NeRP: Implicit Neural Representation Learning with Prior Embedding for Sparsely Sampled Image Reconstruction

Image reconstruction is an inverse problem that solves for a computational image based on sampled sensor measurement. Sparsely sampled image reconstruction poses addition challenges due to limited measurements. In this work, we propose an implicit Neural Representation learning methodology with Prior embedding (NeRP) to reconstruct a computational image from sparsely sampled measurements. The method differs fundamentally from previous deep learning-based image reconstruction approaches in that NeRP exploits the internal information in an image prior, and the physics of the sparsely sampled measurements to produce a representation of the unknown subject. No large-scale data is required to train the NeRP except for a prior image and sparsely sampled measurements. In addition, we demonstrate that NeRP is a general methodology that generalizes to different imaging modalities such as CT and MRI. We also show that NeRP can robustly capture the subtle yet significant image changes required for assessing tumor progression.

A Geometry-Informed Deep Learning Framework for Ultra-Sparse 3D Tomographic Image Reconstruction

Deep learning affords enormous opportunities to augment the armamentarium of biomedical imaging, albeit its design and implementation have potential flaws. Fundamentally, most deep learning models are driven entirely by data without consideration of any prior knowledge, which dramatically increases the complexity of neural networks and limits the application scope and model generalizability. Here we establish a geometry-informed deep learning framework for ultra-sparse 3D tomographic image reconstruction. We introduce a novel mechanism for integrating geometric priors of the imaging system. We demonstrate that the seamless inclusion of known priors is essential to enhance the performance of 3D volumetric computed tomography imaging with ultra-sparse sampling. The study opens new avenues for data-driven biomedical imaging and promises to provide substantially improved imaging tools for various clinical imaging and image-guided interventions.

DualNorm-UNet: Incorporating Global and Local Statistics for Robust Medical Image Segmentation

Batch Normalization (BN) is one of the key components for accelerating network training, and has been widely adopted in the medical image analysis field. However, BN only calculates the global statistics at the batch level, and applies the same affine transformation uniformly across all spatial coordinates, which would suppress the image contrast of different semantic structures. In this paper, we propose to incorporate the semantic class information into normalization layers, so that the activations corresponding to different regions (i.e., classes) can be modulated differently. We thus develop a novel DualNorm-UNet, to concurrently incorporate both global image-level statistics and local region-wise statistics for network normalization. Specifically, the local statistics are integrated by adaptively modulating the activations along different class regions via the learned semantic masks in the normalization layer. Compared with existing methods, our approach exploits semantic knowledge at normalization and yields more discriminative features for robust segmentation results. More importantly, our network demonstrates superior abilities in capturing domain-invariant information from multiple domains (institutions) of medical data. Extensive experiments show that our proposed DualNorm-UNet consistently improves the performance on various segmentation tasks, even in the face of more complex and variable data distributions. Code is available at https://github.com/lambert-x/DualNorm-Unet.

TransCT: Dual-path Transformer for Low Dose Computed Tomography

Low dose computed tomography (LDCT) has attracted more and more attention in routine clinical diagnosis assessment, therapy planning, etc., which can reduce the dose of X-ray radiation to patients. However, the noise caused by low X-ray exposure degrades the CT image quality and then affects clinical diagnosis accuracy. In this paper, we train a transformer-based neural network to enhance the final CT image quality. To be specific, we first decompose the noisy LDCT image into two parts: high-frequency (HF) and low-frequency (LF) compositions. Then, we extract content features (X_{L_c}) and latent texture features (X_{L_t}) from the LF part, as well as HF embeddings (X_{H_f}) from the HF part. Further, we feed X_{L_t} and X_{H_f} into a modified transformer with three encoders and decoders to obtain well-refined HF texture features. After that, we combine these well-refined HF texture features with the pre-extracted X_{L_c} to encourage the restoration of high-quality LDCT images with the assistance of piecewise reconstruction. Extensive experiments on Mayo LDCT dataset show that our method produces superior results and outperforms other methods.

Region-specific Dictionary Learning-based Low-dose Thoracic CT Reconstruction

This paper presents a dictionary learning-based method with region-specific image patches to maximize the utility of the powerful sparse data processing technique for CT image reconstruction. Considering heterogeneous distributions of image features and noise in CT, region-specific customization of dictionaries is utilized in iterative reconstruction. Thoracic CT images are partitioned into several regions according to their structural and noise characteristics. Dictionaries specific to each region are then learned from the segmented thoracic CT images and applied to subsequent image reconstruction of the region. Parameters for dictionary learning and sparse representation are determined according to the structural and noise properties of each region. The proposed method results in better performance than the conventional reconstruction based on a single dictionary in recovering structures and suppressing noise in both simulation and human CT imaging. Quantitatively, the simulation study shows maximum improvement of image quality for the whole thorax can achieve 4.88% and 11.1% in terms of the Structure-SIMilarity (SSIM) and Root-Mean-Square Error (RMSE) indices, respectively. For human imaging data, it is found that the structures in the lungs and heart can be better recovered, while simultaneously decreasing noise around the vertebra effectively. The proposed strategy takes into account inherent regional differences inside of the reconstructed object and leads to improved images. The method can be readily extended to CT imaging of other anatomical regions and other applications.

Deep Sinogram Completion with Image Prior for Metal Artifact Reduction in CT Images

Computed tomography (CT) has been widely used for medical diagnosis, assessment, and therapy planning and guidance. In reality, CT images may be affected adversely in the presence of metallic objects, which could lead to severe metal artifacts and influence clinical diagnosis or dose calculation in radiation therapy. In this paper, we propose a generalizable framework for metal artifact reduction (MAR) by simultaneously leveraging the advantages of image domain and sinogram domain-based MAR techniques. We formulate our framework as a sinogram completion problem and train a neural network (SinoNet) to restore the metal-affected projections. To improve the continuity of the completed projections at the boundary of metal trace and thus alleviate new artifacts in the reconstructed CT images, we train another neural network (PriorNet) to generate a good prior image to guide sinogram learning, and further design a novel residual sinogram learning strategy to effectively utilize the prior image information for better sinogram completion. The two networks are jointly trained in an end-to-end fashion with a differentiable forward projection (FP) operation so that the prior image generation and deep sinogram completion procedures can benefit from each other. Finally, the artifact-reduced CT images are reconstructed using the filtered backward projection (FBP) from the completed sinogram. Extensive experiments on simulated and real artifacts data demonstrate that our method produces superior artifact-reduced results while preserving the anatomical structures and outperforms other MAR methods.

Self-supervised Feature Learning via Exploiting Multi-modal Data for Retinal Disease Diagnosis

The automatic diagnosis of various retinal diseases from fundus images is important to support clinical decision-making. However, developing such automatic solutions is challenging due to the requirement of a large amount of human-annotated data. Recently, unsupervised/self-supervised feature learning techniques receive a lot of attention, as they do not need massive annotations. Most of the current self-supervised methods are analyzed with single imaging modality and there is no method currently utilize multi-modal images for better results. Considering that the diagnostics of various vitreoretinal diseases can greatly benefit from another imaging modality, e.g., FFA, this paper presents a novel self-supervised feature learning method by effectively exploiting multi-modal data for retinal disease diagnosis. To achieve this, we first synthesize the corresponding FFA modality and then formulate a patient feature-based softmax embedding objective. Our objective learns both modality-invariant features and patient-similarity features. Through this mechanism, the neural network captures the semantically shared information across different modalities and the apparent visual similarity between patients. We evaluate our method on two public benchmark datasets for retinal disease diagnosis. The experimental results demonstrate that our method clearly outperforms other self-supervised feature learning methods and is comparable to the supervised baseline.

Multi-Domain Image Completion for Random Missing Input Data

Multi-domain data are widely leveraged in vision applications taking advantage of complementary information from different modalities, e.g., brain tumor segmentation from multi-parametric magnetic resonance imaging (MRI). However, due to possible data corruption and different imaging protocols, the availability of images for each domain could vary amongst multiple data sources in practice, which makes it challenging to build a universal model with a varied set of input data. To tackle this problem, we propose a general approach to complete the random missing domain(s) data in real applications. Specifically, we develop a novel multi-domain image completion method that utilizes a generative adversarial network (GAN) with a representational disentanglement scheme to extract shared skeleton encoding and separate flesh encoding across multiple domains. We further illustrate that the learned representation in multi-domain image completion could be leveraged for high-level tasks, e.g., segmentation, by introducing a unified framework consisting of image completion and segmentation with a shared content encoder. The experiments demonstrate consistent performance improvement on three datasets for brain tumor segmentation, prostate segmentation, and facial expression image completion respectively.

A Mean-Field Theory for Learning the Schönberg Measure of Radial Basis Functions

We develop and analyze a projected particle Langevin optimization method to learn the distribution in the Sch\"{o}nberg integral representation of the radial basis functions from training samples. More specifically, we characterize a distributionally robust optimization method with respect to the Wasserstein distance to optimize the distribution in the Sch\"{o}nberg integral representation. To provide theoretical performance guarantees, we analyze the scaling limits of a projected particle online (stochastic) optimization method in the mean-field regime. In particular, we prove that in the scaling limits, the empirical measure of the Langevin particles converges to the law of a reflected It\^{o} diffusion-drift process. Moreover, the drift is also a function of the law of the underlying process. Using It\^{o} lemma for semi-martingales and Grisanov's change of measure for the Wiener processes, we then derive a Mckean-Vlasov type partial differential equation (PDE) with Robin boundary conditions that describes the evolution of the empirical measure of the projected Langevin particles in the mean-field regime. In addition, we establish the existence and uniqueness of the steady-state solutions of the derived PDE in the weak sense. We apply our learning approach to train radial kernels in the kernel locally sensitive hash (LSH) functions, where the training data-set is generated via a $k$-mean clustering method on a small subset of data-base. We subsequently apply our kernel LSH with a trained kernel for image retrieval task on MNIST data-set, and demonstrate the efficacy of our kernel learning approach. We also apply our kernel learning approach in conjunction with the kernel support vector machines (SVMs) for classification of benchmark data-sets.