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.

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), used to regularize a surface matching term. This paper introduces a novel 3D-3D non-rigid registration method. In contrast to the preceding techniques, our method uniquely incorporates the FEM within the surface matching term itself, ensuring that the estimated deformation maintains geometric consistency throughout the registration process. Additionally, we eliminate the need to determine zero-boundary conditions and applied force locations in the FEM. We achieve this by integrating soft springs into the stiffness matrix and allowing forces to be distributed across the entire liver surface. To further improve robustness, we introduce a regularization technique focused on the gradient of the force magnitudes. This regularization imposes spatial smoothness and helps prevent the overfitting of irregular noise in intraoperative data. Optimization is achieved through an accelerated proximal gradient algorithm, further enhanced by our proposed method for determining the optimal step size. Our method is evaluated and compared to both a learning-based method and a traditional method that features FEM regularization using data collected on our custom-developed phantom, as well as two publicly available datasets. Our method consistently outperforms or is comparable to the baseline techniques. Both the code and dataset will be made publicly available.

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.

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.

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.

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.