arXiv subjects

Sidaty El Hadramy

Publications and source records attributed to Sidaty El Hadramy.

14 recordsLinked to original sources

arXiv2026

AlignUS: MRI-Guided Ultrasound Representation Learning for ALS Classification from Tongue Images

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease in which early assessment remains challenging, particularly in low-resource settings where MRI is often unavailable. High-resolution ultrasound (HRUS) of the tongue offers a portable and low-cost alternative for evaluating bulbar involvement, but learning reliable diagnostic models is limited by small datasets and the difficulty of extracting robust representations from ultrasound alone. We propose AlignUS, a cross-modal knowledge distillation framework that transfers anatomical knowledge from MRI to a HRUS-based classifier while requiring only HRUS at inference time. The model combines classification loss, supervised contrastive learning, and feature-level distillation to align HRUS representations with MRI embeddings. AlignUS achieves a patient-level balanced accuracy of 0.958, macro-F1 of 0.963, and ROC-AUC of 0.990, aggregated across four patient-level cross-validation folds, with consistent improvements over HRUS baselines and cross-modal alternatives. These results demonstrate that MRI-derived supervision can substantially improve ultrasound-based ALS assessment while preserving low-cost, inference-time independence from MRI.

cs.CV↗

arXiv2026

SA-Profile: Automated Sulcus Angle Profiling from Super-Resolution MRI

Trochlear dysplasia (TD) is an abnormality of the femoral trochlea associated with anterior knee pain and patellar instability. The sulcus angle (SA) is used to assess trochlear morphology, but it is typically measured on a single axial MR slice with no clear guidance on which to select, making it sensitive to slice selection and landmark placement. We propose an automatic framework for continuous SA profiling from super-resolved MR volumes. Clinically acquired axial, coronal, and sagittal MR scans are combined using implicit neural representations to reconstruct a high-resolution volume. SA measurements are computed across the trochlear region using two landmark detection U-Net models. The approach was evaluated on the public fastMRI dataset and a small in-house cohort of patients with TD. Compared with conventional manual single-slice SA measurements, the proposed automated method yielded a mean absolute error of 11.6$^\circ$ while providing continuous characterization of trochlear morphology. Population-level analysis demonstrated distinct mean SA profiles between the public cohort and the in-house TD cohort, highlighting the potential of profile-based assessment to characterize TD. By reducing reliance on a single manually selected axial slice, the proposed framework extends conventional SA assessment to a continuous profile-based description of trochlear morphology without additional imaging, while remaining conceptually linked to current clinical assessment. Further validation is required. The code is available: https://github.com/wehrlimi/SA_Profile.

cs.CV↗

arXiv2026

Generalizing Soft Tissue Deformation and Force Prediction Across Material Stiffness and Geometry

Accurate soft tissue simulation is essential for surgical training, pre-operative planning, and haptic feedback systems. While learning-based surrogate models trained on data using the finite element method (FEM) offer a promising path to real-time inference, their reliability depends on well-calibrated constitutive models. Existing approaches neither provide systematic guidance on model selection across stiffness levels, nor generalize across different tissue stiffnesses or geometries. We perform a comprehensive calibration of hyperelastic constitutive models in the SOFA Framework using gravity-loaded silicone beams with different stiffnesses. Using calibrated simulations as training data, we use a softness conditioned equivariant graph neural network, enabling deformation and force prediction across multiple tissue types and unseen geometries. Our model achieves sub-millimeter mean deformation accuracy at 0.010s inference time, while showing that force prediction quality is directly tied to upstream calibration consistency.

cs.AI↗

arXiv2026

HyperShape: Hyperelasticity Across Diverse Shapes

Hyperelastic deformations are highly sensitive to domain geometry and boundary conditions, making generalization across both a critical capability for neural operators applied to these problems. However, existing benchmarks for neural operators on hyperelasticity rely on simple or few geometries, which makes it difficult to assess this capability rigorously. To address this gap, we introduce HyperShape, an extensible framework designed to generate synthetic shapes and their corresponding hyperelastic simulation data, producing a suite of 2D and 3D datasets with adjustable complexity and controllable shape variations. This design enables systematic assessment of generalization across in-distribution, out-of-distribution, and synthetic-to-real transfer settings. Using this framework, we evaluated the performance of several state-of-the-art neural operators over diverse shape distributions. Our findings reveal that neural operators perform well on simple shapes but struggle as shape complexity, geometric diversity, and boundary condition variability increase, requiring large amounts of training data in such regimes. Performance degrades consistently and predictably with geometric complexity highlighting the need for further model development. As an open and extensible benchmark, HyperShape is designed to grow alongside the field: new geometries, material models, loading conditions, and evaluation settings can be easily incorporated to validate hyperelastic surrogate models.

cs.CE↗

arXiv2026

DefSynUS: Real-time Patient-specific Intrahepatic Vessel Identification via Deformation-Aware CT-US Domain Adaptation

Purpose: Laparoscopic ultrasound (LUS) enhances the safety of liver surgery by visualizing intrahepatic vessels in real-time. Still, vessel identification remains difficult due to probe constraints, complex vascular structure, and tissue deformation. This work aims to enable real-time, patient-specific vessel identification that remains robust under deformation through deformable ultrasound augmentation. Methods: Preoperative CT vessel annotations are used to generate synthetic ultrasound data via optimized physics-based rendering, coupled with domain adaptation to intraoperative ultrasound. The rendering is trained end-to-end for vessel identification and patient-specificity, eliminating the need for preoperative ultrasound. A deformation-aware augmentation simulates realistic intraoperative motion and tissue deformation within the rendering pipeline. Results: In abdominal phantom and limited clinical feasibility experiments (single-case clinical evaluation), the framework achieved real-time intrahepatic vessel-branch identification, maintaining performance under new patient poses. Conclusion: The framework enables real-time vessel identification without preoperative ultrasound and supports technical feasibility, but multi-patient validation is still needed for generalizability and clinical feasibility.

cs.CV↗

arXiv2026

End2Reg: Learning Task-Specific Segmentation for Markerless Registration in Spine Surgery

Intraoperative navigation in spine surgery demands millimeter-level accuracy. Currently, this is achieved through radiation-intensive intraoperative imaging and bone-anchored markers that are invasive and disrupt surgical workflow. Markerless RGB-D registration methods offer a promising alternative. However, existing approaches rely on weak segmentation labels to isolate relevant anatomical structures, potentially propagating errors through the registration process. We present End2Reg, an end-to-end deep learning framework that jointly optimizes segmentation and registration, eliminating the need for segmentation labels and manual steps. The network learns task-specific segmentation masks optimized for registration, guided solely by the registration objective without explicit segmentation supervision. End2Reg achieves state-of-the-art performance on ex- and in-vivo benchmarks, reducing median Target Registration Error by 32% and mean Root Mean Square Error by 61%, while maintaining robust performance under partial occlusions. Ablation results confirm that end-to-end optimization significantly improves registration accuracy. Overall, End2Reg advances towards fully automatic, markerless intraoperative navigation. Code and interactive visualizations are available at: https://lorenzopettinari.github.io/end-2-reg/.

cs.CV↗

arXiv2026

NOIR: Neural Operator mapping for Implicit Representations

This paper presents NOIR, a framework that reframes core medical imaging tasks as operator learning between continuous function spaces, challenging the prevailing paradigm of discrete grid-based deep learning. Instead of operating on fixed pixel or voxel grids, NOIR embeds discrete medical signals into shared Implicit Neural Representations and learns a Neural Operator that maps between their latent modulations, enabling resolution-independent function-to-function transformations. We evaluate NOIR across multiple 2D and 3D downstream tasks, including segmentation, shape completion, image-to-image translation, and image synthesis, on several public datasets such as Shenzhen, OASIS-4, SkullBreak, fastMRI, as well as an in-house clinical dataset. It achieves competitive performance at native resolution while demonstrating strong robustness to unseen discretizations, and empirically satisfies key theoretical properties of neural operators. The project page is available here: https://github.com/Sidaty1/NOIR-io.

cs.CV↗

arXiv2025

Soft Tissue Simulation and Force Estimation from Heterogeneous Structures using Equivariant Graph Neural Networks

Accurately simulating soft tissue deformation is crucial for surgical training, pre-operative planning, and real-time haptic feedback systems. While physics-based models such as the finite element method (FEM) provide high-fidelity results, they are often computationally expensive and require extensive preprocessing. We propose a graph neural network (GNN) architecture that predicts both tissue surface deformation and applied force from sparse point clouds. The model incorporates internal anatomical information through binary tissue profiles beneath each point and leverages E(n)-equivariant message passing to improve robustness. We collected experimental data that comprises a real silicone and bone-like phantom, and complemented it with synthetic simulations generated using FEM. Our model achieves a comparable performance to a baseline GNN on standard test cases and significantly outperforms it in rotated and cross-resolution scenarios, showing a strong generalization to unseen orientations and point densities. It also achieves a significant speed improvement, offering a solution for real-time applications. When fine-tuned on experimental data, the model maintains sub-millimeter deformation accuracy despite limited sample size and measurement noise. The results demonstrate that our approach offers an efficient, data-driven alternative to traditional simulations, capable of generalizing across anatomical configurations and supporting interactive surgical environments.

eess.IV↗

arXiv2025

Optimization-Based Calibration for Intravascular Ultrasound Volume Reconstruction

Intraoperative ultrasound images are inherently challenging to interpret in liver surgery due to the limited field of view and complex anatomical structures. Bridging the gap between preoperative and intraoperative data is crucial for effective surgical guidance. 3D IntraVascular UltraSound (IVUS) offers a potential solution by enabling the reconstruction of the entire organ, which facilitates registration between preoperative computed tomography (CT) scans and intraoperative IVUS images. In this work, we propose an optimization-based calibration method using a 3D-printed phantom for accurate 3D Intravascular Ultrasound volume reconstruction. Our approach ensures precise alignment of tracked IVUS data with preoperative CT images, improving intraoperative navigation. We validated our method using in vivo swine liver images, achieving a calibration error from 0.88 to 1.80 mm and a registration error from 3.40 to 5.71 mm between the 3D IVUS data and the corresponding CT scan. Our method provides a reliable and accurate means of calibration and volume reconstruction. It can be used to register intraoperative ultrasound images with preoperative CT images in the context of liver surgery, and enhance intraoperative guidance.

cs.CV↗

arXiv2025

Edge2Prompt: Modality-Agnostic Model for Out-of-Distribution Liver Segmentation

Liver segmentation is essential for preoperative planning in interventions like tumor resection or transplantation, but implementation in clinical workflows faces challenges due to modality-specific tools and data scarcity. We propose Edge2Prompt, a novel pipeline for modality-agnostic liver segmentation that generalizes to out-of-distribution (OOD) data. Our method integrates classical edge detection with foundation models. Modality-agnostic edge maps are first extracted from input images, then processed by a U-Net to generate logit-based prompts. These prompts condition the Segment Anything Model 2 (SAM-2) to generate 2D liver segmentations, which can then be reconstructed into 3D volumes. Evaluated on the multi-modal CHAOS dataset, Edge2Prompt achieves competitive results compared to classical segmentation methods when trained and tested in-distribution (ID), and outperforms them in data-scarce scenarios due to the SAM-2 module. Furthermore, it achieves a mean Dice Score of 86.4% on OOD tasks, outperforming U-Net baselines by 27.4% and other self-prompting methods by 9.1%, demonstrating its effectiveness. This work bridges classical and foundation models for clinically adaptable, data-efficient segmentation.

eess.IV↗

arXiv2025

Towards MR-Based Trochleoplasty Planning

To treat Trochlear Dysplasia (TD), current approaches rely mainly on low-resolution clinical Magnetic Resonance (MR) scans and surgical intuition. The surgeries are planned based on surgeons experience, have limited adoption of minimally invasive techniques, and lead to inconsistent outcomes. We propose a pipeline that generates super-resolved, patient-specific 3D pseudo-healthy target morphologies from conventional clinical MR scans. First, we compute an isotropic super-resolved MR volume using an Implicit Neural Representation (INR). Next, we segment femur, tibia, patella, and fibula with a multi-label custom-trained network. Finally, we train a Wavelet Diffusion Model (WDM) to generate pseudo-healthy target morphologies of the trochlear region. In contrast to prior work producing pseudo-healthy low-resolution 3D MR images, our approach enables the generation of sub-millimeter resolved 3D shapes compatible for pre- and intraoperative use. These can serve as preoperative blueprints for reshaping the femoral groove while preserving the native patella articulation. Furthermore, and in contrast to other work, we do not require a CT for our pipeline - reducing the amount of radiation. We evaluated our approach on 25 TD patients and could show that our target morphologies significantly improve the sulcus angle (SA) and trochlear groove depth (TGD). The code and interactive visualization are available at https://wehrlimi.github.io/sr-3d-planning/.

cs.CV↗

arXiv2025

cIDIR: Conditioned Implicit Neural Representation for Regularized Deformable Image Registration

Regularization is essential in deformable image registration (DIR) to ensure that the estimated Deformation Vector Field (DVF) remains smooth, physically plausible, and anatomically consistent. However, fine-tuning regularization parameters in learning-based DIR frameworks is computationally expensive, often requiring multiple training iterations. To address this, we propose cIDI, a novel DIR framework based on Implicit Neural Representations (INRs) that conditions the registration process on regularization hyperparameters. Unlike conventional methods that require retraining for each regularization hyperparameter setting, cIDIR is trained over a prior distribution of these hyperparameters, then optimized over the regularization hyperparameters by using the segmentations masks as an observation. Additionally, cIDIR models a continuous and differentiable DVF, enabling seamless integration of advanced regularization techniques via automatic differentiation. Evaluated on the DIR-LAB dataset, $\operatorname{cIDIR}$ achieves high accuracy and robustness across the dataset.

cs.CV↗

arXiv2024

Towards Real-time Intrahepatic Vessel Identification in Intraoperative Ultrasound-Guided Liver Surgery

While laparoscopic liver resection is less prone to complications and maintains patient outcomes compared to traditional open surgery, its complexity hinders widespread adoption due to challenges in representing the liver's internal structure. Laparoscopic intraoperative ultrasound offers efficient, cost-effective and radiation-free guidance. Our objective is to aid physicians in identifying internal liver structures using laparoscopic intraoperative ultrasound. We propose a patient-specific approach using preoperative 3D ultrasound liver volume to train a deep learning model for real-time identification of portal tree and branch structures. Our personalized AI model, validated on ex vivo swine livers, achieved superior precision (0.95) and recall (0.93) compared to surgeons, laying groundwork for precise vessel identification in ultrasound-based liver resection. Its adaptability and potential clinical impact promise to advance surgical interventions and improve patient care.

eess.IV↗

arXiv2022

SOniCS: Develop intuition on biomechanical systems through interactive error controlled simulations

This new approach allows the user to experiment with model choices easily and quickly without requiring in-depth expertise, as constitutive models can be modified by one line of code only. This ease in building new models makes SOniCS ideal to develop surrogate, reduced order models and to train machine learning algorithms for uncertainty quantification or to enable patient-specific simulations. SOniCS is thus not only a tool that facilitates the development of surgical training simulations but also, and perhaps more importantly, paves the way to increase the intuition of users or otherwise non-intuitive behaviors of (bio)mechanical systems. The plugin uses new developments of the FEniCSx project enabling automatic generation with FFCx of finite element tensors such as the local residual vector and Jacobian matrix. We validate our approach with numerical simulations such as manufactured solutions, cantilever beams, and benchmarks provided by FEBio. We reach machine precision accuracy and demonstrate the use of the plugin for a real-time haptic simulation involving a surgical tool controlled by the user in contact with a hyperelastic liver. We include complete examples showing the use of our plugin for simulations involving Saint Venant-Kirchhoff, Neo-Hookean, Mooney-Rivlin, and Holzapfel Ogden anisotropic models as supplementary material.

cs.MS↗