Xuanyu Tian

Qing Wu, Chenhe Du, Xuanyu Tian et al.

Motion correction (MoCo) in radial MRI is a particularly challenging problem due to the unpredictability of subject movement. Current state-of-the-art (SOTA) MoCo algorithms often rely on extensive high-quality MR images to pre-train neural networks, which constrains the solution space and leads to outstanding image reconstruction results. However, the need for large-scale datasets significantly increases costs and limits model generalization. In this work, we propose Moner, an unsupervised MoCo method that jointly reconstructs artifact-free MR images and estimates accurate motion from undersampled, rigid motion-corrupted k-space data, without requiring any training data. Our core idea is to leverage the continuous prior of implicit neural representation (INR) to constrain this ill-posed inverse problem, facilitating optimal solutions. Specifically, we integrate a quasi-static motion model into the INR, granting its ability to correct subject's motion. To stabilize model optimization, we reformulate radial MRI reconstruction as a back-projection problem using the Fourier-slice theorem. Additionally, we propose a novel coarse-to-fine hash encoding strategy, significantly enhancing MoCo accuracy. Experiments on multiple MRI datasets show our Moner achieves performance comparable to SOTA MoCo techniques on in-domain data, while demonstrating significant improvements on out-of-domain data. The code is available at: https://github.com/iwuqing/Moner

Chenhe Du, Qing Wu, Xuanyu Tian et al.

3D medical imaging is in high demand and essential for clinical diagnosis and scientific research. Currently, diffusion models (DMs) have become an effective tool for medical imaging reconstruction thanks to their ability to learn rich, high-quality data priors. However, learning the 3D data distribution with DMs in medical imaging is challenging, not only due to the difficulties in data collection but also because of the significant computational burden during model training. A common compromise is to train the DMs on 2D data priors and reconstruct stacked 2D slices to address 3D medical inverse problems. However, the intrinsic randomness of diffusion sampling causes severe inter-slice discontinuities of reconstructed 3D volumes. Existing methods often enforce continuity regularizations along the z-axis, which introduces sensitive hyper-parameters and may lead to over-smoothing results. In this work, we revisit the origin of stochasticity in diffusion sampling and introduce Inter-Slice Consistent Stochasticity (ISCS), a simple yet effective strategy that encourages interslice consistency during diffusion sampling. Our key idea is to control the consistency of stochastic noise components during diffusion sampling, thereby aligning their sampling trajectories without adding any new loss terms or optimization steps. Importantly, the proposed ISCS is plug-and-play and can be dropped into any 2D trained diffusion based 3D reconstruction pipeline without additional computational cost. Experiments on several medical imaging problems show that our method can effectively improve the performance of medical 3D imaging problems based on 2D diffusion models. Our findings suggest that controlling inter-slice stochasticity is a principled and practically attractive route toward high-fidelity 3D medical imaging with 2D diffusion priors. The code is available at: https://github.com/duchenhe/ISCS

Xuanyu Tian, Qing Wu, Hongjiang Wei et al.

Fluorescence microscopy is a key driver to promote discoveries of biomedical research. However, with the limitation of microscope hardware and characteristics of the observed samples, the fluorescence microscopy images are susceptible to noise. Recently, a few self-supervised deep learning (DL) denoising methods have been proposed. However, the training efficiency and denoising performance of existing methods are relatively low in real scene noise removal. To address this issue, this paper proposed self-supervised image denoising method Noise2SR (N2SR) to train a simple and effective image denoising model based on single noisy observation. Our Noise2SR denoising model is designed for training with paired noisy images of different dimensions. Benefiting from this training strategy, Noise2SR is more efficiently self-supervised and able to restore more image details from a single noisy observation. Experimental results of simulated noise and real microscopy noise removal show that Noise2SR outperforms two blind-spot based self-supervised deep learning image denoising methods. We envision that Noise2SR has the potential to improve more other kind of scientific imaging quality.

Lixuan Chen, Xuanyu Tian, Jiangjie Wu et al.

Magnetic Resonance Imaging (MRI) stands as a powerful modality in clinical diagnosis. However, it is known that MRI faces challenges such as long acquisition time and vulnerability to motion-induced artifacts. Despite the success of many existing motion correction algorithms, there has been limited research focused on correcting motion artifacts on the estimated coil sensitivity maps for fast MRI reconstruction. Existing methods might suffer from severe performance degradation due to error propagation resulting from the inaccurate coil sensitivity maps estimation. In this work, we propose to jointly estimate the motion parameters and coil sensitivity maps for under-sampled MRI reconstruction, referred to as JSMoCo. However, joint estimation of motion parameters and coil sensitivities results in a highly ill-posed inverse problem due to an increased number of unknowns. To address this, we introduce score-based diffusion models as powerful priors and leverage the MRI physical principles to efficiently constrain the solution space for this optimization problem. Specifically, we parameterize the rigid motion as three trainable variables and model coil sensitivity maps as polynomial functions. Leveraging the physical knowledge, we then employ Gibbs sampler for joint estimation, ensuring system consistency between sensitivity maps and desired images, avoiding error propagation from pre-estimated sensitivity maps to the reconstructed images. We conduct comprehensive experiments to evaluate the performance of JSMoCo on the fastMRI dataset. The results show that our method is capable of reconstructing high-quality MRI images from sparsely-sampled k-space data, even affected by motion. It achieves this by accurately estimating both motion parameters and coil sensitivities, effectively mitigating motion-related challenges during MRI reconstruction.

Chenhe Du, Xuanyu Tian, Qing Wu et al.

Plug-and-Play diffusion prior (PnPDP) frameworks have emerged as a powerful paradigm for solving imaging inverse problems by treating pretrained generative models as modular priors. However, we identify a critical flaw in prevailing PnP solvers (e.g., based on HQS or Proximal Gradient): they function as memoryless operators, updating estimates solely based on instantaneous gradients. This lack of historical tracking inevitably leads to non-vanishing steady-state bias, where the reconstruction fails to strictly satisfy physical measurements under heavy corruption. To resolve this, we propose Dual-Coupled PnP Diffusion, which restores the classical dual variable to provide integral feedback, theoretically guaranteeing asymptotic convergence to the exact data manifold. However, this rigorous geometric coupling introduces a secondary challenge: the accumulated dual residuals exhibit spectrally colored, structured artifacts that violate the Additive White Gaussian Noise (AWGN) assumption of diffusion priors, causing severe hallucinations. To bridge this gap, we introduce Spectral Homogenization (SH), a frequency-domain adaptation mechanism that modulates these structured residuals into statistically compliant pseudo-AWGN inputs. This effectively aligns the solver's rigorous optimization trajectory with the denoiser's valid statistical manifold. Extensive experiments on CT and MRI reconstruction demonstrate that our approach resolves the bias-hallucination trade-off, achieving state-of-the-art fidelity with significantly accelerated convergence.

Muyu Liu, Chenhe Du, Xuanyu Tian et al.

Low-field (LF) magnetic resonance imaging (MRI) democratizes access to diagnostic imaging but is fundamentally limited by low signal-to-noise ratio and significant tissue contrast distortion due to field-dependent relaxation dynamics. Reconstructing high-field (HF) quality images from LF data is a blind inverse problem, severely challenged by the scarcity of paired training data and the unknown, non-linear contrast transformation operator. Existing zero-shot methods, which assume simplified linear degradation, often fail to recover authentic tissue contrast. In this paper, we propose DACT(Diffusion-Based Adaptive Contrast Transport), a novel zero-shot framework that restores HF-quality images without paired supervision. DACT synergizes a pre-trained HF diffusion prior to ensure anatomical fidelity with a physically-informed adaptive forward model. Specifically, we introduce a differentiable Sinkhorn optimal transport module that explicitly models and corrects the intensity distribution shift between LF and HF domains during the reverse diffusion process. This allows the framework to dynamically learn the intractable contrast mapping while preserving topological consistency. Extensive experiments on simulated and real clinical LF datasets demonstrate that DACT achieves state-of-the-art performance, yielding reconstructions with superior structural detail and correct tissue contrast.

Muyu Liu, Xuanyu Tian, Chenhe Du et al.

Recovering radiometric fidelity from unknown dynamic range compression (UDRC), such as low-light enhancement and HDR reconstruction, is a challenging blind inverse problem, due to the unknown forward model and irreversible information loss introduced by compression. To address this challenge, we first identify monotonicity as the fundamental physical invariant shared across UDRC tasks. Leveraging this insight, we introduce the \textbf{cascaded monotonic Bernstein} (CaMB) operator to parameterize the unknown forward model. CaMB enforces monotonicity as a hard architectural inductive bias, constraining optimization to physically consistent mappings and enabling robust and stable operator estimation. We further integrate CaMB with a plug-and-play diffusion framework, proposing \textbf{CaMB-Diff}. Within this framework, the diffusion model serves as a powerful geometric prior for structural and semantic recovery, while CaMB explicitly models and corrects radiometric distortions through a physically grounded forward operator. Extensive experiments on a variety of zero-shot UDRC tasks, including low-light enhancement, low-field MRI enhancement, and HDR reconstruction, demonstrate that CaMB-Diff significantly outperforms state-of-the-art zero-shot baselines in terms of both signal fidelity and physical consistency. Moreover, we empirically validate the effectiveness of the proposed CaMB parameterization in accurately modeling the unknown forward operator.

Xuanyu Tian, Lixuan Chen, Qing Wu et al.

Cardiac magnetic resonance (CMR) imaging is widely used to characterize cardiac morphology and function. To accelerate CMR imaging, various methods have been proposed to recover high-quality spatiotemporal CMR images from highly undersampled k-t space data. However, current CMR reconstruction techniques either fail to achieve satisfactory image quality or are restricted by the scarcity of ground truth data, leading to limited applicability in clinical scenarios. In this work, we proposed MoCo-INR, a new unsupervised method that integrates implicit neural representations (INR) with the conventional motion-compensated (MoCo) framework. Using explicit motion modeling and the continuous prior of INRs, MoCo-INR can produce accurate cardiac motion decomposition and high-quality CMR reconstruction. Furthermore, we introduce a new INR network architecture tailored to the CMR problem, which significantly stabilizes model optimization. Experiments on retrospective (simulated) datasets demonstrate the superiority of MoCo-INR over state-of-the-art methods, achieving fast convergence and fine-detailed reconstructions at ultra-high acceleration factors (e.g., 20x in VISTA sampling). Additionally, evaluations on prospective (real-acquired) free-breathing CMR scans highlight the clinical practicality of MoCo-INR for real-time imaging. Several ablation studies further confirm the effectiveness of the critical components of MoCo-INR.

Xuanyu Tian, Lixuan Chen, Qing Wu et al.

Emerging unsupervised implicit neural representation (INR) methods, such as NeRP, NeAT, and SCOPE, have shown great potential to address sparse-view computed tomography (SVCT) inverse problems. Although these INR-based methods perform well in relatively dense SVCT reconstructions, they struggle to achieve comparable performance to supervised methods in sparser SVCT scenarios. They are prone to being affected by noise, limiting their applicability in real clinical settings. Additionally, current methods have not fully explored the use of image domain priors for solving SVCsT inverse problems. In this work, we demonstrate that imperfect reconstruction results can provide effective image domain priors for INRs to enhance performance. To leverage this, we introduce Self-prior embedding neural representation (Spener), a novel unsupervised method for SVCT reconstruction that integrates iterative reconstruction algorithms. During each iteration, Spener extracts local image prior features from the previous iteration and embeds them to constrain the solution space. Experimental results on multiple CT datasets show that our unsupervised Spener method achieves performance comparable to supervised state-of-the-art (SOTA) methods on in-domain data while outperforming them on out-of-domain datasets. Moreover, Spener significantly improves the performance of INR-based methods in handling SVCT with noisy sinograms. Our code is available at https://github.com/MeijiTian/Spener.

Qing Wu, Xuanyu Tian, Chenhe Du et al.

Implicit neural representations (INRs) have emerged as a powerful paradigm for medical imaging via physics-informed unsupervised learning. Classical INRs optimize an entire network from scratch for each subject, leading to inefficient training and suboptimal imaging quality. Recent initialization-based approaches attempt to inject population priors into pre-trained networks, yet they rely on high-quality images and often suffer from catastrophic forgetting during fine-tuning. We present DisINR, a novel INR framework that explicitly disentangles shared and subject-specific representations. DisINR introduces a shared encoder-decoder pair and subject-specific encoders, whose features are jointly decoded for image reconstruction. By integrating differentiable forward models, it pre-trains the shared modules directly from limited raw measurements, removing the need for pre-acquired high-quality images. During test-time adaptation, only the subject-specific encoder is optimized, while the shared pair remains frozen, effectively preserving learned priors. Extensive evaluations on three representative medical imaging tasks show that DisINR significantly outperforms state-of-the-art INRs in both reconstruction accuracy and efficiency.

Chenhe Du, Xiyue Lin, Qing Wu et al.

Limited-angle and sparse-view computed tomography (LACT and SVCT) are crucial for expanding the scope of X-ray CT applications. However, they face challenges due to incomplete data acquisition, resulting in diverse artifacts in the reconstructed CT images. Emerging implicit neural representation (INR) techniques, such as NeRF, NeAT, and NeRP, have shown promise in under-determined CT imaging reconstruction tasks. However, the unsupervised nature of INR architecture imposes limited constraints on the solution space, particularly for the highly ill-posed reconstruction task posed by LACT and ultra-SVCT. In this study, we introduce the Diffusion Prior Driven Neural Representation (DPER), an advanced unsupervised framework designed to address the exceptionally ill-posed CT reconstruction inverse problems. DPER adopts the Half Quadratic Splitting (HQS) algorithm to decompose the inverse problem into data fidelity and distribution prior sub-problems. The two sub-problems are respectively addressed by INR reconstruction scheme and pre-trained score-based diffusion model. This combination first injects the implicit image local consistency prior from INR. Additionally, it effectively augments the feasibility of the solution space for the inverse problem through the generative diffusion model, resulting in increased stability and precision in the solutions. We conduct comprehensive experiments to evaluate the performance of DPER on LACT and ultra-SVCT reconstruction with two public datasets (AAPM and LIDC), an in-house clinical COVID-19 dataset and a public raw projection dataset created by Mayo Clinic. The results show that our method outperforms the state-of-the-art reconstruction methods on in-domain datasets, while achieving significant performance improvements on out-of-domain (OOD) datasets.

Jiawen Yang, Yihui Cao, Xuanyu Tian et al.

Orthognathic surgery is a crucial intervention for correcting dentofacial skeletal deformities to enhance occlusal functionality and facial aesthetics. Accurate postoperative facial appearance prediction remains challenging due to the complex nonlinear interactions between skeletal movements and facial soft tissue. Existing biomechanical, parametric models and deep-learning approaches either lack computational efficiency or fail to fully capture these intricate interactions. To address these limitations, we propose Neural Implicit Craniofacial Model (NICE) which employs implicit neural representations for accurate anatomical reconstruction and surgical outcome prediction. NICE comprises a shape module, which employs region-specific implicit Signed Distance Function (SDF) decoders to reconstruct the facial surface, maxilla, and mandible, and a surgery module, which employs region-specific deformation decoders. These deformation decoders are driven by a shared surgical latent code to effectively model the complex, nonlinear biomechanical response of the facial surface to skeletal movements, incorporating anatomical prior knowledge. The deformation decoders output point-wise displacement fields, enabling precise modeling of surgical outcomes. Extensive experiments demonstrate that NICE outperforms current state-of-the-art methods, notably improving prediction accuracy in critical facial regions such as lips and chin, while robustly preserving anatomical integrity. This work provides a clinically viable tool for enhanced surgical planning and patient consultation in orthognathic procedures.

Tianqi Yu, Xuanyu Tian, Jiawen Yang et al.

Biplanar X-ray imaging is widely used in health screening, postoperative rehabilitation evaluation of orthopedic diseases, and injury surgery due to its rapid acquisition, low radiation dose, and straightforward setup. However, 3D volume reconstruction from only two orthogonal projections represents a profoundly ill-posed inverse problem, owing to the intrinsic lack of depth information and irreducible ambiguities in soft-tissue visualization. Some existing methods can reconstruct skeletal structures and Computed Tomography (CT) volumes, they often yield incomplete bone geometry, imprecise tissue boundaries, and a lack of anatomical realism, thereby limiting their clinical utility in scenarios such as surgical planning and postoperative assessment. In this study, we introduce SPIDER, a novel supervised framework designed to reconstruct CT volumes from biplanar X-ray images. SPIDER incorporates tissue structure as prior (e.g., anatomical segmentation) into an implicit neural representation decoder in the form of joint supervision through a unified encoder-decoder architecture. This design enables the model to jointly learn image intensities and anatomical structures in a pixel-aligned fashion. To address the challenges posed by sparse input and structural ambiguity, SPIDER directly embeds anatomical constraints into the reconstruction process, thereby enhancing structural continuity and reducing soft-tissue artifacts. We conduct comprehensive experiments on clinical head CT datasets and show that SPIDER generates anatomically accurate reconstructions from only two projections. Furthermore, our approach demonstrates strong potential in downstream segmentation tasks, underscoring its utility in personalized treatment planning and image-guided surgical navigation.

Xuanyu Tian, Zhuoya Dong, Xiyue Lin et al.

High-resolution electron microscopy (HREM) imaging technique is a powerful tool for directly visualizing a broad range of materials in real-space. However, it faces challenges in denoising due to ultra-low signal-to-noise ratio (SNR) and scarce data availability. In this work, we propose Noise2SR, a zero-shot self-supervised learning (ZS-SSL) denoising framework for HREM. Within our framework, we propose a super-resolution (SR) based self-supervised training strategy, incorporating the Random Sub-sampler module. The Random Sub-sampler is designed to generate approximate infinite noisy pairs from a single noisy image, serving as an effective data augmentation in zero-shot denoising. Noise2SR trains the network with paired noisy images of different resolutions, which is conducted via SR strategy. The SR-based training facilitates the network adopting more pixels for supervision, and the random sub-sampling helps compel the network to learn continuous signals enhancing the robustness. Meanwhile, we mitigate the uncertainty caused by random-sampling by adopting minimum mean squared error (MMSE) estimation for the denoised results. With the distinctive integration of training strategy and proposed designs, Noise2SR can achieve superior denoising performance using a single noisy HREM image. We evaluate the performance of Noise2SR in both simulated and real HREM denoising tasks. It outperforms state-of-the-art ZS-SSL methods and achieves comparable denoising performance with supervised methods. The success of Noise2SR suggests its potential for improving the SNR of images in material imaging domains.