arXiv subjects

Ayberk Acar

Publications and source records attributed to Ayberk Acar.

12 recordsLinked to original sources

arXiv2026

Differentiable Mesh State Estimation via Factor Graph Inference for Deformable Object Reconstruction

Estimating deformable object states remains a fundamental challenge in robotics and simulation. We propose a novel factor graph-based framework for probabilistic mesh state estimation of deformable objects. The method directly updates a tetrahedral mesh, a rich and physically-grounded representation of an environment, by combining physics priors, noisy sensor measurements, and temporal smoothness constraints within a unified probabilistic formulation. The estimation problem is posed as a nonlinear least-squares optimization and solved using Levenberg-Marquardt. Ex vivo central-airway obstruction experiments and simulations on deforming cube models demonstrate reliable and accurate reconstruction under both rigid motion and deformation, highlighting the potential of this probabilistic approach for principled, measurement-driven mesh state estimation in deformable object reconstruction.

cs.RO↗

arXiv2026

Contour-Constrained Deformable Registration with Parameter Characterization for Head and Neck Surgical Guidance

With 890,000 annual new cases globally, head and neck squamous cell carcinoma has one of the highest recurrence rates among solid malignancies. Although frozen section analysis is the standard of care for intraoperative margin assessment, accurately relocating detected positive margins on the resection bed remains challenging due to imprecise alignment between resected specimens and their resection bed, compounded by post-resection mucosal tissue shrinkage. We present a biomechanics-driven deformable registration framework that corrects post-resection tissue deformation to provide intraoperative guidance. Our approach registers 3D specimen meshes to intraoperative resection bed point clouds using a deformable registration approach based on regularized Kelvinlet basis functions. The registration matches surface point clouds, fiducial landmarks, and boundary contour constraints that directly penalize perpendicular distance-to-agreement between specimen and resection bed boundaries. Across nine specimens from skin, buccal mucosa, and tongue sites, the overall mean target registration error was $11.11 \pm 4.07$ mm using rigid registration, which decreased to $8.20 \pm 2.68$ mm (26.19\% reduction) using deformable registration without contour constraint. The proposed contour-constrained deformable registration further reduced the error to $5.62 \pm 2.28$ mm, a 49.41\% reduction relative to rigid registration. We observed the largest reduction in the most clinically challenging tongue specimens. We also performed a systematic two-stage parameter search to characterize the relative importance of surface alignment, fiducial correspondences, contour constraint, and strain energy regularization. This search revealed that contour weighting dominates registration accuracy for tissue types with large lateral deformation, while the algorithm operates over a broad range of parameter combinations.

eess.IV↗

arXiv2026

Open-H-Embodiment: A Large-Scale Dataset for Enabling Foundation Models in Medical Robotics

Autonomous medical robots hold promise to improve patient outcomes, reduce provider workload, democratize access to care, and enable superhuman precision. However, autonomous medical robotics has been limited by a fundamental data problem: existing medical robotic datasets are small, single-embodiment, and rarely shared openly, restricting the development of foundation models that the field needs to advance. We introduce Open-H-Embodiment, the largest open dataset of medical robotic video with synchronized kinematics to date, spanning more than 50 institutions and multiple robotic platforms including the CMR Versius, Intuitive Surgical's da Vinci, da Vinci Research Kit (dVRK), Rob Surgical BiTrack, Virtual Incision's MIRA, Moon Surgical Maestro, and a variety of custom systems, spanning surgical manipulation, robotic ultrasound, and endoscopy procedures. We demonstrate the research enabled by this dataset through two foundation models. GR00T-H is the first open foundation vision-language-action model for medical robotics, which is the only evaluated model to achieve full end-to-end task completion on a structured suturing benchmark (25% of trials vs. 0% for all others) and achieves 64% average success across a 29-step ex vivo suturing sequence. We also train Cosmos-H-Surgical-Simulator, the first action-conditioned world model to enable multi-embodiment surgical simulation from a single checkpoint, spanning nine robotic platforms and supporting in silico policy evaluation and synthetic data generation for the medical domain. These results suggest that open, large-scale medical robot data collection can serve as critical infrastructure for the research community, enabling advances in robot learning, world modeling, and beyond.

cs.RO↗

arXiv2026

Intuitive Surgical SurgToolLoc and SurgVU Challenges Results: 2022-2025

Robotic assisted (RA) surgery promises to transform surgical intervention. Intuitive Surgical is committed to fostering these changes and the machine learning models and algorithms that will enable them. With these goals in mind we have invited the surgical data science community to participate in a yearly competition hosted through the Medical Imaging Computing and Computer Assisted Interventions (MICCAI) conference. With varying changes from year to year, we have challenged the community to solve difficult machine learning problems in the context of advanced RA applications. Here we document the results of these challenges, focusing on surgical tool localization (SurgToolLoc) and surgical visual understanding (SurgVU). The publicly released dataset that accompanies these challenges is detailed in a separate paper arXiv:2501.09209 [1].

cs.CV↗

arXiv2026

PERSEUS: Perception with Semantic Endoscopic Understanding and SLAM

Purpose: Natural orifice surgeries minimize the need for incisions and reduce the recovery time compared to open surgery; however, they require a higher level of expertise due to visualization and orientation challenges. We propose a perception pipeline for these surgeries that allows semantic scene understanding. Methods: We bring learning-based segmentation, depth estimation, and 3D reconstruction modules together to create real-time segmented maps of the surgical scenes. Additionally, we use registration with robot poses to solve the scale ambiguity of mapping from monocular images, and allow the use of semantically informed real-time reconstructions in robotic surgeries. Results: We achieve sub-milimeter reconstruction accuracy based on average one-sided Chamfer distances, average pose registration RMSE of 0.9 mm, and an estimated scale within 2% of ground truth. Conclusion: We present a modular perception pipeline, integrating semantic segmentation with real-time monocular SLAM for natural orifice surgeries. This pipeline offers a promising solution for scene understanding that can facilitate automation or surgeon guidance.

cs.RO↗

arXiv2025

A Supervised Autonomous Resection and Retraction Framework for Transurethral Enucleation of the Prostatic Median Lobe

Concentric tube robots (CTRs) offer dexterous motion at millimeter scales, enabling minimally invasive procedures through natural orifices. This work presents a coordinated model-based resection planner and learning-based retraction network that work together to enable semi-autonomous tissue resection using a dual-arm transurethral concentric tube robot (the Virtuoso). The resection planner operates directly on segmented CT volumes of prostate phantoms, automatically generating tool trajectories for a three-phase median lobe resection workflow: left/median trough resection, right/median trough resection, and median blunt dissection. The retraction network, PushCVAE, trained on surgeon demonstrations, generates retractions according to the procedural phase. The procedure is executed under Level-3 (supervised) autonomy on a prostate phantom composed of hydrogel materials that replicate the mechanical and cutting properties of tissue. As a feasibility study, we demonstrate that our combined autonomous system achieves a 97.1% resection of the targeted volume of the median lobe. Our study establishes a foundation for image-guided autonomy in transurethral robotic surgery and represents a first step toward fully automated minimally-invasive prostate enucleation.

cs.RO↗

arXiv2025

Monocular absolute depth estimation from endoscopy via domain-invariant feature learning and latent consistency

Monocular depth estimation (MDE) is a critical task to guide autonomous medical robots. However, obtaining absolute (metric) depth from an endoscopy camera in surgical scenes is difficult, which limits supervised learning of depth on real endoscopic images. Current image-level unsupervised domain adaptation methods translate synthetic images with known depth maps into the style of real endoscopic frames and train depth networks using these translated images with their corresponding depth maps. However a domain gap often remains between real and translated synthetic images. In this paper, we present a latent feature alignment method to improve absolute depth estimation by reducing this domain gap in the context of endoscopic videos of the central airway. Our methods are agnostic to the image translation process and focus on the depth estimation itself. Specifically, the depth network takes translated synthetic and real endoscopic frames as input and learns latent domain-invariant features via adversarial learning and directional feature consistency. The evaluation is conducted on endoscopic videos of central airway phantoms with manually aligned absolute depth maps. Compared to state-of-the-art MDE methods, our approach achieves superior performance on both absolute and relative depth metrics, and consistently improves results across various backbones and pretrained weights. Our code is available at https://github.com/MedICL-VU/MDE.

cs.CV↗

arXiv2025

NAVIUS: Navigated Augmented Reality Visualization for Ureteroscopic Surgery

Ureteroscopy is the standard of care for diagnosing and treating kidney stones and tumors. However, current ureteroscopes have a limited field of view, requiring significant experience to adequately navigate the renal collecting system. This is evidenced by the fact that inexperienced surgeons have higher rates of missed stones. One-third of patients with residual stones require re-operation within 20 months. In order to aid surgeons to fully explore the kidney, this study presents the Navigated Augmented Reality Visualization for Ureteroscopic Surgery (NAVIUS) system. NAVIUS assists surgeons by providing 3D maps of the target anatomy, real-time scope positions, and preoperative imaging overlays. To enable real-time navigation and visualization, we integrate an electromagnetic tracker-based navigation pipeline with augmented reality visualizations. NAVIUS connects to 3D Slicer and Unity with OpenIGTLink, and uses HoloLens 2 as a holographic interface. We evaluate NAVIUS through a user study where surgeons conducted ureteroscopy on kidney phantoms with and without visual guidance. With our proposed system, we observed that surgeons explored more areas within the collecting system with NAVIUS (average 23.73% increase), and NASA-TLX metrics were improved (up to 27.27%). NAVIUS acts as a step towards better surgical outcomes and surgeons' experience. The codebase for the system will be available at: https://github.com/vu-maple-lab/NAVIUS.

cs.HC↗

arXiv2025

From Monocular Vision to Autonomous Action: Guiding Tumor Resection via 3D Reconstruction

Surgical automation requires precise guidance and understanding of the scene. Current methods in the literature rely on bulky depth cameras to create maps of the anatomy, however this does not translate well to space-limited clinical applications. Monocular cameras are small and allow minimally invasive surgeries in tight spaces but additional processing is required to generate 3D scene understanding. We propose a 3D mapping pipeline that uses only RGB images to create segmented point clouds of the target anatomy. To ensure the most precise reconstruction, we compare different structure from motion algorithms' performance on mapping the central airway obstructions, and test the pipeline on a downstream task of tumor resection. In several metrics, including post-procedure tissue model evaluation, our pipeline performs comparably to RGB-D cameras and, in some cases, even surpasses their performance. These promising results demonstrate that automation guidance can be achieved in minimally invasive procedures with monocular cameras. This study is a step toward the complete autonomy of surgical robots.

cs.CV↗

arXiv2025

An Effectiveness Study Across Baseline and Learning-based Force Estimation Methods on the da Vinci Research Kit Si System

Robot-assisted minimally invasive surgery, such as through the da Vinci systems, improves precision and patient outcomes. However, da Vinci systems prior to da Vinci 5, lacked direct force-sensing capabilities, forcing surgeons to operate without the haptic feedback they get through laparoscopy. Our prior work restored force sensing through machine learning-based force estimation for the da Vinci Research Kit (dVRK) Classic. This study extends our previous method to the newer dVRK system, the dVRK-Si. Additionally, we benchmark the performance of the learning-based algorithm against baseline methods (which make simplifying assumptions on the torque) to study how the two systems differ. Results show the learning-based method achieves an average root-mean-square-error (RMSE) of 5.21\%, for the dVRK-Si, which is comparable to the dVRK Classic. In both systems, the learning-based method outperforms baselines, but the difference is much larger in the dVRK-Si. Nonetheless, dVRK-Si force estimation accuracy lags behind the dVRK Classic, with RMSE 2 to 3 times higher. Further analysis reveals poor PID control in the dVRK-Si. We hypothesize that this is due to the lack of gravity compensation, as unlike the dVRK Classic, the dVRK-Si is not mechanically balanced. This study advances the understanding of learning-based force estimation and is the first work to characterize the dynamics of the new dVRK-Si system.

cs.RO↗

arXiv2024

MeshBrush: Painting the Anatomical Mesh with Neural Stylization for Endoscopy

Style transfer is a promising approach to close the sim-to-real gap in medical endoscopy. Rendering synthetic endoscopic videos by traversing pre-operative scans (such as MRI or CT) can generate structurally accurate simulations as well as ground truth camera poses and depth maps. Although image-to-image (I2I) translation models such as CycleGAN can imitate realistic endoscopic images from these simulations, they are unsuitable for video-to-video synthesis due to the lack of temporal consistency, resulting in artifacts between frames. We propose MeshBrush, a neural mesh stylization method to synthesize temporally consistent videos with differentiable rendering. MeshBrush uses the underlying geometry of patient imaging data while leveraging existing I2I methods. With learned per-vertex textures, the stylized mesh guarantees consistency while producing high-fidelity outputs. We demonstrate that mesh stylization is a promising approach for creating realistic simulations for downstream tasks such as training networks and preoperative planning. Although our method is tested and designed for ureteroscopy, its components are transferable to general endoscopic and laparoscopic procedures. The code will be made public on GitHub.

eess.IV↗

arXiv2024

Depth Anything in Medical Images: A Comparative Study

Monocular depth estimation (MDE) is a critical component of many medical tracking and mapping algorithms, particularly from endoscopic or laparoscopic video. However, because ground truth depth maps cannot be acquired from real patient data, supervised learning is not a viable approach to predict depth maps for medical scenes. Although self-supervised learning for MDE has recently gained attention, the outputs are difficult to evaluate reliably and each MDE's generalizability to other patients and anatomies is limited. This work evaluates the zero-shot performance of the newly released Depth Anything Model on medical endoscopic and laparoscopic scenes. We compare the accuracy and inference speeds of Depth Anything with other MDE models trained on general scenes as well as in-domain models trained on endoscopic data. Our findings show that although the zero-shot capability of Depth Anything is quite impressive, it is not necessarily better than other models in both speed and performance. We hope that this study can spark further research in employing foundation models for MDE in medical scenes.

cs.CV↗