Xiaoran Zhang

Xiaoran Zhang, Chenyu You, Shawn Ahn et al.

Learning spatial-temporal correspondences in cardiac motion from images is important for understanding the underlying dynamics of cardiac anatomical structures. Many methods explicitly impose smoothness constraints such as the $\mathcal{L}_2$ norm on the displacement vector field (DVF), while usually ignoring biomechanical feasibility in the transformation. Other geometric constraints either regularize specific regions of interest such as imposing incompressibility on the myocardium or introduce additional steps such as training a separate network-based regularizer on physically simulated datasets. In this work, we propose an explicit biomechanics-informed prior as regularization on the predicted DVF in modeling a more generic biomechanically plausible transformation within all cardiac structures without introducing additional training complexity. We validate our methods on two publicly available datasets in the context of 2D MRI data and perform extensive experiments to illustrate the effectiveness and robustness of our proposed methods compared to other competing regularization schemes. Our proposed methods better preserve biomechanical properties by visual assessment and show advantages in segmentation performance using quantitative evaluation metrics. The code is publicly available at \url{https://github.com/Voldemort108X/bioinformed_reg}.

Chenyu You, Jinlin Xiang, Kun Su et al.

Many medical datasets have recently been created for medical image segmentation tasks, and it is natural to question whether we can use them to sequentially train a single model that (1) performs better on all these datasets, and (2) generalizes well and transfers better to the unknown target site domain. Prior works have achieved this goal by jointly training one model on multi-site datasets, which achieve competitive performance on average but such methods rely on the assumption about the availability of all training data, thus limiting its effectiveness in practical deployment. In this paper, we propose a novel multi-site segmentation framework called incremental-transfer learning (ITL), which learns a model from multi-site datasets in an end-to-end sequential fashion. Specifically, "incremental" refers to training sequentially constructed datasets, and "transfer" is achieved by leveraging useful information from the linear combination of embedding features on each dataset. In addition, we introduce our ITL framework, where we train the network including a site-agnostic encoder with pre-trained weights and at most two segmentation decoder heads. We also design a novel site-level incremental loss in order to generalize well on the target domain. Second, we show for the first time that leveraging our ITL training scheme is able to alleviate challenging catastrophic forgetting problems in incremental learning. We conduct experiments using five challenging benchmark datasets to validate the effectiveness of our incremental-transfer learning approach. Our approach makes minimal assumptions on computation resources and domain-specific expertise, and hence constitutes a strong starting point in multi-site medical image segmentation.

Xiaoran Zhang, Jian Ding, Yuxing Duan et al.

Turbulence mitigation (TM) is highly ill-posed due to the stochastic nature of atmospheric turbulence. Most methods rely on multiple frames recorded by conventional cameras to capture stable patterns in natural scenarios. However, they inevitably suffer from a trade-off between accuracy and efficiency: more frames enhance restoration at the cost of higher system latency and larger data overhead. Event cameras, equipped with microsecond temporal resolution and efficient sensing of dynamic changes, offer an opportunity to break the bottleneck. In this work, we present EHETM, a high-quality and efficient TM method inspired by the superiority of events to model motions in continuous sequences. We discover two key phenomena: (1) turbulence-induced events exhibit distinct polarity alternation correlated with sharp image gradients, providing structural cues for restoring scenes; and (2) dynamic objects form spatiotemporally coherent ``event tubes'' in contrast to irregular patterns within turbulent events, providing motion priors for disentangling objects from turbulence. Based on these insights, we design two complementary modules that respectively leverage polarity-weighted gradients for scene refinement and event-tube constraints for motion decoupling, achieving high-quality restoration with few frames. Furthermore, we construct two real-world event-frame turbulence datasets covering atmospheric and thermal cases. Experiments show that EHETM outperforms SOTA methods, especially under scenes with dynamic objects, while reducing data overhead and system latency by approximately 77.3% and 89.5%, respectively. Our code is available at: https://github.com/Xavier667/EHETM.

Ziqi Gao, Nicha Dvornek, Xiaoran Zhang et al.

Low-field (LF) magnetic resonance imaging (MRI) improves accessibility and reduces costs but generally has lower signal-to-noise ratios and degraded contrast compared to high field (HF) MRI, limiting its clinical utility. Simulating LF MRI from HF MRI enables virtual evaluation of novel imaging devices and development of LF algorithms. Existing low field simulators rely on noise injection and smoothing, which fail to capture the contrast degradation seen in LF acquisitions. To this end, we introduce an end-to-end LF-MRI synthesis framework that learns HF to LF image degradation directly from a small number of paired HF-LF MRIs. Specifically, we introduce a novel HF to LF coordinate-image decoupled neural operator (H2LO) to model the underlying degradation process, and tailor it to capture high-frequency noise textures and image structure. Experimental results in T1w and T2w MRI demonstrate that H2LO produces more faithful simulated low-field images than existing parameterized noise synthesis models and popular image-to-image translation models. Furthermore, it improves performance in downstream image enhancement tasks, showcasing its potential to enhance LF MRI diagnostic capabilities.

Xiaoran Zhang, Yu Liu, Jinyu Liang et al.

Cross-modal Thermal Geo-localization (TG) provides a robust, all-weather solution for Unmanned Aerial Vehicles (UAVs) in Global Navigation Satellite System (GNSS)-denied environments. However, profound thermal-visible modality gaps introduce severe feature ambiguity, systematically corrupting conventional coarse-to-fine registration. To dismantle this bottleneck, we propose SCC-Loc, a unified Semantic-Cascade-Consensus localization framework. By sharing a single DINOv2 backbone across global retrieval and MINIMA$_{\text{RoMa}}$ matching, it minimizes memory footprint and achieves zero-shot, highly accurate absolute position estimation. Specifically, we tackle modality ambiguity by introducing three cohesive components. First, we design the Semantic-Guided Viewport Alignment (SGVA) module to adaptively optimize satellite crop regions, effectively correcting initial spatial deviations. Second, we develop the Cascaded Spatial-Adaptive Texture-Structure Filtering (C-SATSF) mechanism to explicitly enforce geometric consistency, thereby eradicating dense cross-modal outliers. Finally, we propose the Consensus-Driven Reliability-Aware Position Selection (CD-RAPS) strategy to derive the optimal solution through a synergy of physically constrained pose optimization. To address data scarcity, we construct Thermal-UAV, a comprehensive dataset providing 11,890 diverse thermal queries referenced against a large-scale satellite ortho-photo and corresponding spatially aligned Digital Surface Model (DSM). Extensive experiments demonstrate that SCC-Loc establishes a new state-of-the-art, suppressing the mean localization error to 9.37 m and providing a 7.6-fold accuracy improvement within a strict 5-m threshold over the strongest baseline. Code and dataset are available at https://github.com/FloralHercules/SCC-Loc.

Daniel H. Pak, Shubh Thaker, Kyle Baylous et al.

High-quality volumetric meshing from medical images is a key bottleneck for physics-based simulations in personalized medicine. For volumetric meshing of complex medical structures, recent studies have often utilized deep learning (DL)-based template deformation approaches to enable fast test-time generation with high spatial accuracy. However, these approaches still exhibit limitations, such as limited flexibility at high-curvature areas and unrealistic inter-part distances. In this study, we introduce a simple yet effective snap-and-tune strategy that sequentially applies DL and test-time optimization, which combines fast initial shape fitting with more detailed sample-specific mesh corrections. Our method provides significant improvements in both spatial accuracy and mesh quality, while being fully automated and requiring no additional training labels. Finally, we demonstrate the versatility and usefulness of our newly generated meshes via solid mechanics simulations in two different software platforms. Our code is available at https://github.com/danpak94/Deep-Cardiac-Volumetric-Mesh.

Xiaoran Zhang, Eric Z. Chen, Lin Zhao et al.

We propose a novel approach that adapts hierarchical vision foundation models for real-time ultrasound image segmentation. Existing ultrasound segmentation methods often struggle with adaptability to new tasks, relying on costly manual annotations, while real-time approaches generally fail to match state-of-the-art performance. To overcome these limitations, we introduce an adaptive framework that leverages the vision foundation model Hiera to extract multi-scale features, interleaved with DINOv2 representations to enhance visual expressiveness. These enriched features are then decoded to produce precise and robust segmentation. We conduct extensive evaluations on six public datasets and one in-house dataset, covering both cardiac and thyroid ultrasound segmentation. Experiments show that our approach outperforms state-of-the-art methods across multiple datasets and excels with limited supervision, surpassing nnUNet by over 20\% on average in the 1\% and 10\% data settings. Our method achieves $\sim$77 FPS inference speed with TensorRT on a single GPU, enabling real-time clinical applications.

Xiaoran Zhang, Byung-Woo Hong, Hyoungseob Park et al.

We propose a model-agnostic, progressive test-time energy adaptation approach for medical image segmentation. Maintaining model performance across diverse medical datasets is challenging, as distribution shifts arise from inconsistent imaging protocols and patient variations. Unlike domain adaptation methods that require multiple passes through target data - impractical in clinical settings - our approach adapts pretrained models progressively as they process test data. Our method leverages a shape energy model trained on source data, which assigns an energy score at the patch level to segmentation maps: low energy represents in-distribution (accurate) shapes, while high energy signals out-of-distribution (erroneous) predictions. By minimizing this energy score at test time, we refine the segmentation model to align with the target distribution. To validate the effectiveness and adaptability, we evaluated our framework on eight public MRI (bSSFP, T1- and T2-weighted) and X-ray datasets spanning cardiac, spinal cord, and lung segmentation. We consistently outperform baselines both quantitatively and qualitatively.

Younjoon Chung, Hyoungseob Park, Patrick Rim et al.

We propose a method for test-time adaptation of pretrained depth completion models. Depth completion models, trained on some ``source'' data, often predict erroneous outputs when transferred to ``target'' data captured in novel environmental conditions due to a covariate shift. The crux of our method lies in quantifying the likelihood of depth predictions belonging to the source data distribution. The challenge is in the lack of access to out-of-distribution (target) data prior to deployment. Hence, rather than making assumptions regarding the target distribution, we utilize adversarial perturbations as a mechanism to explore the data space. This enables us to train an energy model that scores local regions of depth predictions as in- or out-of-distribution. We update the parameters of pretrained depth completion models at test time to minimize energy, effectively aligning test-time predictions to those of the source distribution. We call our method ``Energy-based Test-time Adaptation'', or ETA for short. We evaluate our method across three indoor and three outdoor datasets, where ETA improve over the previous state-of-the-art method by an average of 6.94% for outdoors and 10.23% for indoors. Project Page: https://fuzzythecat.github.io/eta.

Ziwei Shi, Xiaoran Zhang, Wenjing Xu et al.

We tackle the challenge of LiDAR-based place recognition, which traditionally depends on costly and time-consuming prior 3D maps. To overcome this, we first construct LiRSI-XA dataset, which encompasses approximately $110,000$ remote sensing submaps and $13,000$ LiDAR point cloud submaps captured in urban scenes, and propose a novel method, L2RSI, for cross-view LiDAR place recognition using high-resolution Remote Sensing Imagery. This approach enables large-scale localization capabilities at a reduced cost by leveraging readily available overhead images as map proxies. L2RSI addresses the dual challenges of cross-view and cross-modal place recognition by learning feature alignment between point cloud submaps and remote sensing submaps in the semantic domain. Additionally, we introduce a novel probability propagation method based on particle estimation to refine position predictions, effectively leveraging temporal and spatial information. This approach enables large-scale retrieval and cross-scene generalization without fine-tuning. Extensive experiments on LiRSI-XA demonstrate that, within a $100km^2$ retrieval range, L2RSI accurately localizes $83.27\%$ of point cloud submaps within a $30m$ radius for top-$1$ retrieved location. Our project page is publicly available at https://shizw695.github.io/L2RSI/.

Lei Li, Fuping Wu, Sihan Wang et al.

Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore potential of solutions, as well as to provide a benchmark for future research. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. Note that MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (www.sdspeople.fudan.edu.cn/zhuangxiahai/0/myops20/).

Bijie Bai, Hongda Wang, Yuzhu Li et al.

The immunohistochemical (IHC) staining of the human epidermal growth factor receptor 2 (HER2) biomarker is widely practiced in breast tissue analysis, preclinical studies and diagnostic decisions, guiding cancer treatment and investigation of pathogenesis. HER2 staining demands laborious tissue treatment and chemical processing performed by a histotechnologist, which typically takes one day to prepare in a laboratory, increasing analysis time and associated costs. Here, we describe a deep learning-based virtual HER2 IHC staining method using a conditional generative adversarial network that is trained to rapidly transform autofluorescence microscopic images of unlabeled/label-free breast tissue sections into bright-field equivalent microscopic images, matching the standard HER2 IHC staining that is chemically performed on the same tissue sections. The efficacy of this virtual HER2 staining framework was demonstrated by quantitative analysis, in which three board-certified breast pathologists blindly graded the HER2 scores of virtually stained and immunohistochemically stained HER2 whole slide images (WSIs) to reveal that the HER2 scores determined by inspecting virtual IHC images are as accurate as their immunohistochemically stained counterparts. A second quantitative blinded study performed by the same diagnosticians further revealed that the virtually stained HER2 images exhibit a comparable staining quality in the level of nuclear detail, membrane clearness, and absence of staining artifacts with respect to their immunohistochemically stained counterparts. This virtual HER2 staining framework bypasses the costly, laborious, and time-consuming IHC staining procedures in laboratory, and can be extended to other types of biomarkers to accelerate the IHC tissue staining used in life sciences and biomedical workflow.

Xiaoran Zhang, Michelle Noga, David Glynn Martin et al.

This study proposes a fully automated approach for the left atrial segmentation from routine cine long-axis cardiac magnetic resonance image sequences using deep convolutional neural networks and Bayesian filtering. The proposed approach consists of a classification network that automatically detects the type of long-axis sequence and three different convolutional neural network models followed by unscented Kalman filtering (UKF) that delineates the left atrium. Instead of training and predicting all long-axis sequence types together, the proposed approach first identifies the image sequence type as to 2, 3 and 4 chamber views, and then performs prediction based on neural nets trained for that particular sequence type. The datasets were acquired retrospectively and ground truth manual segmentation was provided by an expert radiologist. In addition to neural net based classification and segmentation, another neural net is trained and utilized to select image sequences for further processing using UKF to impose temporal consistency over cardiac cycle. A cyclic dynamic model with time-varying angular frequency is introduced in UKF to characterize the variations in cardiac motion during image scanning. The proposed approach was trained and evaluated separately with varying amount of training data with images acquired from 20, 40, 60 and 80 patients. Evaluations over 1515 images with equal number of images from each chamber group acquired from an additional 20 patients demonstrated that the proposed model outperformed state-of-the-art and yielded a mean Dice coefficient value of 94.1%, 93.7% and 90.1% for 2, 3 and 4-chamber sequences, respectively, when trained with datasets from 80 patients.

Xiaoran Zhang, Michelle Noga, Kumaradevan Punithakumar

Myocardial characterization is essential for patients with myocardial infarction and other myocardial diseases, and the assessment is often performed using cardiac magnetic resonance (CMR) sequences. In this study, we propose a fully automated approach using deep convolutional neural networks (CNN) for cardiac pathology segmentation, including left ventricular (LV) blood pool, right ventricular blood pool, LV normal myocardium, LV myocardial edema (ME) and LV myocardial scars (MS). The input to the network consists of three CMR sequences, namely, late gadolinium enhancement (LGE), T2 and balanced steady state free precession (bSSFP). The proposed approach utilized the data provided by the MyoPS challenge hosted by MICCAI 2020 in conjunction with STACOM. The training set for the CNN model consists of images acquired from 25 cases, and the gold standard labels are provided by trained raters and validated by radiologists. The proposed approach introduces a data augmentation module, linear encoder and decoder module and a network module to increase the number of training samples and improve the prediction accuracy for LV ME and MS. The proposed approach is evaluated by the challenge organizers with a test set including 20 cases and achieves a mean dice score of $46.8\%$ for LV MS and $55.7\%$ for LV ME+MS

Xiaoran Zhang, Hexiang Dong, Di Gao et al.

Image registration algorithms can be generally categorized into two groups: non-rigid and rigid. Recently, many deep learning-based algorithms employ a neural net to characterize non-rigid image registration function. However, do they always perform better? In this study, we compare the state-of-art deep learning-based non-rigid registration approach with rigid registration approach. The data is generated from Kaggle Dog vs Cat Competition \url{https://www.kaggle.com/c/dogs-vs-cats/} and we test the algorithms' performance on rigid transformation including translation, rotation, scaling, shearing and pixelwise non-rigid transformation. The Voxelmorph is trained on rigidset and nonrigidset separately for comparison and we also add a gaussian blur layer to its original architecture to improve registration performance. The best quantitative results in both root-mean-square error (RMSE) and mean absolute error (MAE) metrics for rigid registration are produced by SimpleElastix and non-rigid registration by Voxelmorph. We select representative samples for visual assessment.