Unified Supervised-Unsupervised (SUPER) Learning for X-Ray CT Image Reconstruction

Low-dose CT reconstruction using dataset-free learning

Low-Dose computer tomography (LDCT) is an ideal alternative to reduce radiation risk in clinical applications. Although supervised-deep-learning-based reconstruction methods have demonstrated superior performance compared to conventional model-driven reconstruction algorithms, they require collecting massive pairs of low-dose and norm-dose CT images for neural network training, which limits their practical application in LDCT imaging. In this paper, we propose an unsupervised and training data-free learning reconstruction method for LDCT imaging that avoids the requirement for training data. The proposed method is a post-processing technique that aims to enhance the initial low-quality reconstruction results, and it reconstructs the high-quality images by neural work training that minimizes the ℓ1-norm distance between the CT measurements and their corresponding simulated sinogram data, as well as the total variation (TV) value of the reconstructed image. Moreover, the proposed method does not require to set the weights for both the data fidelity term and the plenty term. Experimental results on the AAPM challenge data and LoDoPab-CT data demonstrate that the proposed method is able to effectively suppress the noise and preserve the tiny structures. Also, these results demonstrate the rapid convergence and low computational cost of the proposed method. The source code is available at https://github.com/linfengyu77/IRLDCT.

Multi-layer clustering-based residual sparsifying transform for low-dose CT image reconstruction

PURPOSE

The recently proposed sparsifying transform (ST) models incur low computational cost and have been applied to medical imaging. Meanwhile, deep models with nested network structure reveal great potential for learning features in different layers. In this study, we propose a network-structured ST learning approach for X-ray computed tomography (CT), which we refer to as multi-layer clustering-based residual sparsifying transform (MCST) learning. The proposed MCST scheme learns multiple different unitary transforms in each layer by dividing each layer's input into several classes. We apply the MCST model to low-dose CT (LDCT) reconstruction by deploying the learned MCST model into the regularizer in penalized weighted least squares (PWLS) reconstruction.

METHODS

The proposed MCST model combines a multi-layer sparse representation structure with multiple clusters for the features in each layer that are modeled by a rich collection of transforms. We train the MCST model in an unsupervised manner via a block coordinate descent (BCD) algorithm. Since our method is patch-based, the training can be performed with a limited set of images. For CT image reconstruction, we devise a novel algorithm called PWLS-MCST by integrating the pre-learned MCST signal model with PWLS optimization.

RESULTS

We conducted LDCT reconstruction experiments on XCAT phantom data, Numerical Mayo Clinical CT dataset and "LDCT image and projection dataset" (Clinical LDCT dataset). We trained the MCST model with two (or three) layers and with five clusters in each layer. The learned transforms in the same layer showed rich features while additional information is extracted from representation residuals. Our simulation results and clinical results demonstrate that PWLS-MCST achieves better image reconstruction quality than the conventional filtered back-projection (FBP) method and PWLS with edge-preserving (EP) regularizer. It also outperformed recent advanced methods like PWLS with a learned multi-layer residual sparsifying transform (MARS) prior and PWLS with a union of learned transforms (ULTRA), especially for displaying clear edges and preserving subtle details.

CONCLUSIONS

In this work, a multi-layer sparse signal model with a nested network structure is proposed. We refer this novel model as the MCST model that exploits multi-layer residual maps to sparsify the underlying image and clusters the inputs in each layer for accurate sparsification. We presented a new PWLS framework with a learned MCST regularizer for LDCT reconstruction. Experimental results show that the proposed PWLS-MCST provides clearer reconstructions than several baseline methods. The code for PWLS-MCST is released at https://github.com/Xikai97/PWLS-MCST.

An optimized EBRSA-Bi LSTM model for highly undersampled rapid CT image reconstruction

COVID-19 has spread all over the world, causing serious panic around the globe. Chest computed tomography (CT) images are integral in confirming COVID positive patients. Several investigations were conducted to improve or maintain the image reconstruction quality for the sample image reconstruction. Deep learning (DL) methods have recently been proposed to achieve fast reconstruction, but many have focused on a single domain, such as the image domain of k-space. In this research, the highly under-sampled enhanced battle royale self-attention based bi-directional long short-term (EBRSA-bi LSTM) CT image reconstruction model is proposed to reconstruct the image from the under-sampled data. The research is adapted with two phases, namely, pre-processing and reconstruction. The extended cascaded filter (ECF) is proposed for image pre-processing and tends to suppress the noise and enhance the reconstruction accuracy. In the reconstruction model, the battle royale optimization (BrO) is intended to diminish the loss function of the reconstruction network model and weight updation. The proposed model is tested with two datasets, COVID-CT- and SARS-CoV-2 CT. The reconstruction accuracy of the proposed model with two datasets is 93.5 % and 97.7 %, respectively. Also, the image quality assessment parameters such as Peak-Signal to Noise Ratio (PSNR), Root Mean Square Error (RMSE) and Structural Similarity Index metric (SSIM) are evaluated, and it yields an outcome of (45 and 46 dB), (0.0026 and 0.0022) and (0.992, 0.996) with two datasets.

Physics-/Model-Based and Data-Driven Methods for Low-Dose Computed Tomography: A survey

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. 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.

Towards artificial intelligence to multi-omics characterization of tumor heterogeneity in esophageal cancer

Esophageal cancer is a unique and complex heterogeneous malignancy, with substantial tumor heterogeneity: at the cellular levels, tumors are composed of tumor and stromal cellular components; at the genetic levels, they comprise genetically distinct tumor clones; at the phenotypic levels, cells in distinct microenvironmental niches acquire diverse phenotypic features. This heterogeneity affects almost every process of esophageal cancer progression from onset to metastases and recurrence, etc. Intertumoral and intratumoral heterogeneity are major obstacles in the treatment of esophageal cancer, but also offer the potential to manipulate the heterogeneity themselves as a new therapeutic strategy. The high-dimensional, multi-faceted characterization of genomics, epigenomics, transcriptomics, proteomics, metabonomics, etc. of esophageal cancer has opened novel horizons for dissecting tumor heterogeneity. Artificial intelligence especially machine learning and deep learning algorithms, are able to make decisive interpretations of data from multi-omics layers. To date, artificial intelligence has emerged as a promising computational tool for analyzing and dissecting esophageal patient-specific multi-omics data. This review provides a comprehensive review of tumor heterogeneity from a multi-omics perspective. Especially, we discuss the novel techniques single-cell sequencing and spatial transcriptomics, which have revolutionized our understanding of the cell compositions of esophageal cancer and allowed us to determine novel cell types. We focus on the latest advances in artificial intelligence in integrating multi-omics data of esophageal cancer. Artificial intelligence-based multi-omics data integration computational tools exert a key role in tumor heterogeneity assessment, which will potentially boost the development of precision oncology in esophageal cancer.