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Sebastien Ourselin

Publications and source records attributed to Sebastien Ourselin.

At least 19 recordsLinked to original sources

Metadata Supervised Imaging Representations for Modelling and Controlling Acquisition Variability

Biomedical imaging data exhibit substantial acquisition variability, where identical biological structures can appear markedly different due to differences in imaging devices, acquisition protocols, sites, and reconstruction settings. Consequently, learned representations often entangle underlying biological information with acquisition-dependent appearance, limiting interpretability, generalisation, and clinical deployment. We show that these sources of variation can be disentangled by jointly modelling medical images and acquisition metadata. Using large-scale clinical brain MRI data as a case study, we learn representations that disentangle anatomical structure from contrast-dependent appearance. The resulting framework enables the organisation of heterogeneous imaging protocols, sequence understanding, the detection of image-metadata inconsistencies and imaging artifacts, while preserving biologically relevant anatomical features across diverse acquisitions. Building on these disentangled representations, it further supports generative and translational capabilities, performing both metadata-conditioned synthesis of realistic 3D brain MRIs and anatomy-preserving harmonisation for cross-modality and cross-site adaptation. Our findings demonstrate that acquisition variability is a structured component of the imaging process that can be modeled, audited, synthesised, and controlled, establishing a foundation for acquisition-aware representation learning in large-scale biomedical imaging.

cs.CV

WeakMCN: Multi-task Collaborative Network for Weakly Supervised Referring Expression Comprehension and Segmentation

Weakly supervised referring expression comprehension(WREC) and segmentation(WRES) aim to learn object grounding based on a given expression using weak supervision signals like image-text pairs. While these tasks have traditionally been modeled separately, we argue that they can benefit from joint learning in a multi-task framework. To this end, we propose WeakMCN, a novel multi-task collaborative network that effectively combines WREC and WRES with a dual-branch architecture. Specifically, the WREC branch is formulated as anchor-based contrastive learning, which also acts as a teacher to supervise the WRES branch. In WeakMCN, we propose two innovative designs to facilitate multi-task collaboration, namely Dynamic Visual Feature Enhancement(DVFE) and Collaborative Consistency Module(CCM). DVFE dynamically combines various pre-trained visual knowledge to meet different task requirements, while CCM promotes cross-task consistency from the perspective of optimization. Extensive experimental results on three popular REC and RES benchmarks, i.e., RefCOCO, RefCOCO+, and RefCOCOg, consistently demonstrate performance gains of WeakMCN over state-of-the-art single-task alternatives, e.g., up to 3.91% and 13.11% on RefCOCO for WREC and WRES tasks, respectively. Furthermore, experiments also validate the strong generalization ability of WeakMCN in both semi-supervised REC and RES settings against existing methods, e.g., +8.94% for semi-REC and +7.71% for semi-RES on 1% RefCOCO. The code is publicly available at https://github.com/MRUIL/WeakMCN.

cs.CV

A cautionary tale on the cost-effectiveness of collaborative AI in real-world medical applications

Federated learning (FL) has gained wide popularity as a collaborative learning paradigm allowing collaborative Artificial Intelligence (AI) in sensitive healthcare applications. Nevertheless, the practical implementation of FL presents technical and organizational challenges, as it generally requires complex communication infrastructures. In this context, consensus-based learning (CBL) may represent a promising alternative for collaborative learning, allowing the combination of local knowledge into a federated decision system, while potentially reducing deployment overhead. Nevertheless, a comprehensive assessment of the viability of consensus-based learning as a cost-effective and sustainable alternative to federated learning has not yet been conducted. In this work we propose an extensive benchmark of the accuracy, cost-effectiveness, and sustainability of a panel of FL and CBL methods in a wide range of collaborative medical data analysis scenarios. The benchmark includes 7 different medical datasets, encompassing 3 machine learning tasks, 8 different data modalities, and multi-centric settings involving 3 to 23 clients. Our results reveal that CBL is a cost-effective and more sustainable alternative to FL. When compared across the panel of medical datasets in the considered benchmark, CBL methods provide equivalent accuracy to the one achieved by FL. Nonetheless, CBL significantly reduces training time and communication cost (resp. 15 fold and 131 fold decrease) (p-value < 0.05). This study opens a novel perspective on the deployment of collaborative AI in real-world applications, whereas the adoption of cost-effective methods is instrumental to achieve sustainability and democratization of AI by alleviating the need for extensive computational resources.

cs.LG

MambaX-Net: Dual-Input Mamba-Enhanced Cross-Attention Network for Longitudinal Prostate MRI Segmentation

Active Surveillance (AS) is a treatment option for managing low and intermediate-risk prostate cancer (PCa), aiming to avoid overtreatment while monitoring disease progression through serial MRI and clinical follow-up. Accurate prostate segmentation is an important preliminary step for automating this process, enabling automated detection and diagnosis of PCa. However, existing deep-learning segmentation models are often trained on single-time-point, expertly annotated datasets, making them unsuitable for longitudinal AS analysis, where multiple time points and a scarcity of expert labels hinder effective fine-tuning. To address these challenges, we propose MambaX-Net, a novel semi-supervised, dual-scan 3D segmentation architecture that computes the segmentation for time point t by leveraging the MRI and the corresponding segmentation mask from the previous time point. We introduce two new components: (i) a Mamba-enhanced Cross-Attention Module, which integrates the Mamba block into cross-attention to efficiently capture temporal evolution and long-range spatial dependencies, and (ii) a Shape Extractor Module that encodes the previous segmentation mask into a latent anatomical representation for refined zone delineation. Moreover, we use a semi-supervised self-training strategy that leverages pseudo-labels generated from a pre-trained nnU-Net, enabling effective learning without expert annotations. MambaX-Net was evaluated on a longitudinal AS dataset, and results showed that it significantly outperforms state-of-the-art U-Net and Transformer-based models, achieving superior prostate zone segmentation even when trained on limited and noisy data.

cs.CV

Progressive Experience Fusion for Multi-Task World Model Control in Endovascular Navigation

Autonomous endovascular navigation could support the delivery of mechanical thrombectomy to underserved areas, but controllers must navigate long, multi-stage paths across varying vascular anatomies. This study investigates Progressive Experience Fusion (PEF) to train a multi-task TD-MPC2 controller. We additionally evaluate a heuristic that changes the Model Predictive Path Integral planning horizon using residual action-sequence dispersion, and fine-tuning in a patient-specific simulation. Across five subtasks in ten known training anatomies with held-out targets, PEF achieved a mean success rate of 74%, compared with 37% for Soft Actor-Critic (p < 0.001) and 65% for base TD-MPC2 (p = 0.053). A PEF controller with adaptive-horizon planning trained on 30 vasculatures achieved a mean success rate of 90% in ten held-out vasculatures. The PEF agent successfully transferred to an unseen in vitro stroke patient vasculature under fluoroscopy, achieving a mean path ratio improvement from 63% to 80% with fine-tuning (p < 0.001), following 40x103 fine-tuning steps (corresponding to approximately 107 min of clinical inter-hospital transfer time). This work represents a proof of concept for multi-vasculature training and patient-specific adaptation, while further validation is required before clinical deployment.

cs.RO

Eversion-based robots can enable safe access,steering and endoscopic imaging within the spinal subarachnoid space

Safe navigation within the spinal subarachnoid space is constrained by its narrow, compliant, and delicate anatomy. Conventional catheters and continuum robots rely on proximal pushing, generating friction and shear along the tissue device interface that limit distal controllability and increase the risk of neural injury. Here, we present a 2 mm diameter eversion-growing robotic platform that enables friction minimised extension and steering within the human spinal subarachnoid space, validated through computational modelling, phantom experiments, and intact human cadaver studies. The robot integrates a miniature endoscope for real time intrathecal visualisation and advances by pressure driven tip eversion, localising motion to the distal tip while minimising translational sliding of the deployed body. Phantom experiments demonstrated reductions of 65.2% in mean interaction force and 48.0% in peak interaction force compared with matched push-based insertion. Physics based modelling showed that eversion based growth redistributed tissue loading, reducing local stress concentrations and interfacial shear relative to conventional insertion. In an intact human cadaver, the system achieved 150 mm of controlled intrathecal extension with concurrent fluoroscopic and endoscopic visualisation, providing access across multiple vertebral levels from a standard lumbar entry point. Postprocedural laminectomy and durotomy revealed no observable macroscopic disruption of the dura mater or surrounding neural structures. These results provide the first mechanically characterised and multimodally validated demonstration of eversion-based robotic navigation in intact human spinal anatomy, establishing a quantitative and procedural foundation for future intrathecal interventions. Further validation in larger anatomical cohorts and under physiological conditions will be required before clinical translation.

cs.RO

Stabilizing Temporal Inference Dynamics for Online Surgical Phase Recognition

Online Surgical Phase Recognition (SPR) models can reach high frame-wise accuracy, yet their predictions often lack temporal stability, fragmenting workflow understanding and reducing the reliability of downstream assistance. We show that this instability is not random noise but arises from two mechanisms: early misclassifications corrupt temporal feature states and propagate forward to form error cascades, and phase transitions follow evidence-accumulation dynamics whereas most online SPR systems rely on memoryless frame-wise decisions, making them sensitive to transient confidence fluctuations. We propose a unified Train-Inference-Evaluation framework that explicitly stabilizes temporal inference dynamics using model-agnostic, plug-and-play components. For training, the Temporal Error-Cascade (TEC) loss suppresses error onset and mitigates forward error propagation by stabilizing temporal feature evolution. For inference, the Evidence-Gated Transition Predictor (EGTP) enforces evidence-driven state transitions, allowing phase changes only when accumulated evidence exceeds a confidence boundary. For evaluation, we introduce the Temporal Fragmentation Index (TFI), a reliability-aware metric that quantifies instability-induced temporal disagreement beyond conventional frame-wise and token-based measures. Experiments on Cholec80 and AutoLaparo across three representative backbones show that the proposed framework substantially improves temporal stability and reduces prediction fragmentation, while maintaining or modestly improving frame-wise performance.

cs.CV

Real-time 3D Ultrasonic Needle Tracking with a Photoacoustic Beacon

Many minimally invasive procedures, such as core needle biopsy of focal liver lesions, nerve blocks, and fetal and vascular interventions, are typically performed under ultrasound guidance, which provides real-time, high-resolution visualisation of tissue anatomy. Accurate and efficient localisation of the needle tip relative to patient anatomy is essential for guiding the needle towards the procedure target, avoiding adverse events and reducing the need for repeat procedures. However, the 3D nature of the procedure and poor image contrast of the needle in heterogeneous tissue or at steep insertion angles often lead to confusion over the true location of the tip within the 2D guidance images, and existing methods to enhance needle visibility largely remain limited to 2D. Here, we present a novel interventional ultrasound system capable of 2D B-mode imaging and 3D needle tracking. The tip location is determined from the time-of-flight of ultrasound generated by a photoacoustic beacon embedded in the needle bevel and received by a sparse receiver array distributed around the imaging system's curvilinear ultrasound probe. The measured tracking accuracy was better than 2 mm for depths up to 140 mm in water, and approximately 2 mm on average in an ex vivo tissue phantom, with referenced positions derived from X-ray computed tomography. In a usability study involving 12 clinicians performing biopsy procedures in a ex vivo tissue phantom, the failure rate was reduced by 35%, from 15.8% to 10.3% after only a few minutes of training. These results demonstrate that the proposed system has strong potential to support a wide range of minimally invasive procedures by enabling clinicians to accurately target small anatomical structures, improving the efficiency and effectiveness of diagnostic sampling and therapeutic delivery or ablation, and reducing the risk of adverse events.

physics.med-ph

Three-dimensional intraoperative light field fluorescence imaging system for PpIX-guided tumour resection

Conventional 2D fluorescence imaging in glioma surgery cannot separate intrinsic fluorophore strength from attenuation with depth, creating depth-intensity ambiguity that can compromise assessment of residual tumour and fluorescence based grading. This study develops and validates a dual mode light field imaging system that could capture 3D structure and depth corrected fluorescence in a single snapshot by adapting a commercial Lytro Illum camera. A custom 3D printed depth standard was used to optimise main lens focal length and to derive a grayscale - distance linearity from Lytro Desktop depth maps. CdSe/ZnS quantum dot targets and fluorescent brain phantoms were imaged to establish fluorescence intensity distance attenuation models and to recover intrinsic fluorescence. In system optimisation, the increasing FU strengthened grayscale depth linearity and achieved millimetre scale vertical resolution ($R^{2}$ > 0.95) for FU $\ge$ 60 mm. Higher concentration quantum dot wells of the fluorescent target showed consistent attenuation. In fluorescence mode, the deviations of distance estimations across six regions of a fluorescent brain phantom were 0.14 to 2.45% with intensity prediction errors from -11.73% to 6.08% based on the fluorescence intensity-distance model, enabling recovery of intrinsic quantum dot concentrations which are mimicking PpIX characteristics in glioma. This research supports light field imaging as a practical approach for depth resolved quantitative fluorescence and improved intraoperative tumour characterisation.

physics.med-ph

CLoPA: Continual Low Parameter Adaptation of Interactive Segmentation for Medical Image Annotation

Interactive segmentation enables clinicians to guide annotation, but existing zero-shot models like nnInteractive fail to consistently reach expert-level performance across diverse medical imaging tasks. Because annotation campaigns produce a growing stream of task-specific labelled data, online adaptation of the segmentation model is a natural complement to zero-shot inference. We propose CLoPA, a continual adaptation strategy that tunes a small fraction of nnInteractive's parameters on the annotation cache, triggered by lightweight episode scheduling. CLoPA requires no new parameters or changes to the inference pipeline, and operates entirely within the existing annotation workflow. Across eight Medical Segmentation Decathlon tasks spanning diverse anatomical targets and imaging characteristics, CLoPA rapidly elevates performance to expert-level, even for tasks where nnInteractive previously failed, with the majority of gains realised after a single training episode. We show that the benefits of tuning different parameter groups depends on task characteristics and data regimes. Also, that for targets with complex geometries (e.g., hepatic vessels), instance normalisation and low-level feature tuning saturates, suggesting a need for deeper feature-representation alignment in the most challenging scenarios.

cs.CV

Deep generative computed perfusion-deficit mapping of ischaemic stroke

Focal deficits in ischaemic stroke result from impaired perfusion downstream of a critical vascular occlusion. While parenchymal lesions are traditionally used to predict clinical deficits, the underlying pattern of disrupted perfusion provides information upstream of the lesion, potentially yielding earlier predictive and localizing signals. Such perfusion maps can be derived from routine CT angiography (CTA) widely deployed in clinical practice. Analysing computed perfusion maps from 1,393 CTA-imaged-patients with acute ischaemic stroke, we use deep generative inference to localise neural substrates of NIHSS sub-scores. We show that our approach replicates known lesion-deficit relations without knowledge of the lesion itself and reveals novel neural dependents. The high achieved anatomical fidelity suggests acute CTA-derived computed perfusion maps may be of substantial clinical-and-scientific value in rich phenotyping of acute stroke. Using only hyperacute imaging, deep generative inference could power highly expressive models of functional anatomical relations in ischaemic stroke within the pre-interventional window.

q-bio.QM

From Pre- to Intra-operative MRI: Predicting Brain Shift in Temporal Lobe Resection for Epilepsy Surgery

Introduction: In neurosurgery, image-guided Neurosurgery Systems (IGNS) highly rely on preoperative brain magnetic resonance images (MRI) to assist surgeons in locating surgical targets and determining surgical paths. However, brain shift invalidates the preoperative MRI after dural opening. Updated intraoperative brain MRI with brain shift compensation is crucial for enhancing the precision of neuronavigation systems and ensuring the optimal outcome of surgical interventions. Methodology: We propose NeuralShift, a U-Net-based model that predicts brain shift entirely from pre-operative MRI for patients undergoing temporal lobe resection. We evaluated our results using Target Registration Errors (TREs) computed on anatomical landmarks located on the resection side and along the midline, and DICE scores comparing predicted intraoperative masks with masks derived from intraoperative MRI. Results: Our experimental results show that our model can predict the global deformation of the brain (DICE of 0.97) with accurate local displacements (achieve landmark TRE as low as 1.12 mm), compensating for large brain shifts during temporal lobe removal neurosurgery. Conclusion: Our proposed model is capable of predicting the global deformation of the brain during temporal lobe resection using only preoperative images, providing potential opportunities to the surgical team to increase safety and efficiency of neurosurgery and better outcomes to patients. Our contributions will be publicly available after acceptance in https://github.com/SurgicalDataScienceKCL/NeuralShift.

cs.CV

UltraFlwr -- An Efficient Federated Surgical Object Detection Framework

Surgical object detection in laparoscopic videos enables real-time instrument identification for workflow analysis and skills assessment, but training robust models such as You Only Look Once (YOLO) is challenged by limited data, privacy constraints, and inter-institutional variability. Federated learning (FL) enables collaborative training without sharing raw data, yet practical support for modern YOLO pipelines under heterogeneous surgical data remains limited. We present UltraFlwr, an open-source, communication-efficient, and edge-deployable framework that integrates Ultralytics YOLO with the Flower FL platform and supports native Partial Aggregation (PA) of YOLO components (backbone, neck, head). Using two public laparoscopic surgical tool detection datasets, we conduct a systematic empirical study of federated YOLO training under Independent and Identically Distributed (IID) and multiple clinically motivated heterogeneous scenarios, including differences in data curation, video length, and label availability. Results show that standard FL aggregators (e.g., FedAvg) do not consistently match centralized training per client, but reduce inter-client performance variability. Aggregating both backbone and neck components achieves performance comparable to full aggregation with lower communication costs. Also, improving within-client data consistency can benefit FL even when it increases distribution shift across clients. These findings provide practical guidance for deploying federated YOLO-based object detection in heterogeneous surgical environments. UltraFlwr is publicly available at https://github.com/KCL-BMEIS/UltraFlwr.

cs.CV

Enabling High-Curvature Navigation in Eversion Robots through Buckle-Inducing Constrictive Bands

Tip-growing eversion robots are renowned for their ability to access remote spaces through narrow passages. However, achieving reliable navigation remains a significant challenge. Existing solutions often rely on artificial muscles integrated into the robot body or active tip-steering mechanisms. While effective, these additions introduce structural complexity and compromise the defining advantages of eversion robots: their inherent softness and compliance. In this paper, we propose a passive approach to reduce bending stiffness by purposefully introducing buckling points along the robot's outer wall. We achieve this by integrating inextensible diameter-reducing circumferential bands at regular intervals along the robot body facilitating forward motion through tortuous, obstacle cluttered paths. Rather than relying on active steering, our approach leverages the robot's natural interaction with the environment, allowing for smooth, compliant navigation. We present a Cosserat rod-based mathematical model to quantify this behavior, capturing the local stiffness reductions caused by the constricting bands and their impact on global bending mechanics. Experimental results demonstrate that these bands reduce the robot's stiffness when bent at the tip by up to 91 percent, enabling consistent traversal of 180 degree bends with a bending radius of as low as 25 mm-notably lower than the 35 mm achievable by standard eversion robots under identical conditions. The feasibility of the proposed method is further demonstrated through a case study in a colon phantom. By significantly improving maneuverability without sacrificing softness or increasing mechanical complexity, this approach expands the applicability of eversion robots in highly curved pathways, whether in relation to pipe inspection or medical procedures such as colonoscopy.

cs.RO

Volumetric ultrasound imaging with a sparse matrix array and integrated fiber-optic sensing for robust needle tracking in interventional procedures

Accurate visualization of interventional devices, such as medical needles, is essential for the safe and effective guidance of minimally invasive procedures. Ultrasound (US) imaging is widely used for needle guidance, but the two-dimensional nature of most clinical probes limits accurate three-dimensional (3D) localization, particularly of the needle tip. We present a novel system that integrates volumetric US imaging with 3D needle tracking by combining a fiber-optic hydrophone embedded in the needle and a sparse spiral US array. Real-time volumetric imaging was achieved using plane-wave techniques, while precise needle tip tracking was enabled through communication between the probe and hydrophone. The feasibility of the approach was demonstrated using a nerve block training phantom. This proof-of-concept system enables simultaneous volumetric anatomical imaging and 3D needle tip tracking, with strong potential to enhance the efficacy and safety of image-guided interventional procedures.

physics.med-ph

DIST-CLIP: Arbitrary Metadata and Image Guided MRI Harmonization via Disentangled Anatomy-Contrast Representations

Deep learning holds immense promise for transforming medical image analysis, yet its clinical generalization remains profoundly limited. A major barrier is data heterogeneity. This is particularly true in Magnetic Resonance Imaging, where scanner hardware differences, diverse acquisition protocols, and varying sequence parameters introduce substantial domain shifts that obscure underlying biological signals. Data harmonization methods aim to reduce these instrumental and acquisition variability, but existing approaches remain insufficient. When applied to imaging data, image-based harmonization approaches are often restricted by the need for target images, while existing text-guided methods rely on simplistic labels that fail to capture complex acquisition details or are typically restricted to datasets with limited variability, failing to capture the heterogeneity of real-world clinical environments. To address these limitations, we propose DIST-CLIP (Disentangled Style Transfer with CLIP Guidance), a unified framework for MRI harmonization that flexibly uses either target images or DICOM metadata for guidance. Our framework explicitly disentangles anatomical content from image contrast, with the contrast representations being extracted using pre-trained CLIP encoders. These contrast embeddings are then integrated into the anatomical content via a novel Adaptive Style Transfer module. We trained and evaluated DIST-CLIP on diverse real-world clinical datasets, and showed significant improvements in performance when compared against state-of-the-art methods in both style translation fidelity and anatomical preservation, offering a flexible solution for style transfer and standardizing MRI data. Our code and weights will be made publicly available upon publication.

cs.CV

Advancing Embodied Intelligence in Robotic-Assisted Endovascular Procedures: A Systematic Review of AI Solutions

Endovascular procedures have revolutionized vascular disease treatment, yet their manual execution is challenged by the demands for high precision, operator fatigue, and radiation exposure. Robotic systems have emerged as transformative solutions to mitigate these inherent limitations. A pivotal moment has arrived, where a confluence of pressing clinical needs and breakthroughs in AI creates an opportunity for a paradigm shift toward Embodied Intelligence (EI), enabling robots to navigate complex vascular networks and adapt to dynamic physiological conditions. Data-driven approaches, leveraging advanced computer vision, medical image analysis, and machine learning, drive this evolution by enabling real-time vessel segmentation, device tracking, and anatomical landmark detection. Reinforcement learning and imitation learning further enhance navigation strategies and replicate expert techniques. This review systematically analyzes the integration of EI into endovascular robotics, identifying profound systemic challenges such as the heterogeneity in validation standards and the gap between human mimicry and machine-native capabilities. Based on this analysis, a conceptual roadmap is proposed that reframes the ultimate objective away from systems that supplant clinical decision-making. This vision of augmented intelligence, where the clinician's role evolves into that of a high-level supervisor, provides a principled foundation for the future of the field.

cs.RO

LIHE: Linguistic Instance-Split Hyperbolic-Euclidean Framework for Generalized Weakly-Supervised Referring Expression Comprehension

Existing Weakly-Supervised Referring Expression Comprehension (WREC) methods, while effective, are fundamentally limited by a one-to-one mapping assumption, hindering their ability to handle expressions corresponding to zero or multiple targets in realistic scenarios. To bridge this gap, we introduce the Weakly-Supervised Generalized Referring Expression Comprehension task (WGREC), a more practical paradigm that handles expressions with variable numbers of referents. However, extending WREC to WGREC presents two fundamental challenges: supervisory signal ambiguity, where weak image-level supervision is insufficient for training a model to infer the correct number and identity of referents, and semantic representation collapse, where standard Euclidean similarity forces hierarchically-related concepts into non-discriminative clusters, blurring categorical boundaries. To tackle these challenges, we propose a novel WGREC framework named Linguistic Instance-Split Hyperbolic-Euclidean (LIHE), which operates in two stages. The first stage, Referential Decoupling, predicts the number of target objects and decomposes the complex expression into simpler sub-expressions. The second stage, Referent Grounding, then localizes these sub-expressions using HEMix, our innovative hybrid similarity module that synergistically combines the precise alignment capabilities of Euclidean proximity with the hierarchical modeling strengths of hyperbolic geometry. This hybrid approach effectively prevents semantic collapse while preserving fine-grained distinctions between related concepts. Extensive experiments demonstrate LIHE establishes the first effective weakly supervised WGREC baseline on gRefCOCO and Ref-ZOM, while HEMix achieves consistent improvements on standard REC benchmarks, improving IoU@0.5 by up to 2.5\%. The code is available at https://anonymous.4open.science/r/LIHE.

cs.CV