arXiv subjects

Ipek Oguz

Publications and source records attributed to Ipek Oguz.

At least 19 recordsLinked to original sources

arXiv2026

LISynSeg: Data-Centric Label-to-Image Synthesis for Cross-Modality Whole-Heart Segmentation

Whole-heart segmentation (WHS) in computed tomography (CT) and magnetic resonance imaging (MRI) is affected by acquisition shifts and heterogeneous cardiac annotations. Existing WHS systems combine architectural design, transfer learning, and generic spatial or intensity augmentation. We investigate whether changes to data augmentation and training supervision can improve cross-modality WHS while the segmentation architecture is held constant. We present LISynSeg, a data-centric approach that augments real-image nnU-Net training with label-to-image synthesis. Synthetic volumes are generated from cardiac label maps using contrast and acquisition perturbations calibrated to the training cohort, then mixed with real images to retain thoracic context absent from the labels (and thus the synthesized images). We model cardiac label variation through controlled changes in myocardial wall thickness and partial supervision of uncertain vessel endpoints. On the CARE Whole-Heart benchmark, synthetic-only training performs worse than the real-image nnU-Net baseline, whereas calibrated real-synthetic training improves cross-modality segmentation without changing the architecture; the improvement is larger for MRI than for CT. The results show that modifying the training data strategy can benefit model development for heterogeneous cardiac data. Code and trained weights will be released at https://github.com/MedICL-VU/Care26_LISynSeg.

cs.CV↗

arXiv2026

crossMoDA Challenge: Evolution of Cross-Modality Domain Adaptation Techniques for Vestibular Schwannoma and Cochlea Segmentation from 2021 to 2023

The cross-Modality Domain Adaptation (crossMoDA) challenge series, initiated in 2021 in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), focuses on unsupervised cross-modality segmentation, learning from contrast-enhanced T1 (ceT1) and transferring to T2 MRI. The task is an extreme example of domain shift chosen to serve as a meaningful and illustrative benchmark. From a clinical application perspective, it aims to automate Vestibular Schwannoma (VS) and cochlea segmentation on T2 scans for more cost-effective VS management. Over time, the challenge objectives have evolved to enhance its clinical relevance. The challenge evolved from using single-institutional data and basic segmentation in 2021 to incorporating multi-institutional data and Koos grading in 2022, and by 2023, it included heterogeneous routine data and sub-segmentation of intra- and extra-meatal tumour components. In this work, we report the findings of the 2022 and 2023 editions and perform a retrospective analysis of the challenge progression over the years. The observations from the successive challenge contributions indicate that the number of outliers decreases with an expanding dataset. This is notable since the diversity of scanning protocols of the datasets concurrently increased. The winning approach of the 2023 edition reduced the number of outliers on the 2021 and 2022 testing data, demonstrating how increased data heterogeneity can enhance segmentation performance even on homogeneous data. However, the cochlea Dice score declined in 2023, likely due to the added complexity from tumour sub-annotations affecting overall segmentation performance. While progress is still needed for clinically acceptable VS segmentation, the plateauing performance suggests that a more challenging cross-modal task may better serve future benchmarking.

eess.IV↗

arXiv2026

IntraStyler: Intra-Domain Style Synthesis for Cross-Modality MRI Domain Adaptation

Segmentation of vestibular schwannoma and cochlea from T2 MRI is clinically important yet annotation-intensive. Domain adaptation (DA) has been widely adopted to bridge the gap between labeled contrast-enhanced T1 and unlabeled T2 datasets. While existing methods focus on cross-domain alignment, intra-domain variability within the target domain remains largely overlooked. Images from the same domain may vary substantially due to different scanners, field strengths, and acquisition protocols. Ignoring this variability produces homogeneous synthetic images that limit the generalizability of downstream segmentation models. To address this, we propose IntraStyler, a 3D unpaired image translation method that automatically discovers fine-grained intra-domain styles without any predefined sub-domains, and synthesizes diverse target domain images using per-image style references. To this end, we design a 3D style encoder trained with a novel contrastive learning objective to extract style-only embeddings disentangled from anatomy. IntraStyler is built upon the 1st place CrossMoDA challenge solution and further advances it, generating more diverse synthetic data and achieving more reliable downstream segmentation. Code is available at https://github.com/MedICL-VU/IntraStyler.

cs.CV↗

arXiv2026

Towards Verified and Targeted Explanations through Formal Methods

As deep neural networks are deployed in safety-critical domains such as autonomous driving and medical diagnosis, stakeholders need explanations that are interpretable but also trustworthy with formal guarantees. Existing XAI methods fall short: heuristic attribution techniques (e.g., LIME, Integrated Gradients) highlight influential features but offer no mathematical guarantees about decision boundaries, while formal methods verify robustness yet remain untargeted, analyzing the nearest boundary regardless of whether it represents a critical risk. In safety-critical systems, not all misclassifications carry equal consequences; confusing a "Stop" sign for a "60 kph" sign is far more dangerous than confusing it with a "No Passing" sign. We introduce ViTaX (Verified and Targeted Explanations), a formal XAI framework that generates targeted semifactual explanations with mathematical guarantees. For a given input (class y) and a user-specified critical alternative (class t), ViTaX: (1) identifies the minimal feature subset most sensitive to the y->t transition, and (2) applies formal reachability analysis to guarantee that perturbing these features by epsilon cannot flip the classification to t. We formalize this through Targeted epsilon-Robustness, certifying whether a feature subset remains robust under perturbation toward a specific target class. ViTaX is the first method to provide formally guaranteed explanations of a model's resilience against user-identified alternatives. Evaluations on MNIST, GTSRB, EMNIST, and TaxiNet demonstrate over 30% fidelity improvement with minimal explanation cardinality.

cs.LG↗

arXiv2026

ProbeMDE: Uncertainty-Guided Active Proprioception for Monocular Depth Estimation in Surgical Robotics

Monocular depth estimation (MDE) provides a useful tool for robotic perception, but its predictions are often uncertain and inaccurate in challenging environments such as surgical scenes where textureless surfaces, specular reflections, and occlusions are common. To address this, we propose ProbeMDE, a cost-aware active sensing framework that combines RGB images with sparse proprioceptive measurements for MDE. Our approach utilizes an ensemble of MDE models to predict dense depth maps conditioned on both RGB images and on a sparse set of known depth measurements obtained via proprioception, where the robot has touched the environment in a known configuration. We quantify predictive uncertainty via the ensemble's variance and measure the gradient of the uncertainty with respect to candidate measurement locations. To prevent mode collapse while selecting maximally informative locations to propriocept (touch), we leverage Stein Variational Gradient Descent (SVGD) over this gradient map. We validate our method in both simulated and physical experiments on central airway obstruction surgical phantoms. Our results demonstrate that our approach outperforms baseline methods across standard depth estimation metrics, achieving higher accuracy while minimizing the number of required proprioceptive measurements. Project page: https://brittonjordan.github.io/probe_mde/

cs.RO↗

arXiv2026

VAMOS-OCTA: Vessel-Aware Multi-Axis Orthogonal Supervision for Inpainting Motion-Corrupted OCT Angiography Volumes

Handheld Optical Coherence Tomography Angiography (OCTA) enables noninvasive retinal imaging in uncooperative or pediatric subjects, but is highly susceptible to motion artifacts that severely degrade volumetric image quality. Sudden motion during 3D acquisition can lead to unsampled retinal regions across entire B-scans (cross-sectional slices), resulting in blank bands in en face projections. We propose VAMOS-OCTA, a deep learning framework for inpainting motion-corrupted B-scans using vessel-aware multi-axis supervision. We employ a 2.5D U-Net architecture that takes a stack of neighboring B-scans as input to reconstruct a corrupted center B-scan, guided by a novel Vessel-Aware Multi-Axis Orthogonal Supervision (VAMOS) loss. This loss combines vessel-weighted intensity reconstruction with axial and lateral projection consistency, encouraging vascular continuity in native B-scans and across orthogonal planes. Unlike prior work that focuses primarily on restoring the en face MIP, VAMOS-OCTA jointly enhances both cross-sectional B-scan sharpness and volumetric projection accuracy, even under severe motion corruptions. We trained our model on both synthetic and real-world corrupted volumes and evaluated its performance using both perceptual quality and pixel-wise accuracy metrics. VAMOS-OCTA consistently outperforms prior methods, producing reconstructions with sharp capillaries, restored vessel continuity, and clean en face projections. These results demonstrate that multi-axis supervision offers a powerful constraint for restoring motion-degraded 3D OCTA data. Our source code is available at https://github.com/MedICL-VU/VAMOS-OCTA.

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

EndoStreamDepth: Temporally Consistent Monocular Depth Estimation for Endoscopic Video Streams

This work presents EndoStreamDepth, a monocular depth estimation framework for endoscopic video streams. It provides accurate depth maps with sharp anatomical boundaries for each frame, temporally consistent predictions across frames, and real-time throughput. Unlike prior work that uses batched inputs, EndoStreamDepth processes individual frames with a temporal module to propagate inter-frame information. The framework contains three main components: (1) a single-frame depth network with endoscopy-specific transformation to produce accurate depth maps, (2) multi-level Mamba temporal modules that leverage inter-frame information to improve accuracy and stabilize predictions, and (3) a hierarchical design with comprehensive multi-scale supervision, where complementary loss terms jointly improve local boundary sharpness and global geometric consistency. We conduct comprehensive evaluations on two publicly available colonoscopy depth estimation datasets. Compared to state-of-the-art monocular depth estimation methods, EndoStreamDepth substantially improves performance, and it produces depth maps with sharp, anatomically aligned boundaries, which are essential to support downstream tasks such as automation for robotic surgery. The code is publicly available at https://github.com/MedICL-VU/EndoStreamDepth

cs.CV↗

arXiv2025

Endo-SemiS: Towards Robust Semi-Supervised Image Segmentation for Endoscopic Video

In this paper, we present Endo-SemiS, a semi-supervised segmentation framework for providing reliable segmentation of endoscopic video frames with limited annotation. EndoSemiS uses 4 strategies to improve performance by effectively utilizing all available data, particularly unlabeled data: (1) Cross-supervision between two individual networks that supervise each other; (2) Uncertainty-guided pseudo-labels from unlabeled data, which are generated by selecting high-confidence regions to improve their quality; (3) Joint pseudolabel supervision, which aggregates reliable pixels from the pseudo-labels of both networks to provide accurate supervision for unlabeled data; and (4) Mutual learning, where both networks learn from each other at the feature and image levels, reducing variance and guiding them toward a consistent solution. Additionally, a separate corrective network that utilizes spatiotemporal information from endoscopy video to improve segmentation performance. Endo-SemiS is evaluated on two clinical applications: kidney stone laser lithotomy from ureteroscopy and polyp screening from colonoscopy. Compared to state-of-the-art segmentation methods, Endo-SemiS substantially achieves superior results on both datasets with limited labeled data. The code is publicly available at https://github.com/MedICL-VU/Endo-SemiS

cs.CV↗

arXiv2025

DEMIST: Decoupled Multi-stream latent diffusion for Quantitative Myelin Map Synthesis

Quantitative magnetization transfer (qMT) imaging provides myelin-sensitive biomarkers, such as the pool size ratio (PSR), which is valuable for multiple sclerosis (MS) assessment. However, qMT requires specialized 20-30 minute scans. We propose DEMIST to synthesize PSR maps from standard T1w and FLAIR images using a 3D latent diffusion model with three complementary conditioning mechanisms. Our approach has two stages: first, we train separate autoencoders for PSR and anatomical images to learn aligned latent representations. Second, we train a conditional diffusion model in this latent space on top of a frozen diffusion foundation backbone. Conditioning is decoupled into: (i) \textbf{semantic} tokens via cross-attention, (ii) \textbf{spatial} per-scale residual hints via a 3D ControlNet branch, and (iii) \textbf{adaptive} LoRA-modulated attention. We include edge-aware loss terms to preserve lesion boundaries and alignment losses to maintain quantitative consistency, while keeping the number of trainable parameters low and retaining the inductive bias of the pretrained model. We evaluate on 163 scans from 99 subjects using 5-fold cross-validation. Our method outperforms VAE, GAN and diffusion baselines on multiple metrics, producing sharper boundaries and better quantitative agreement with ground truth. Our code is publicly available at https://github.com/MedICL-VU/MS-Synthesis-3DcLDM.

eess.IV↗

arXiv2025

Probabilistic Robustness Analysis in High Dimensional Space: Application to Semantic Segmentation Network

Semantic segmentation networks (SSNs) are central to safety-critical applications such as medical imaging and autonomous driving, where robustness under uncertainty is essential. However, existing probabilistic verification methods often fail to scale with the complexity and dimensionality of modern segmentation tasks, producing guarantees that are overly conservative and of limited practical value. We propose a probabilistic verification framework that is architecture-agnostic and scalable to high-dimensional input-output spaces. Our approach employs conformal inference (CI), enhanced by a novel technique that we call the \textbf{clipping block}, to provide provable guarantees while mitigating the excessive conservatism of prior methods. Experiments on large-scale segmentation models across CamVid, OCTA-500, Lung Segmentation, and Cityscapes demonstrate that our framework delivers reliable safety guarantees while substantially reducing conservatism compared to state-of-the-art approaches on segmentation tasks. We also provide a public GitHub repository (https://github.com/Navidhashemicodes/SSN_Reach_CLP_Surrogate) for this approach, to support reproducibility.

cs.CV↗

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

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↗

arXiv2024

SynStitch: a Self-Supervised Learning Network for Ultrasound Image Stitching Using Synthetic Training Pairs and Indirect Supervision

Ultrasound (US) image stitching can expand the field-of-view (FOV) by combining multiple US images from varied probe positions. However, registering US images with only partially overlapping anatomical contents is a challenging task. In this work, we introduce SynStitch, a self-supervised framework designed for 2DUS stitching. SynStitch consists of a synthetic stitching pair generation module (SSPGM) and an image stitching module (ISM). SSPGM utilizes a patch-conditioned ControlNet to generate realistic 2DUS stitching pairs with known affine matrix from a single input image. ISM then utilizes this synthetic paired data to learn 2DUS stitching in a supervised manner. Our framework was evaluated against multiple leading methods on a kidney ultrasound dataset, demonstrating superior 2DUS stitching performance through both qualitative and quantitative analyses. The code will be made public upon acceptance of the paper.

eess.IV↗

arXiv2024

AdaptDiff: Cross-Modality Domain Adaptation via Weak Conditional Semantic Diffusion for Retinal Vessel Segmentation

Deep learning has shown remarkable performance in medical image segmentation. However, despite its promise, deep learning has many challenges in practice due to its inability to effectively transition to unseen domains, caused by the inherent data distribution shift and the lack of manual annotations to guide domain adaptation. To tackle this problem, we present an unsupervised domain adaptation (UDA) method named AdaptDiff that enables a retinal vessel segmentation network trained on fundus photography (FP) to produce satisfactory results on unseen modalities (e.g., OCT-A) without any manual labels. For all our target domains, we first adopt a segmentation model trained on the source domain to create pseudo-labels. With these pseudo-labels, we train a conditional semantic diffusion probabilistic model to represent the target domain distribution. Experimentally, we show that even with low quality pseudo-labels, the diffusion model can still capture the conditional semantic information. Subsequently, we sample on the target domain with binary vessel masks from the source domain to get paired data, i.e., target domain synthetic images conditioned on the binary vessel map. Finally, we fine-tune the pre-trained segmentation network using the synthetic paired data to mitigate the domain gap. We assess the effectiveness of AdaptDiff on seven publicly available datasets across three distinct modalities. Our results demonstrate a significant improvement in segmentation performance across all unseen datasets. Our code is publicly available at https://github.com/DeweiHu/AdaptDiff.

cs.CV↗

arXiv2024

PRISM Lite: A lightweight model for interactive 3D placenta segmentation in ultrasound

Placenta volume measured from 3D ultrasound (3DUS) images is an important tool for tracking the growth trajectory and is associated with pregnancy outcomes. Manual segmentation is the gold standard, but it is time-consuming and subjective. Although fully automated deep learning algorithms perform well, they do not always yield high-quality results for each case. Interactive segmentation models could address this issue. However, there is limited work on interactive segmentation models for the placenta. Despite their segmentation accuracy, these methods may not be feasible for clinical use as they require relatively large computational power which may be especially prohibitive in low-resource environments, or on mobile devices. In this paper, we propose a lightweight interactive segmentation model aiming for clinical use to interactively segment the placenta from 3DUS images in real-time. The proposed model adopts the segmentation from our fully automated model for initialization and is designed in a human-in-the-loop manner to achieve iterative improvements. The Dice score and normalized surface Dice are used as evaluation metrics. The results show that our model can achieve superior performance in segmentation compared to state-of-the-art models while using significantly fewer parameters. Additionally, the proposed model is much faster for inference and robust to poor initial masks. The code is available at https://github.com/MedICL-VU/PRISM-placenta.

eess.IV↗

arXiv2024

Deep Learning-based Unsupervised Domain Adaptation via a Unified Model for Prostate Lesion Detection Using Multisite Bi-parametric MRI Datasets

Our hypothesis is that UDA using diffusion-weighted images, generated with a unified model, offers a promising and reliable strategy for enhancing the performance of supervised learning models in multi-site prostate lesion detection, especially when various b-values are present. This retrospective study included data from 5,150 patients (14,191 samples) collected across nine different imaging centers. A novel UDA method using a unified generative model was developed for multi-site PCa detection. This method translates diffusion-weighted imaging (DWI) acquisitions, including apparent diffusion coefficient (ADC) and individual DW images acquired using various b-values, to align with the style of images acquired using b-values recommended by Prostate Imaging Reporting and Data System (PI-RADS) guidelines. The generated ADC and DW images replace the original images for PCa detection. An independent set of 1,692 test cases (2,393 samples) was used for evaluation. The area under the receiver operating characteristic curve (AUC) was used as the primary metric, and statistical analysis was performed via bootstrapping. For all test cases, the AUC values for baseline SL and UDA methods were 0.73 and 0.79 (p<.001), respectively, for PI-RADS>=3, and 0.77 and 0.80 (p<.001) for PI-RADS>=4 PCa lesions. In the 361 test cases under the most unfavorable image acquisition setting, the AUC values for baseline SL and UDA were 0.49 and 0.76 (p<.001) for PI-RADS>=3, and 0.50 and 0.77 (p<.001) for PI-RADS>=4 PCa lesions. The results indicate the proposed UDA with generated images improved the performance of SL methods in multi-site PCa lesion detection across datasets with various b values, especially for images acquired with significant deviations from the PI-RADS recommended DWI protocol (e.g. with an extremely high b-value).

eess.IV↗