Wenjun Xia

Ziyuan Yang, Wenjun Xia, Zexin Lu et al.

Computed tomography (CT) is of great importance in clinical practice due to its powerful ability to provide patients' anatomical information without any invasive inspection, but its potential radiation risk is raising people's concerns. Deep learning-based methods are considered promising in CT reconstruction, but these network models are usually trained with the measured data obtained from specific scanning protocol and need to centralizedly collect large amounts of data, which will lead to serious data domain shift, and privacy concerns. To relieve these problems, in this paper, we propose a hypernetwork-based federated learning method for personalized CT imaging, dubbed as HyperFed. The basic assumption of HyperFed is that the optimization problem for each institution can be divided into two parts: the local data adaption problem and the global CT imaging problem, which are implemented by an institution-specific hypernetwork and a global-sharing imaging network, respectively. The purpose of global-sharing imaging network is to learn stable and effective common features from different institutions. The institution-specific hypernetwork is carefully designed to obtain hyperparameters to condition the global-sharing imaging network for personalized local CT reconstruction. Experiments show that HyperFed achieves competitive performance in CT reconstruction compared with several other state-of-the-art methods. It is believed as a promising direction to improve CT imaging quality and achieve personalized demands of different institutions or scanners without privacy data sharing. The codes will be released at https://github.com/Zi-YuanYang/HyperFed.

Wenjun Xia, Hongming Shan, Ge Wang et al.

Since 2016, deep learning (DL) has advanced tomographic imaging with remarkable successes, especially in low-dose computed tomography (LDCT) imaging. Despite being driven by big data, the LDCT denoising and pure end-to-end reconstruction networks often suffer from the black box nature and major issues such as instabilities, which is a major barrier to apply deep learning methods in low-dose CT applications. An emerging trend is to integrate imaging physics and model into deep networks, enabling a hybridization of physics/model-based and data-driven elements. %This type of hybrid methods has become increasingly influential. In this paper, we systematically review the physics/model-based data-driven methods for LDCT, summarize the loss functions and training strategies, evaluate the performance of different methods, and discuss relevant issues and future directions.

Wenjun Xia, Wenxiang Cong, Ge Wang

Sparse-view computed tomography (CT) can be used to reduce radiation dose greatly but is suffers from severe image artifacts. Recently, the deep learning based method for sparse-view CT reconstruction has attracted a major attention. However, neural networks often have a limited ability to remove the artifacts when they only work in the image domain. Deep learning-based sinogram processing can achieve a better anti-artifact performance, but it inevitably requires feature maps of the whole image in a video memory, which makes handling large-scale or three-dimensional (3D) images rather challenging. In this paper, we propose a patch-based denoising diffusion probabilistic model (DDPM) for sparse-view CT reconstruction. A DDPM network based on patches extracted from fully sampled projection data is trained and then used to inpaint down-sampled projection data. The network does not require paired full-sampled and down-sampled data, enabling unsupervised learning. Since the data processing is patch-based, the deep learning workflow can be distributed in parallel, overcoming the memory problem of large-scale data. Our experiments show that the proposed method can effectively suppress few-view artifacts while faithfully preserving textural details.

Wenjun Xia, Yongyi Shi, Chuang Niu et al.

Computed tomography (CT) involves a patient's exposure to ionizing radiation. To reduce the radiation dose, we can either lower the X-ray photon count or down-sample projection views. However, either of the ways often compromises image quality. To address this challenge, here we introduce an iterative reconstruction algorithm regularized by a diffusion prior. Drawing on the exceptional imaging prowess of the denoising diffusion probabilistic model (DDPM), we merge it with a reconstruction procedure that prioritizes data fidelity. This fusion capitalizes on the merits of both techniques, delivering exceptional reconstruction results in an unsupervised framework. To further enhance the efficiency of the reconstruction process, we incorporate the Nesterov momentum acceleration technique. This enhancement facilitates superior diffusion sampling in fewer steps. As demonstrated in our experiments, our method offers a potential pathway to high-definition CT image reconstruction with minimized radiation.

Yongyi Shi, Wenjun Xia, Ge Wang et al.

Lowering radiation dose per view and utilizing sparse views per scan are two common CT scan modes, albeit often leading to distorted images characterized by noise and streak artifacts. Blind image quality assessment (BIQA) strives to evaluate perceptual quality in alignment with what radiologists perceive, which plays an important role in advancing low-dose CT reconstruction techniques. An intriguing direction involves developing BIQA methods that mimic the operational characteristic of the human visual system (HVS). The internal generative mechanism (IGM) theory reveals that the HVS actively deduces primary content to enhance comprehension. In this study, we introduce an innovative BIQA metric that emulates the active inference process of IGM. Initially, an active inference module, implemented as a denoising diffusion probabilistic model (DDPM), is constructed to anticipate the primary content. Then, the dissimilarity map is derived by assessing the interrelation between the distorted image and its primary content. Subsequently, the distorted image and dissimilarity map are combined into a multi-channel image, which is inputted into a transformer-based image quality evaluator. Remarkably, by exclusively utilizing this transformer-based quality evaluator, we won the second place in the MICCAI 2023 low-dose computed tomography perceptual image quality assessment grand challenge. Leveraging the DDPM-derived primary content, our approach further improves the performance on the challenge dataset.

Wenjun Xia, Hsin Wu Tseng, Chuang Niu et al.

Breast cancer is the most prevalent cancer among women worldwide, and early detection is crucial for reducing its mortality rate and improving quality of life. Dedicated breast computed tomography (CT) scanners offer better image quality than mammography and tomosynthesis in general but at higher radiation dose. To enable breast CT for cancer screening, the challenge is to minimize the radiation dose without compromising image quality, according to the ALARA principle (as low as reasonably achievable). Over the past years, deep learning has shown remarkable successes in various tasks, including low-dose CT especially few-view CT. Currently, the diffusion model presents the state of the art for CT reconstruction. To develop the first diffusion model-based breast CT reconstruction method, here we report innovations to address the large memory requirement for breast cone-beam CT reconstruction and high computational cost of the diffusion model. Specifically, in this study we transform the cutting-edge Denoising Diffusion Probabilistic Model (DDPM) into a parallel framework for sub-volume-based sparse-view breast CT image reconstruction in projection and image domains. This novel approach involves the concurrent training of two distinct DDPM models dedicated to processing projection and image data synergistically in the dual domains. Our experimental findings reveal that this method delivers competitive reconstruction performance at half to one-third of the standard radiation doses. This advancement demonstrates an exciting potential of diffusion-type models for volumetric breast reconstruction at high-resolution with much-reduced radiation dose and as such hopefully redefines breast cancer screening and diagnosis.

Wenjun Xia, Qing Lyu, Ge Wang

Low-dose computed tomography (LDCT) is an important topic in the field of radiology over the past decades. LDCT reduces ionizing radiation-induced patient health risks but it also results in a low signal-to-noise ratio (SNR) and a potential compromise in the diagnostic performance. In this paper, to improve the LDCT denoising performance, we introduce the conditional denoising diffusion probabilistic model (DDPM) and show encouraging results with a high computational efficiency. Specifically, given the high sampling cost of the original DDPM model, we adapt the fast ordinary differential equation (ODE) solver for a much-improved sampling efficiency. The experiments show that the accelerated DDPM can achieve 20x speedup without compromising image quality.

Chuang Niu, Wenjun Xia, Hongming Shan et al.

Self-supervised learning (SSL) has emerged as a crucial technique in image processing, encoding, and understanding, especially for developing today's vision foundation models that utilize large-scale datasets without annotations to enhance various downstream tasks. This study introduces a novel SSL approach, Information-Maximized Soft Variable Discretization (IMSVD), for image representation learning. Specifically, IMSVD softly discretizes each variable in the latent space, enabling the estimation of their probability distributions over training batches and allowing the learning process to be directly guided by information measures. Motivated by the MultiView assumption, we propose an information-theoretic objective function to learn transform-invariant, non-travail, and redundancy-minimized representation features. We then derive a joint-cross entropy loss function for self-supervised image representation learning, which theoretically enjoys superiority over the existing methods in reducing feature redundancy. Notably, our non-contrastive IMSVD method statistically performs contrastive learning. Extensive experimental results demonstrate the effectiveness of IMSVD on various downstream tasks in terms of both accuracy and efficiency. Thanks to our variable discretization, the embedding features optimized by IMSVD offer unique explainability at the variable level. IMSVD has the potential to be adapted to other learning paradigms. Our code is publicly available at https://github.com/niuchuangnn/IMSVD.

Abuobaida M. Khair, Wenjing Jiang, Yousuf Babiker M. Osman et al.

This study presents a hybrid deep learning framework, the Vision Transformer with Residual Feature Network (VRF-Net), for recovering high-resolution system matrices in Magnetic Particle Imaging (MPI). MPI resolution often suffers from downsampling and coil sensitivity variations. VRF-Net addresses these challenges by combining transformer-based global attention with residual convolutional refinement, enabling recovery of both large-scale structures and fine details. To reflect realistic MPI conditions, the system matrix is degraded using a dual-stage downsampling strategy. Training employed paired-image super-resolution on the public Open MPI dataset and a simulated dataset incorporating variable coil sensitivity profiles. For system matrix recovery on the Open MPI dataset, VRF-Net achieved nRMSE = 0.403, pSNR = 39.08 dB, and SSIM = 0.835 at 2x scaling, and maintained strong performance even at challenging scale 8x (pSNR = 31.06 dB, SSIM = 0.717). For the simulated dataset, VRF-Net achieved nRMSE = 4.44, pSNR = 28.52 dB, and SSIM = 0.771 at 2x scaling, with stable performance at higher scales. On average, it reduced nRMSE by 88.2%, increased pSNR by 44.7%, and improved SSIM by 34.3% over interpolation and CNN-based methods. In image reconstruction of Open MPI phantoms, VRF-Net further reduced reconstruction error to nRMSE = 1.79 at 2x scaling, while preserving structural fidelity (pSNR = 41.58 dB, SSIM = 0.960), outperforming existing methods. These findings demonstrate that VRF-Net enables sharper, artifact-free system matrix recovery and robust image reconstruction across multiple scales, offering a promising direction for future in vivo applications.

Anthony Zhang, Mahmut Gokmen, Dennis Hein et al.

The Poisson Flow Consistency Model (PFCM) is a consistency-style model based on the robust Poisson Flow Generative Model++ (PFGM++) which has achieved success in unconditional image generation and CT image denoising. Yet the PFCM can only be trained in distillation which limits the potential of the PFCM in many data modalities. The objective of this research was to create a method to train the PFCM in isolation called Poisson Flow Consistency Training (PFCT). The perturbation kernel was leveraged to remove the pretrained PFGM++, and the sinusoidal discretization schedule and Beta noise distribution were introduced in order to facilitate adaptability and improve sample quality. The model was applied to the task of low dose computed tomography image denoising and improved the low dose image in terms of LPIPS and SSIM. It also displayed similar denoising effectiveness as models like the Consistency Model. PFCT is established as a valid method of training the PFCM from its effectiveness in denoising CT images, showing potential with competitive results to other generative models. Further study is needed in the precise optimization of PFCT and in its applicability to other generative modeling tasks. The framework of PFCT creates more flexibility for the ways in which a PFCM can be created and can be applied to the field of generative modeling.

Wenjun Xia, Chuang Niu, Ge Wang

Computed tomography (CT) is a major medical imaging modality. Clinical CT scenarios, such as low-dose screening, sparse-view scanning, and metal implants, often lead to severe noise and artifacts in reconstructed images, requiring improved reconstruction techniques. The introduction of deep learning has significantly advanced CT image reconstruction. However, obtaining paired training data remains rather challenging due to patient motion and other constraints. Although deep learning methods can still perform well with approximately paired data, they inherently carry the risk of hallucination due to data inconsistencies and model instability. In this paper, we integrate the data fidelity with the state-of-the-art generative AI model, referred to as the Poisson flow generative model (PFGM) with a generalized version PFGM++, and propose a novel CT framework: Flow-Oriented Reconstruction Conditioning Engine (FORCE). In our experiments, the proposed method shows superior performance in various CT imaging tasks, outperforming existing unsupervised reconstruction approaches.

Chenyu Shen, Wenjun Xia, Hongwei Ye et al.

Positron emission tomography (PET) reconstruction has become an ill-posed inverse problem due to low-count projection data, and a robust algorithm is urgently required to improve imaging quality. Recently, the deep image prior (DIP) has drawn much attention and has been successfully applied in several image restoration tasks, such as denoising and inpainting, since it does not need any labels (reference image). However, overfitting is a vital defect of this framework. Hence, many methods have been proposed to mitigate this problem, and DeepRED is a typical representation that combines DIP and regularization by denoising (RED). In this article, we leverage DeepRED from a Bayesian perspective to reconstruct PET images from a single corrupted sinogram without any supervised or auxiliary information. In contrast to the conventional denoisers customarily used in RED, a DnCNN-like denoiser, which can add an adaptive constraint to DIP and facilitate the computation of derivation, is employed. Moreover, to further enhance the regularization, Gaussian noise is injected into the gradient updates, deriving a Markov chain Monte Carlo (MCMC) sampler. Experimental studies on brain and whole-body datasets demonstrate that our proposed method can achieve better performance in terms of qualitative and quantitative results compared to several classic and state-of-the-art methods.

Zhiwen Wang, Wenjun Xia, Zexin Lu et al.

Magnetic resonance imaging (MRI) acquisition, reconstruction, and segmentation are usually processed independently in the conventional practice of MRI workflow. It is easy to notice that there are significant relevances among these tasks and this procedure artificially cuts off these potential connections, which may lead to losing clinically important information for the final diagnosis. To involve these potential relations for further performance improvement, a sequential multi-task joint learning network model is proposed to train a combined end-to-end pipeline in a differentiable way, aiming at exploring the mutual influence among those tasks simultaneously. Our design consists of three cascaded modules: 1) deep sampling pattern learning module optimizes the $k$-space sampling pattern with predetermined sampling rate; 2) deep reconstruction module is dedicated to reconstructing MR images from the undersampled data using the learned sampling pattern; 3) deep segmentation module encodes MR images reconstructed from the previous module to segment the interested tissues. The proposed model retrieves the latently interactive and cyclic relations among those tasks, from which each task will be mutually beneficial. The proposed framework is verified on MRB dataset, which achieves superior performance on other SOTA methods in terms of both reconstruction and segmentation.

Qingchao Zhang, Mehrdad Alvandipour, Wenjun Xia et al.

We propose a provably convergent method, called Efficient Learned Descent Algorithm (ELDA), for low-dose CT (LDCT) reconstruction. ELDA is a highly interpretable neural network architecture with learned parameters and meanwhile retains convergence guarantee as classical optimization algorithms. To improve reconstruction quality, the proposed ELDA also employs a new non-local feature mapping and an associated regularizer. We compare ELDA with several state-of-the-art deep image methods, such as RED-CNN and Learned Primal-Dual, on a set of LDCT reconstruction problems. Numerical experiments demonstrate improvement of reconstruction quality using ELDA with merely 19 layers, suggesting the promising performance of ELDA in solution accuracy and parameter efficiency.

Tao Wang, Wenjun Xia, Zexin Lu et al.

Due to the presence of metallic implants, the imaging quality of computed tomography (CT) would be heavily degraded. With the rapid development of deep learning, several network models have been proposed for metal artifact reduction (MAR). Since the dual-domain MAR methods can leverage the hybrid information from both sinogram and image domains, they have significantly improved the performance compared to single-domain methods. However,current dual-domain methods usually operate on both domains in a specific order, which implicitly imposes a certain priority prior into MAR and may ignore the latent information interaction between both domains. To address this problem, in this paper, we propose a novel interactive dualdomain parallel network for CT MAR, dubbed as IDOLNet. Different from existing dual-domain methods, the proposed IDOL-Net is composed of two modules. The disentanglement module is utilized to generate high-quality prior sinogram and image as the complementary inputs. The follow-up refinement module consists of two parallel and interactive branches that simultaneously operate on image and sinogram domain, fully exploiting the latent information interaction between both domains. The simulated and clinical results demonstrate that the proposed IDOL-Net outperforms several state-of-the-art models in both qualitative and quantitative aspects.

Zexin Lu, Wenjun Xia, Yongqiang Huang et al.

Lowering the radiation dose in computed tomography (CT) can greatly reduce the potential risk to public health. However, the reconstructed images from the dose-reduced CT or low-dose CT (LDCT) suffer from severe noise, compromising the subsequent diagnosis and analysis. Recently, convolutional neural networks have achieved promising results in removing noise from LDCT images; the network architectures used are either handcrafted or built on top of conventional networks such as ResNet and U-Net. Recent advance on neural network architecture search (NAS) has proved that the network architecture has a dramatic effect on the model performance, which indicates that current network architectures for LDCT may be sub-optimal. Therefore, in this paper, we make the first attempt to apply NAS to LDCT and propose a multi-scale and multi-level NAS for LDCT denoising, termed MANAS. On the one hand, the proposed MANAS fuses features extracted by different scale cells to capture multi-scale image structural details. On the other hand, the proposed MANAS can search a hybrid cell- and network-level structure for better performance. Extensively experimental results on three different dose levels demonstrate that the proposed MANAS can achieve better performance in terms of preserving image structural details than several state-of-the-art methods. In addition, we also validate the effectiveness of the multi-scale and multi-level architecture for LDCT denoising.

Tao Wang, Wenjun Xia, Yongqiang Huang et al.

Metal implants can heavily attenuate X-rays in computed tomography (CT) scans, leading to severe artifacts in reconstructed images, which significantly jeopardize image quality and negatively impact subsequent diagnoses and treatment planning. With the rapid development of deep learning in the field of medical imaging, several network models have been proposed for metal artifact reduction (MAR) in CT. Despite the encouraging results achieved by these methods, there is still much room to further improve performance. In this paper, a novel Dual-domain Adaptive-scaling Non-local network (DAN-Net) for MAR. We correct the corrupted sinogram using adaptive scaling first to preserve more tissue and bone details as a more informative input. Then, an end-to-end dual-domain network is adopted to successively process the sinogram and its corresponding reconstructed image generated by the analytical reconstruction layer. In addition, to better suppress the existing artifacts and restrain the potential secondary artifacts caused by inaccurate results of the sinogram-domain network, a novel residual sinogram learning strategy and nonlocal module are leveraged in the proposed network model. In the experiments, the proposed DAN-Net demonstrates performance competitive with several state-of-the-art MAR methods in both qualitative and quantitative aspects.

Yi Zhang, Hu Chen, Wenjun Xia et al.

Compressed sensing (CS) computed tomography has been proven to be important for several clinical applications, such as sparse-view computed tomography (CT), digital tomosynthesis and interior tomography. Traditional compressed sensing focuses on the design of handcrafted prior regularizers, which are usually image-dependent and time-consuming. Inspired by recently proposed deep learning-based CT reconstruction models, we extend the state-of-the-art LEARN model to a dual-domain version, dubbed LEARN++. Different from existing iteration unrolling methods, which only involve projection data in the data consistency layer, the proposed LEARN++ model integrates two parallel and interactive subnetworks to perform image restoration and sinogram inpainting operations on both the image and projection domains simultaneously, which can fully explore the latent relations between projection data and reconstructed images. The experimental results demonstrate that the proposed LEARN++ model achieves competitive qualitative and quantitative results compared to several state-of-the-art methods in terms of both artifact reduction and detail preservation.

Xiang Chen, Wenjun Xia, Yan Liu et al.

Spectral computed tomography (CT) can reconstruct spectral images from different energy bins using photon counting detectors (PCDs). However, due to the limited photons and counting rate in the corresponding spectral fraction, the reconstructed spectral images usually suffer from severe noise. In this paper, a fourth-order nonlocal tensor decomposition model for spectral CT image reconstruction (FONT-SIR) method is proposed. Similar patches are collected in both spatial and spectral dimensions simultaneously to form the basic tensor unit. Additionally, principal component analysis (PCA) is applied to extract latent features from the patches for a robust and efficient similarity measure. Then, low-rank and sparsity decomposition is performed on the produced fourth-order tensor unit, and the weighted nuclear norm and total variation (TV) norm are used to enforce the low-rank and sparsity constraints, respectively. The alternating direction method of multipliers (ADMM) is adopted to optimize the objective function. The experimental results with our proposed FONT-SIR demonstrates a superior qualitative and quantitative performance for both simulated and real data sets relative to several state-of-the-art methods, in terms of noise suppression and detail preservation.

Wenjun Xia, Zexin Lu, Yongqiang Huang et al.

Current mainstream of CT reconstruction methods based on deep learning usually needs to fix the scanning geometry and dose level, which will significantly aggravate the training cost and need more training data for clinical application. In this paper, we propose a parameter-dependent framework (PDF) which trains data with multiple scanning geometries and dose levels simultaneously. In the proposed PDF, the geometry and dose level are parameterized and fed into two multi-layer perceptrons (MLPs). The MLPs are leveraged to modulate the feature maps of CT reconstruction network, which condition the network outputs on different scanning geometries and dose levels. The experiments show that our proposed method can obtain competing performance similar to the original network trained with specific geometry and dose level, which can efficiently save the extra training cost for multiple scanning geometries and dose levels.

Peng Bao, Wenjun Xia, Kang Yang et al.

Over the past few years, dictionary learning (DL)-based methods have been successfully used in various image reconstruction problems. However, traditional DL-based computed tomography (CT) reconstruction methods are patch-based and ignore the consistency of pixels in overlapped patches. In addition, the features learned by these methods always contain shifted versions of the same features. In recent years, convolutional sparse coding (CSC) has been developed to address these problems. In this paper, inspired by several successful applications of CSC in the field of signal processing, we explore the potential of CSC in sparse-view CT reconstruction. By directly working on the whole image, without the necessity of dividing the image into overlapped patches in DL-based methods, the proposed methods can maintain more details and avoid artifacts caused by patch aggregation. With predetermined filters, an alternating scheme is developed to optimize the objective function. Extensive experiments with simulated and real CT data were performed to validate the effectiveness of the proposed methods. Qualitative and quantitative results demonstrate that the proposed methods achieve better performance than several existing state-of-the-art methods.

Peng Bao, Wenjun Xia, Kang Yang et al.

Traditional dictionary learning based CT reconstruction methods are patch-based and the features learned with these methods often contain shifted versions of the same features. To deal with these problems, the convolutional sparse coding (CSC) has been proposed and introduced into various applications. In this paper, inspired by the successful applications of CSC in the field of signal processing, we propose a novel sparse-view CT reconstruction method based on CSC with gradient regularization on feature maps. By directly working on whole image, which need not to divide the image into overlapped patches like dictionary learning based methods, the proposed method can maintain more details and avoid the artifacts caused by patch aggregation. Experimental results demonstrate that the proposed method has better performance than several existing algorithms in both qualitative and quantitative aspects.