Jinglun Yu

Zhangxing Bian, Fangxu Xing, Jinglun Yu et al.

Tagged magnetic resonance imaging~(MRI) has been used for decades to observe and quantify the detailed motion of deforming tissue. However, this technique faces several challenges such as tag fading, large motion, long computation times, and difficulties in obtaining diffeomorphic incompressible flow fields. To address these issues, this paper presents a novel unsupervised phase-based 3D motion estimation technique for tagged MRI. We introduce two key innovations. First, we apply a sinusoidal transformation to the harmonic phase input, which enables end-to-end training and avoids the need for phase interpolation. Second, we propose a Jacobian determinant-based learning objective to encourage incompressible flow fields for deforming biological tissues. Our method efficiently estimates 3D motion fields that are accurate, dense, and approximately diffeomorphic and incompressible. The efficacy of the method is assessed using human tongue motion during speech, and includes both healthy controls and patients that have undergone glossectomy. We show that the method outperforms existing approaches, and also exhibits improvements in speed, robustness to tag fading, and large tongue motion. The code is available: https://github.com/jasonbian97/DRIMET-tagged-MRI

Rosalinda Xiong, Jinglun Yu, Yaning Wang et al.

Robotic deep anterior lamellar keratoplasty (DALK) requires accurate real time depth feedback to approach Descemet's membrane (DM) without perforation. M-mode intraoperative optical coherence tomography (OCT) provides high temporal resolution depth traces, but speckle noise, attenuation, and instrument induced shadowing often result in discontinuous or ambiguous layer interfaces that challenge anatomically consistent segmentation at deployment frame rates. We present a lightweight, topology aware M-mode segmentation pipeline based on UNeXt that incorporates anatomical topology regularization to stabilize boundary continuity and layer ordering under low signal to noise ratio conditions. The proposed system achieves end to end throughput exceeding 80 Hz measured over the complete preprocessing inference overlay pipeline on a single GPU, demonstrating practical real time guidance beyond model only timing. This operating margin provides temporal headroom to reject low quality or dropout frames while maintaining a stable effective depth update rate. Evaluation on a standard rabbit eye M-mode dataset using an established baseline protocol shows improved qualitative boundary stability compared with topology agnostic controls, while preserving deployable real time performance.

Jinglun Yu, Yaning Wang, Rosalinda Xiong et al.

Training deep learning models for corneal optical coherence tomography (OCT) imaging is limited by the availability of large, well-annotated datasets. We present a configurable Monte Carlo simulation framework that generates synthetic corneal B-scan optical OCT images with pixel-level five-layer segmentation labels derived directly from the simulation geometry. A five-layer corneal model with Gaussian surfaces captures curvature and thickness variability in healthy and keratoconic eyes. Each layer is assigned optical properties from the literature and light transport is simulated using Monte Carlo modeling of light transport in multi-layered tissues (MCML), while incorporating system features such as the confocal PSF and sensitivity roll-off. This approach produces over 10,000 high-resolution (1024x1024) image-label pairs and supports customization of geometry, photon count, noise, and system parameters. The resulting dataset enables systematic training, validation, and benchmarking of AI models under controlled, ground-truth conditions, providing a reproducible and scalable resource to support the development of diagnostic and surgical guidance applications in image-guided ophthalmology.

Jinglun Yu, Yaning Wang, Wenhan Guo et al.

Inverse scattering in optical coherence tomography (OCT) seeks to recover both structural images and intrinsic tissue optical properties, including refractive index, scattering coefficient, and anisotropy. This inverse problem is challenging due to attenuation, speckle noise, and strong coupling among parameters. We propose a regularized end-to-end deep learning framework that jointly reconstructs optical parameter maps and speckle-reduced OCT structural intensity for layer visualization. Trained with Monte Carlo-simulated ground truth, our network incorporates a physics-based OCT forward model that generates predicted signals from the estimated parameters, providing physics-consistent supervision for parameter recovery and artifact suppression. Experiments on the synthetic corneal OCT dataset demonstrate robust optical map recovery under noise, improved resolution, and enhanced structural fidelity. This approach enables quantitative multi-parameter tissue characterization and highlights the benefit of combining physics-informed modeling with deep learning for computational OCT.

Yaning Wang, Jinglun Yu, Wenhan Guo et al.

We propose an OCT super-resolution framework based on a plug-and-play diffusion model (PnP-DM) to reconstruct high-quality images from sparse measurements (OCT B-mode corneal images). Our method formulates reconstruction as an inverse problem, combining a diffusion prior with Markov chain Monte Carlo sampling for efficient posterior inference. We collect high-speed under-sampled B-mode corneal images and apply a deep learning-based up-sampling pipeline to build realistic training pairs. Evaluations on in vivo and ex vivo fish-eye corneal models show that PnP-DM outperforms conventional 2D-UNet baselines, producing sharper structures and better noise suppression. This approach advances high-fidelity OCT imaging in high-speed acquisition for clinical applications.