understanding. While recent surgical foundation models pretrained on large-scale vision-language data offer promising transferability, their zero-shot performance remains constrained by domain shifts, limiting their utility in unseen surgical environments. To address this, we introduce Surgical Phase Anywhere (SPA), a lightweight framework for versatile surgical workflow understanding that adapts foundation models to institutional settings with minimal annotation. SPA leverages few-shot spatial adaptation to align multi-modal embeddings with institution-specific surgical scenes and phases. It also ensures temporal consistency through diffusion modeling, which encodes task-graph priors derived from institutional procedure protocols. Finally, SPA employs dynamic test-time adaptation, exploiting the mutual agreement between multi-modal phase prediction streams to adapt the model to a given test video in a self-supervised manner, enhancing the reliability under test-time distribution shifts. SPA is a lightweight adaptation framework, allowing hospitals to rapidly customize phase recognition models by defining phases in natural language text, annotating a few images with the phase labels, and providing a task graph defining phase transitions. The experimental results show that the SPA framework achieves state-of-the-art performance in few-shot surgical phase recognition across multiple institutions and procedures, even outperforming full-shot models with 32-shot labeled data. Code is available at https://github.com/CAMMA-public/SPA

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Multi-modal Representations for Fine-grained Multi-label Critical View of Safety Recognition

The Critical View of Safety (CVS) is crucial for safe laparoscopic cholecystectomy, yet assessing CVS criteria remains a complex and challenging task, even for experts. Traditional models for CVS recognition depend on vision-only models learning with costly, labor-intensive spatial annotations. This study investigates how text can be harnessed as a powerful tool for both training and inference in multi-modal surgical foundation models to automate CVS recognition. Unlike many existing multi-modal models, which are primarily adapted for multi-class classification, CVS recognition requires a multi-label framework. Zero-shot evaluation of existing multi-modal surgical models shows a significant performance gap for this task. To address this, we propose CVS-AdaptNet, a multi-label adaptation strategy that enhances fine-grained, binary classification across multiple labels by aligning image embeddings with textual descriptions of each CVS criterion using positive and negative prompts. By adapting PeskaVLP, a state-of-the-art surgical foundation model, on the Endoscapes-CVS201 dataset, CVS-AdaptNet achieves 57.6 mAP, improving over the ResNet50 image-only baseline (51.5 mAP) by 6 points. Our results show that CVS-AdaptNet's multi-label, multi-modal framework, enhanced by textual prompts, boosts CVS recognition over image-only methods. We also propose text-specific inference methods, that helps in analysing the image-text alignment. While further work is needed to match state-of-the-art spatial annotation-based methods, this approach highlights the potential of adapting generalist models to specialized surgical tasks. Code: https://github.com/CAMMA-public/CVS-AdaptNet

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Adaptation of Multi-modal Representation Models for Multi-task Surgical Computer Vision

Surgical AI often involves multiple tasks within a single procedure, like phase recognition or assessing the Critical View of Safety in laparoscopic cholecystectomy. Traditional models, built for one task at a time, lack flexibility, requiring a separate model for each. To address this, we introduce MML-SurgAdapt, a unified multi-task framework with Vision-Language Models (VLMs), specifically CLIP, to handle diverse surgical tasks through natural language supervision. A key challenge in multi-task learning is the presence of partial annotations when integrating different tasks. To overcome this, we employ Single Positive Multi-Label (SPML) learning, which traditionally reduces annotation burden by training models with only one positive label per instance. Our framework extends this approach to integrate data from multiple surgical tasks within a single procedure, enabling effective learning despite incomplete or noisy annotations. We demonstrate the effectiveness of our model on a combined dataset consisting of Cholec80, Endoscapes2023, and CholecT50, utilizing custom prompts. Extensive evaluation shows that MML-SurgAdapt performs comparably to task-specific benchmarks, with the added advantage of handling noisy annotations. It also outperforms the existing SPML frameworks for the task. By reducing the required labels by 23%, our approach proposes a more scalable and efficient labeling process, significantly easing the annotation burden on clinicians. To our knowledge, this is the first application of SPML to integrate data from multiple surgical tasks, presenting a novel and generalizable solution for multi-task learning in surgical computer vision. Implementation is available at: https://github.com/CAMMA-public/MML-SurgAdapt

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