arXiv subjects

Richard Simon

Publications and source records attributed to Richard Simon.

15 recordsLinked to original sources

arXiv2026

Toward Vision Language Model-based Assessment of Clinical Quality and Usability of LGE-MR Images for Cardiac Ablation Planning

LGE cardiac MRI is widely used for left atrial fibrosis assessment and ablation planning in atrial fibrillation patients as knowledge of fibrotic tissue regions identified from LGE-MRI is critical for catheter ablation. Often, poor quality images used during ablation planning can cause mis-localization of ablation targets, directly impacting procedure safety and outcome. The decision of whether a scan meets the minimum quality threshold for ablation planning is currently made informally by the reviewing radiologist and is not captured by any automated system, yet it is arguably the most safety-critical output of the image quality assessment (IQA) process. However, variations in image quality caused by noise, motion artifacts, and poor boundary definition significantly compromise the reliability of downstream segmentation and clinical decision-making tasks. Manual quality assessment by expert radiologists is subjective and difficult to scale, while existing automated methods produce scalar scores without interpretable clinical reasoning. In this work, we propose a two-stage vision language model (VLM) framework for clinically grounded image quality assessment of left atrial LGE-MRI. In the first stage, a fine-tuned VLM generates structured radiology-style quality reports predicting five radiologist-defined criteria: Noise, Motion Artifact, LA Boundary Accuracy, PV Region Accuracy, and Under-segmentation Severity. In the second stage, a GPT-based reasoning module maps the predicted quality and reports to a structured quality scores and binary clinical usability decision for ablation planning. We curate a dataset of 60 annotated image slice-text pairs from 20 patients and benchmark four state-of-the-art VLM architectures. InternVL2 achieves the highest criterion-level accuracy (Avg ACC=0.65, PLCC=0.79), while DeepSeek achieves perfect clinical usability agreement (Acc=1.00, kappa=1.00).

eess.IV↗

arXiv2026

Toward Mask Annotation-Free Surgical Instrument Segmentation from Endoscopic Images Using Text-Prompted Segment Anything Model 3 (SAM3)

Surgical instrument segmentation is a fundamental task for computer-assisted interventions, yet most existing methods rely on pixel-level annotations or manual spatial prompts, which limit scalability and automation. The recently introduced Segment Anything Model 3 (SAM3) offers a pathway to annotation-free, automatic segmentation via text-based prompting; however, the instrument name as a text prompt could not be directly used due to a large domain gap. To overcome these limitations, we propose a two-stage framework that achieves instance-level segmentation without requiring ground truth masks or manual interaction. In the first stage, we leverage a natural-language-aligned generic prompt - "tool" - to produce binary masks using SAM3's zero-shot capability. In the second stage, these masks are extended to instance-level by integrating a vision-language model (Qwen) that is fine-tuned on SAM3-generated masked regions for instrument classification. We evaluate our approach on the EndoVis 2017 and 2018 datasets. Results show that, while our two-stage approach does not reach the performance of current fully supervised methods, it significantly outperforms the direct use of SAM3 for instance-level instrument segmentation with text prompts. Overall, our findings highlight both the limitations and potential of SAM3, suggesting a promising direction toward annotation-free surgical instrument segmentation.

cs.CV↗

arXiv2026

Evaluating Large Vision-language Models for Surgical Tool Detection

Surgery is a highly complex process, and artificial intelligence has emerged as a transformative force in supporting surgical guidance and decision-making. However, the unimodal nature of most current AI systems limits their ability to achieve a holistic understanding of surgical workflows. This highlights the need for general-purpose surgical AI systems capable of comprehensively modeling the interrelated components of surgical scenes. Recent advances in large vision-language models that integrate multimodal data processing offer strong potential for modeling surgical tasks and providing human-like scene reasoning and understanding. Despite their promise, systematic investigations of VLMs in surgical applications remain limited. In this study, we evaluate the effectiveness of large VLMs for the fundamental surgical vision task of detecting surgical tools. Specifically, we investigate three state-of-the-art VLMs, Qwen2.5, LLaVA1.5, and InternVL3.5, on the GraSP robotic surgery dataset under both zero-shot and parameter-efficient LoRA fine-tuning settings. Our results demonstrate that Qwen2.5 consistently achieves superior detection performance in both configurations among the evaluated VLMs. Furthermore, compared with the open-set detection baseline Grounding DINO, Qwen2.5 exhibits stronger zero-shot generalization and comparable fine-tuned performance. Notably, Qwen2.5 shows superior instrument recognition, while Grounding DINO demonstrates stronger localization.

cs.CV↗

arXiv2025

2D Ultrasound Elasticity Imaging of Abdominal Aortic Aneurysms Using Deep Neural Networks

Abdominal aortic aneurysms (AAA) pose a significant clinical risk due to their potential for rupture, which is often asymptomatic but can be fatal. Although maximum diameter is commonly used for risk assessment, diameter alone is insufficient as it does not capture the properties of the underlying material of the vessel wall, which play a critical role in determining the risk of rupture. To overcome this limitation, we propose a deep learning-based framework for elasticity imaging of AAAs with 2D ultrasound. Leveraging finite element simulations, we generate a diverse dataset of displacement fields with their corresponding modulus distributions. We train a model with U-Net architecture and normalized mean squared error (NMSE) to infer the spatial modulus distribution from the axial and lateral components of the displacement fields. This model is evaluated across three experimental domains: digital phantom data from 3D COMSOL simulations, physical phantom experiments using biomechanically distinct vessel models, and clinical ultrasound exams from AAA patients. Our simulated results demonstrate that the proposed deep learning model is able to reconstruct modulus distributions, achieving an NMSE score of 0.73\%. Similarly, in phantom data, the predicted modular ratio closely matches the expected values, affirming the model's ability to generalize to phantom data. We compare our approach with an iterative method which shows comparable performance but higher computation time. In contrast, the deep learning method can provide quick and effective estimates of tissue stiffness from ultrasound images, which could help assess the risk of AAA rupture without invasive procedures.

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arXiv2025

Toward Patient-specific Partial Point Cloud to Surface Completion for Pre- to Intra-operative Registration in Image-guided Liver Interventions

Intra-operative data captured during image-guided surgery lacks sub-surface information, where key regions of interest, such as vessels and tumors, reside. Image-to-physical registration enables the fusion of pre-operative information and intra-operative data, typically represented as a point cloud. However, this registration process struggles due to partial visibility of the intra-operative point cloud. In this research, we propose a patient-specific point cloud completion approach to assist with the registration process. Specifically, we leverage VN-OccNet to generate a complete liver surface from a partial intra-operative point cloud. The network is trained in a patient-specific manner, where simulated deformations from the pre-operative model are used to train the model. First, we conduct an in-depth analysis of VN-OccNet's rotation-equivariant property and its effectiveness in recovering complete surfaces from partial intra-operative surfaces. Next, we integrate the completed intra-operative surface into the Go-ICP registration algorithm to demonstrate its utility in improving initial rigid registration outcomes. Our results highlight the promise of this patient-specific completion approach in mitigating the challenges posed by partial intra-operative visibility. The rotation equivariant and surface generation capabilities of VN-OccNet hold strong promise for developing robust registration frameworks for variations of the intra-operative point cloud.

cs.CV↗

arXiv2025

Evaluation of Intra-operative Patient-specific Methods for Point Cloud Completion for Minimally Invasive Liver Interventions

The registration between the pre-operative model and the intra-operative surface is crucial in image-guided liver surgery, as it facilitates the effective use of pre-operative information during the procedure. However, the intra-operative surface, usually represented as a point cloud, often has limited coverage, especially in laparoscopic surgery, and is prone to holes and noise, posing significant challenges for registration methods. Point cloud completion methods have the potential to alleviate these issues. Thus, we explore six state-of-the-art point cloud completion methods to identify the optimal completion method for liver surgery applications. We focus on a patient-specific approach for liver point cloud completion from a partial liver surface under three cases: canonical pose, non-canonical pose, and canonical pose with noise. The transformer-based method, AdaPoinTr, outperforms all other methods to generate a complete point cloud from the given partial liver point cloud under the canonical pose. On the other hand, our findings reveal substantial performance degradation of these methods under non-canonical poses and noisy settings, highlighting the limitations of these methods, which suggests the need for a robust point completion method for its application in image-guided liver surgery.

cs.CV↗

arXiv2025

Multi-Scale Feature Fusion with Image-Driven Spatial Integration for Left Atrium Segmentation from Cardiac MRI Images

Accurate segmentation of the left atrium (LA) from late gadolinium-enhanced magnetic resonance imaging plays a vital role in visualizing diseased atrial structures, enabling the diagnosis and management of cardiovascular diseases. It is particularly essential for planning treatment with ablation therapy, a key intervention for atrial fibrillation (AF). However, manual segmentation is time-intensive and prone to inter-observer variability, underscoring the need for automated solutions. Class-agnostic foundation models like DINOv2 have demonstrated remarkable feature extraction capabilities in vision tasks. However, their lack of domain specificity and task-specific adaptation can reduce spatial resolution during feature extraction, impacting the capture of fine anatomical detail in medical imaging. To address this limitation, we propose a segmentation framework that integrates DINOv2 as an encoder with a UNet-style decoder, incorporating multi-scale feature fusion and input image integration to enhance segmentation accuracy. The learnable weighting mechanism dynamically prioritizes hierarchical features from different encoder blocks of the foundation model, optimizing feature selection for task relevance. Additionally, the input image is reintroduced during the decoding stage to preserve high-resolution spatial details, addressing limitations of downsampling in the encoder. We validate our approach on the LAScarQS 2022 dataset and demonstrate improved performance with a 92.3% Dice and 84.1% IoU score for giant architecture compared to the nnUNet baseline model. These findings emphasize the efficacy of our approach in advancing the field of automated left atrium segmentation from cardiac MRI.

cs.CV↗

arXiv2024

Resolving the Ambiguity of Complete-to-Partial Point Cloud Registration for Image-Guided Liver Surgery with Patches-to-Partial Matching

In image-guided liver surgery, the initial rigid alignment between preoperative and intraoperative data, often represented as point clouds, is crucial for providing sub-surface information from preoperative CT/MRI images to the surgeon during the procedure. Currently, this alignment is typically performed using semi-automatic methods, which, while effective to some extent, are prone to errors that demand manual correction. Point cloud correspondence-based registration methods are promising to serve as a fully automatic solution. However, they may struggle in scenarios with limited intraoperative surface visibility, a common challenge in liver surgery, particularly in laparoscopic procedures, which we refer to as complete-to-partial ambiguity. We first illustrate this ambiguity by evaluating the performance of state-of-the-art learning-based point cloud registration methods on our carefully constructed in silico and in vitro datasets. Then, we propose a patches-to-partial matching strategy as a plug-and-play module to resolve the ambiguity, which can be seamlessly integrated into learning-based registration methods without disrupting their end-to-end structure. It has proven effective and efficient in improving registration performance for cases with limited intraoperative visibility. The constructed benchmark and the proposed module establish a solid foundation for advancing applications of point cloud correspondence-based registration methods in image-guided liver surgery.

cs.CV↗

arXiv2024

Assessing the Performance of the DINOv2 Self-supervised Learning Vision Transformer Model for the Segmentation of the Left Atrium from MRI Images

Accurate left atrium (LA) segmentation from pre-operative scans is crucial for diagnosing atrial fibrillation, treatment planning, and supporting surgical interventions. While deep learning models are key in medical image segmentation, they often require extensive manually annotated data. Foundation models trained on larger datasets have reduced this dependency, enhancing generalizability and robustness through transfer learning. We explore DINOv2, a self-supervised learning vision transformer trained on natural images, for LA segmentation using MRI. The challenges for LA's complex anatomy, thin boundaries, and limited annotated data make accurate segmentation difficult before & during the image-guided intervention. We demonstrate DINOv2's ability to provide accurate & consistent segmentation, achieving a mean Dice score of .871 & a Jaccard Index of .792 for end-to-end fine-tuning. Through few-shot learning across various data sizes & patient counts, DINOv2 consistently outperforms baseline models. These results suggest that DINOv2 effectively adapts to MRI with limited data, highlighting its potential as a competitive tool for segmentation & encouraging broader use in medical imaging.

eess.IV↗

arXiv2024

Boundary Constraint-free Biomechanical Model-Based Surface Matching for Intraoperative Liver Deformation Correction

In image-guided liver surgery, 3D-3D non-rigid registration methods play a crucial role in estimating the mapping between the preoperative model and the intraoperative surface represented as point clouds, addressing the challenge of tissue deformation. Typically, these methods incorporate a biomechanical model, represented as a finite element model (FEM), into the strain energy term to regularize a surface matching term. We propose a 3D-3D non-rigid registration method that incorporates a modified FEM into the surface matching term. The modified FEM alleviates the need to specify boundary conditions, which is achieved by modifying the stiffness matrix of a FEM and using diagonal loading for stabilization. As a result, the modified surface matching term does not require the specification of boundary conditions or an additional strain energy term to regularize the surface matching term. Optimization is achieved through an accelerated gradient algorithm, further enhanced by our proposed method for determining the optimal step size. We evaluated our method and compared it to several state-of-the-art methods across various datasets. Our straightforward and effective approach consistently outperformed or achieved comparable performance to the state-of-the-art methods. Our code and datasets are available at https://github.com/zixinyang9109/BCF-FEM.

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arXiv2023

A Disparity Refinement Framework for Learning-based Stereo Matching Methods in Cross-domain Setting for Laparoscopic Images

Purpose: Stereo matching methods that enable depth estimation are crucial for visualization enhancement applications in computer-assisted surgery (CAS). Learning-based stereo matching methods are promising to predict accurate results on laparoscopic images. However, they require a large amount of training data, and their performance may be degraded due to domain shifts. Methods: Maintaining robustness and improving the accuracy of learning-based methods are still open problems. To overcome the limitations of learning-based methods, we propose a disparity refinement framework consisting of a local disparity refinement method and a global disparity refinement method to improve the results of learning-based stereo matching methods in a cross-domain setting. Those learning-based stereo matching methods are pre-trained on a large public dataset of natural images and are tested on two datasets of laparoscopic images. Results: Qualitative and quantitative results suggest that our proposed disparity framework can effectively refine disparity maps when they are noise-corrupted on an unseen dataset, without compromising prediction accuracy when the network can generalize well on an unseen dataset. Conclusion: Our proposed disparity refinement framework could work with learning-based methods to achieve robust and accurate disparity prediction. Yet, as a large laparoscopic dataset for training learning-based methods does not exist and the generalization ability of networks remains to be improved, the incorporation of the proposed disparity refinement framework into existing networks will contribute to improving their overall accuracy and robustness associated with depth estimation.

cs.CV↗

arXiv2022

Learning Feature Descriptors for Pre- and Intra-operative Point Cloud Matching for Laparoscopic Liver Registration

Purpose: In laparoscopic liver surgery (LLS), pre-operative information can be overlaid onto the intra-operative scene by registering a 3D pre-operative model to the intra-operative partial surface reconstructed from the laparoscopic video. To assist with this task, we explore the use of learning-based feature descriptors, which, to our best knowledge, have not been explored for use in laparoscopic liver registration. Furthermore, a dataset to train and evaluate the use of learning-based descriptors does not exist. Methods: We present the LiverMatch dataset consisting of 16 preoperative models and their simulated intra-operative 3D surfaces. We also propose the LiverMatch network designed for this task, which outputs per-point feature descriptors, visibility scores, and matched points. Results: We compare the proposed LiverMatch network with anetwork closest to LiverMatch, and a histogram-based 3D descriptor on the testing split of the LiverMatch dataset, which includes two unseen pre-operative models and 1400 intra-operative surfaces. Results suggest that our LiverMatch network can predict more accurate and dense matches than the other two methods and can be seamlessly integrated with a RANSAC-ICP-based registration algorithm to achieve an accurate initial alignment. Conclusion: The use of learning-based feature descriptors in LLR is promising, as it can help achieve an accurate initial rigid alignment, which, in turn, serves as an initialization for subsequent non-rigid registration. We will release the dataset and code upon acceptance.

cs.CV↗

arXiv2022

Use of Non-concurrent Common Control in Master Protocols in Oncology Trials: Report of an American Statistical Association Biopharmaceutical Section Open Forum Discussion

This article summarizes the discussions from the American Statistical Association (ASA) Biopharmaceutical (BIOP) Section Open Forum that took place on December 10, 2020 and was organized by the ASA BIOP Statistical Methods in Oncology Scientific Working Group, in coordination with the US FDA Oncology Center of Excellence. Diverse stakeholders including experts from international regulatory agencies, academicians, and representatives of the pharmaceutical industry engaged in a discussion on the use of non-concurrent control in Master Protocols for oncology trials. While the use of non-concurrent control with the concurrent control may increase the power of detecting the therapeutic difference between a treatment and the control, the panelists had diverse opinion on the statistical approaches for modeling non-concurrent and concurrent controls. Some were more concerned about the temporality of the non-concurrent control and bias introduced by different confounders related to time, e.g., changes in standard of care, changes in patient population, changes in recruiting strategies, changes in assessment of endpoints. Nevertheless, in some situations such as when the recruitment is extremely challenging for a rare disease, the panelists concluded that the use of a non-concurrent control can be justified.

stat.AP↗

arXiv2021

CNN-based Cardiac Motion Extraction to Generate Deformable Geometric Left Ventricle Myocardial Models from Cine MRI

Patient-specific left ventricle (LV) myocardial models have the potential to be used in a variety of clinical scenarios for improved diagnosis and treatment plans. Cine cardiac magnetic resonance (MR) imaging provides high resolution images to reconstruct patient-specific geometric models of the LV myocardium. With the advent of deep learning, accurate segmentation of cardiac chambers from cine cardiac MR images and unsupervised learning for image registration for cardiac motion estimation on a large number of image datasets is attainable. Here, we propose a deep leaning-based framework for the development of patient-specific geometric models of LV myocardium from cine cardiac MR images, using the Automated Cardiac Diagnosis Challenge (ACDC) dataset. We use the deformation field estimated from the VoxelMorph-based convolutional neural network (CNN) to propagate the isosurface mesh and volume mesh of the end-diastole (ED) frame to the subsequent frames of the cardiac cycle. We assess the CNN-based propagated models against segmented models at each cardiac phase, as well as models propagated using another traditional nonrigid image registration technique.

eess.IV↗

arXiv2013

On Estimating Many Means, Selection Bias, and the Bootstrap

With recent advances in high throughput technology, researchers often find themselves running a large number of hypothesis tests (thousands+) and esti- mating a large number of effect-sizes. Generally there is particular interest in those effects estimated to be most extreme. Unfortunately naive estimates of these effect-sizes (even after potentially accounting for multiplicity in a testing procedure) can be severely biased. In this manuscript we explore this bias from a frequentist perspective: we give a formal definition, and show that an oracle estimator using this bias dominates the naive maximum likelihood estimate. We give a resampling estimator to approximate this oracle, and show that it works well on simulated data. We also connect this to ideas in empirical Bayes.

stat.ML↗