A novel deep learning-based magnetic resonance imaging reconstruction pipeline was designed to address fundamental image quality limitations of conventional reconstruction to provide high-resolution, low-noise MR images. This pipeline's unique aims were to convert truncation artifact into improved image sharpness while jointly denoising images to improve image quality. This new approach, now commercially available at AIR Recon DL (GE Healthcare, Waukesha, WI), includes a deep convolutional neural network (CNN) to aid in the reconstruction of raw data, ultimately producing clean, sharp images. Here we describe key features of this pipeline and its CNN, characterize its performance in digital reference objects, phantoms, and in-vivo, and present sample images and protocol optimization strategies that leverage image quality improvement for reduced scan time. This new deep learning-based reconstruction pipeline represents a powerful new tool to increase the diagnostic and operational performance of an MRI scanner.
Recovering a high dynamic range (HDR) image from a single low dynamic range (LDR) input image is challenging due to missing details in under-/over-exposed regions caused by quantization and saturation of camera sensors. In contrast to existing learning-based methods, our core idea is to incorporate the domain knowledge of the LDR image formation pipeline into our model. We model the HDRto-LDR image formation pipeline as the (1) dynamic range clipping, (2) non-linear mapping from a camera response function, and (3) quantization. We then propose to learn three specialized CNNs to reverse these s…
Microsoft Research（微软研究院）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；University of Minnesota（明尼苏达大学）；Stanford University（斯坦福大学）
Deep learning techniques have emerged as a promising approach to highly accelerated MRI. However, recent reconstruction challenges have shown several drawbacks in current deep learning approaches, including the loss of fine image details even using models that perform well in terms of global quality metrics. In this study, we propose an end-to-end deep learning framework for image reconstruction and pathology detection, which enables a clinically aware evaluation of deep learning reconstruction quality. The solution is demonstrated for a use case in detecting meniscal tears on knee MRI studies…
Purpose of this study was to evaluate the effect of a robust magnetic resonance reconstruction pipeline equipped with a deep convolutional neural network on the overall image quality, in terms of Gibbs artifact reduction, and SNR improvement. Sixteen (16) healthy volunteers enrolled in this study and were imaged at 3T. Representative images of each image series that were reconstructed through the pipeline that leverages a deep learning (DL) algorithm were retrospectively benchmarked against corresponding images reconstructed through a conventional pipeline. DL-reconstructed images showed signi…
Imperial College London（帝国理工学院）；King’s College London（伦敦国王学院）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）；Technical University of Munich（慕尼黑工业大学）
We present CortexODE, a deep learning framework for cortical surface reconstruction. CortexODE leverages neural ordinary differential equations (ODEs) to deform an input surface into a target shape by learning a diffeomorphic flow. The trajectories of the points on the surface are modeled as ODEs, where the derivatives of their coordinates are parameterized via a learnable Lipschitz-continuous deformation network. This provides theoretical guarantees for the prevention of self-intersections. CortexODE can be integrated to an automatic learning-based pipeline, which reconstructs cortical surfac…
Biomedical image reconstruction research has been developed for more than five decades, giving rise to various techniques such as central and filtered back projection. With the rise of deep learning technology, biomedical image reconstruction field has undergone a massive paradigm shift from analytical and iterative methods to deep learning methods To drive scientific discussion on advanced deep learning techniques for biomedical image reconstruction, a workshop focusing on deep biomedical image reconstruction, MLMIR, is introduced and is being held yearly since 2018. This survey paper is aime…
Washington University in St. Louis（圣路易斯华盛顿大学）；Mallinckrodt Institute of Radiology（马林克罗特放射学研究所）
One of the key limitations in conventional deep learning based image reconstruction is the need for registered pairs of training images containing a set of high-quality groundtruth images. This paper addresses this limitation by proposing a novel unsupervised deep registration-augmented reconstruction method (U-Dream) for training deep neural nets to reconstruct high-quality images by directly mapping pairs of unregistered and artifact-corrupted images. The ability of U-Dream to circumvent the need for accurately registered data makes it widely applicable to many biomedical image reconstructio…
This paper proposes a novel learning based high-dynamic-range (HDR) reconstruction method using a polarization camera. We utilize a previous observation that polarization filters with different orientations can attenuate natural light differently, and we treat the multiple images acquired by the polarization camera as a set acquired under different exposure times, to introduce the development of solutions for the HDR reconstruction problem. We propose a deep HDR reconstruction framework with a feature masking mechanism that uses polarimetric cues available from the polarization camera, called …
Tel-Aviv University（特拉维夫大学）；Technion – Israel Institute of Technology（以色列理工学院）
We present DeepISP, a full end-to-end deep neural model of the camera image signal processing (ISP) pipeline. Our model learns a mapping from the raw low-light mosaiced image to the final visually compelling image and encompasses low-level tasks such as demosaicing and denoising as well as higher-level tasks such as color correction and image adjustment. The training and evaluation of the pipeline were performed on a dedicated dataset containing pairs of low-light and well-lit images captured by a Samsung S7 smartphone camera in both raw and processed JPEG formats. The proposed solution achiev…
Biomedical Imaging Research Institute, Cedars-Sinai Medical Center（西达赛奈医疗中心生物医学影像研究所）；UCLA（加州大学洛杉矶分校）
Non-Cartesian sampling with subspace-constrained image reconstruction is a popular approach to dynamic MRI, but slow iterative reconstruction limits its clinical application. Data-consistent (DC) deep learning can accelerate reconstruction with good image quality, but has not been formulated for non-Cartesian subspace imaging. In this study, we propose a DC non-Cartesian deep subspace learning framework for fast, accurate dynamic MR image reconstruction. Four novel DC formulations are developed and evaluated: two gradient decent approaches, a directly solved approach, and a conjugate gradient …
Harvard Medical School（哈佛医学院）；Boston Children’s Hospital（波士顿儿童医院）
Fast data acquisition in Magnetic Resonance Imaging (MRI) is vastly in demand and scan time directly depends on the number of acquired k-space samples. Conventional MRI reconstruction methods for fast MRI acquisition mostly relied on different regularizers which represent analytical models of sparsity. However, recent data-driven methods based on deep learning has resulted in promising improvements in image reconstruction algorithms. In this paper, we propose a deep plug-and-play prior framework for parallel MRI reconstruction problems which utilize a deep neural network (DNN) as an advanced d…
Nanchang University（南昌大学）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）
Purpose: Although recent deep energy-based generative models (EBMs) have shown encouraging results in many image generation tasks, how to take advantage of the self-adversarial cogitation in deep EBMs to boost the performance of Magnetic Resonance Imaging (MRI) reconstruction is still desired. Methods: With the successful application of deep learning in a wide range of MRI reconstruction, a line of emerging research involves formulating an optimization-based reconstruction method in the space of a generative model. Leveraging this, a novel regularization strategy is introduced in this article …
Fast data acquisition in Magnetic Resonance Imaging (MRI) is vastly in demand and scan time directly depends on the number of acquired k-space samples. The data-driven methods based on deep neural networks have resulted in promising improvements, compared to the conventional methods, in image reconstruction algorithms. The connection between deep neural network and Ordinary Differential Equation (ODE) has been observed and studied recently. The studies show that different residual networks can be interpreted as Euler discretization of an ODE. In this paper, we propose an ODE-based deep network…
X-ray computed tomography (CT) is widely used in clinical practice. The involved ionizing X-ray radiation, however, could increase cancer risk. Hence, the reduction of the radiation dose has been an important topic in recent years. Few-view CT image reconstruction is one of the main ways to minimize radiation dose and potentially allow a stationary CT architecture. In this paper, we propose a deep encoder-decoder adversarial reconstruction (DEAR) network for 3D CT image reconstruction from few-view data. Since the artifacts caused by few-view reconstruction appear in 3D instead of 2D geometry,…
University of Florida（佛罗里达大学）；Georgia State University（佐治亚州立大学）
We propose a novel deep neural network architecture by mapping the robust proximal gradient scheme for fast image reconstruction in parallel MRI (pMRI) with regularization function trained from data. The proposed network learns to adaptively combine the multi-coil images from incomplete pMRI data into a single image with homogeneous contrast, which is then passed to a nonlinear encoder to efficiently extract sparse features of the image. Unlike most of existing deep image reconstruction networks, our network does not require knowledge of sensitivity maps, which can be difficult to estimate acc…
Rensselaer Polytechnic Institute（伦斯勒理工学院）；Southeast University（东南大学）；Fudan University（复旦大学）；University of Massachusetts Lowell（马萨诸塞大学洛厄尔分校）；The University of Hong Kong（香港大学）
Tomographic image reconstruction with deep learning is an emerging field, but a recent landmark study reveals that several deep reconstruction networks are unstable for computed tomography (CT) and magnetic resonance imaging (MRI). Specifically, three kinds of instabilities were reported: (1) strong image artefacts from tiny perturbations, (2) small features missing in a deeply reconstructed image, and (3) decreased imaging performance with increased input data. On the other hand, compressed sensing (CS) inspired reconstruction methods do not suffer from these instabilities because of their bu…
National University of Singapore（新加坡国立大学）；University of Cambridge（剑桥大学）
Indirect image registration is a promising technique to improve image reconstruction quality by providing a shape prior for the reconstruction task. In this paper, we propose a novel hybrid method that seeks to reconstruct high quality images from few measurements whilst requiring low computational cost. With this purpose, our framework intertwines indirect registration and reconstruction tasks is a single functional. It is based on two major novelties. Firstly, we introduce a model based on deep nets to solve the indirect registration problem, in which the inversion and registration mappings …
The integration of Time-of-Flight (TOF) information in the reconstruction process of Positron Emission Tomography (PET) yields improved image properties. However, implementing the cutting-edge model-based deep learning methods for TOF-PET reconstruction is challenging due to the substantial memory requirements. In this study, we present a novel model-based deep learning approach, LMPDNet, for TOF-PET reconstruction from list-mode data. We address the issue of real-time parallel computation of the projection matrix for list-mode data, and propose an iterative model-based module that utilizes a …
College of Computer Science, Sichuan University（四川大学计算机学院）；College of Electrical Engineering, Sichuan University（四川大学电气工程学院）；Chengdu University of Information Technology（成都信息工程大学）
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, aimin…
Facebook AI Research（Facebook人工智能研究）；fastMRI team（fastMRI团队）
Deep learning approaches to accelerated MRI take a matrix of sampled Fourier-space lines as input and produce a spatial image as output. In this work we show that by careful choice of the offset used in the sampling procedure, the symmetries in k-space can be better exploited, producing higher quality reconstructions than given by standard equally-spaced samples or randomized samples motivated by compressed sensing.
Self-supervised Deep Unrolled Reconstruction Using Regularization by Denoising
State University of New York at Buffalo（纽约州立大学布法罗分校）；Cleveland Clinic（克利夫兰诊所）；Paul C. Lauterbur Research Center for Biomedical Imaging, SIAT, CAS（中国科学院深圳先进技术研究院保罗·C·劳特伯生物医学成像研究中心）
United Imaging Intelligence（联影智能）；UIH America, Inc.（联影美国公司）；United Imaging Healthcare（联影医疗）
Retrospectively gated cine (retro-cine) MRI is the clinical standard for cardiac functional analysis. Deep learning (DL) based methods have been proposed for the reconstruction of highly undersampled MRI data and show superior image quality and magnitude faster reconstruction time than CS-based methods. Nevertheless, it remains unclear whether DL reconstruction is suitable for cardiac function analysis. To address this question, in this study we evaluate and compare the cardiac functional values (EDV, ESV and EF for LV and RV, respectively) obtained from highly accelerated MRI acquisition usin…
Khalifa University of Science and Technology（哈利法科学技术大学）
This article proposes and documents a machine-learning framework and tutorial for classifying images using mobile phones. Compared to computers, the performance of deep learning model performance degrades when deployed on a mobile phone and requires a systematic approach to find a model that performs optimally on both computers and mobile phones. By following the proposed pipeline, which consists of various computational tools, simple procedural recipes, and technical considerations, one can bring the power of deep learning medical image classification to mobile devices, potentially unlocking …
Lawrence Livermore National Laboratory（劳伦斯利弗莫尔国家实验室）
Reconstruction of few-view x-ray Computed Tomography (CT) data is a highly ill-posed problem. It is often used in applications that require low radiation dose in clinical CT, rapid industrial scanning, or fixed-gantry CT. Existing analytic or iterative algorithms generally produce poorly reconstructed images, severely deteriorated by artifacts and noise, especially when the number of x-ray projections is considerably low. This paper presents a deep network-driven approach to address extreme few-view CT by incorporating convolutional neural network-based inference into state-of-the-art iterativ…
Generative AI Pipeline for Interactive Prompt-driven 2D-to-3D Vascular Reconstruction for Fontan Geometries from Contrast-Enhanced X-Ray Fluoroscopy Imaging
University of Pittsburgh（匹兹堡大学）；The American Association for Thoracic Surgery (AATS)（美国胸外科医师协会）
DEALing with Image Reconstruction: Deep Attentive Least Squares
Biomedical Imaging Group, EPFL Lausanne, Switzerland（瑞士洛桑联邦理工学院生物医学成像组）；Institute for Virtual Morphology, Johannes Kepler University Linz（林茨约翰内斯·开普勒大学虚拟形态学研究所）；Faculty of Mathematics, TU Chemnitz, Germany（德国 Chemnitz 工业大学数学学院）
The main focus of this work is a novel framework for the joint reconstruction and segmentation of parallel MRI (PMRI) brain data. We introduce an image domain deep network for calibrationless recovery of undersampled PMRI data. The proposed approach is the deep-learning (DL) based generalization of local low-rank based approaches for uncalibrated PMRI recovery including CLEAR [6]. Since the image domain approach exploits additional annihilation relations compared to k-space based approaches, we expect it to offer improved performance. To minimize segmentation errors resulting from undersamplin…
Current deep learning based detection models tackle detection and segmentation tasks by casting them to pixel or patch-wise classification. To automate the initial mass lesion detection and segmentation on the whole mammographic images and avoid the computational redundancy of patch-based and sliding window approaches, the conditional generative adversarial network (cGAN) was used in this study. Subsequently, feeding the detected regions to the trained densely connected network (DenseNet), the binary classification of benign versus malignant was predicted. We used a combination of publicly ava…
In this work, we investigate the application of deep learning methods for computed tomography in the context of having a low-data regime. As motivation, we review some of the existing approaches and obtain quantitative results after training them with different amounts of data. We find that the learned primal-dual has an outstanding performance in terms of reconstruction quality and data efficiency. However, in general, end-to-end learned methods have two issues: a) lack of classical guarantees in inverse problems and b) lack of generalization when not trained with enough data. To overcome the…
While Model Based Iterative Reconstruction (MBIR) of CT scans has been shown to have better image quality than Filtered Back Projection (FBP), its use has been limited by its high computational cost. More recently, deep convolutional neural networks (CNN) have shown great promise in both denoising and reconstruction applications. In this research, we propose a fast reconstruction algorithm, which we call Deep Learning MBIR (DL-MBIR), for approximating MBIR using a deep residual neural network. The DL-MBIR method is trained to produce reconstructions that approximate true MBIR images using a 16…
Brain MRI segmentation results should always undergo a quality control (QC) process, since automatic segmentation tools can be prone to errors. In this work, we propose two deep learning-based architectures for performing QC automatically. First, we used generative adversarial networks for creating error maps that highlight the locations of segmentation errors. Subsequently, a 3D convolutional neural network was implemented to predict segmentation quality. The present pipeline was shown to achieve promising results and, in particular, high sensitivity in both tasks.
Breast CT provides image volumes with isotropic resolution in high contrast, enabling detection of small calcification (down to a few hundred microns in size) and subtle density differences. Since breast is sensitive to x-ray radiation, dose reduction of breast CT is an important topic, and for this purpose, few-view scanning is a main approach. In this article, we propose a Deep Efficient End-to-end Reconstruction (DEER) network for few-view breast CT image reconstruction. The major merits of our network include high dose efficiency, excellent image quality, and low model complexity. By the d…
Shanghai Jiao Tong University（上海交通大学）；National University of Singapore（新加坡国立大学）；South China University of Technology（华南理工大学）
Low-dose CT (LDCT) imaging attracted a considerable interest for the reduction of the object's exposure to X-ray radiation. In recent years, supervised deep learning (DL) has been extensively studied for LDCT image reconstruction, which trains a network over a dataset containing many pairs of normal-dose and low-dose images. However, the challenge on collecting many such pairs in the clinical setup limits the application of such supervised-learning-based methods for LDCT image reconstruction in practice. Aiming at addressing the challenges raised by the collection of training dataset, this pap…
Paul C. Lauterbur Research Center for Biomedical Imaging（保罗·C·劳特伯生物医学成像研究中心）；Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences（中国科学院大学深圳先进技术学院）；University at Buffalo, the State University of New York（纽约州立大学布法罗分校）
Image reconstruction from undersampled k-space data has been playing an important role for fast MRI. Recently, deep learning has demonstrated tremendous success in various fields and also shown potential to significantly speed up MR reconstruction with reduced measurements. This article gives an overview of deep learning-based image reconstruction methods for MRI. Three types of deep learning-based approaches are reviewed, the data-driven, model-driven and integrated approaches. The main structure of each network in three approaches is explained and the analysis of common parts of reviewed net…
Recent advances in photoacoustic (PA) imaging have enabled detailed images of microvascular structure and quantitative measurement of blood oxygenation or perfusion. Standard reconstruction methods for PA imaging are based on solving an inverse problem using appropriate signal and system models. For handheld scanners, however, the ill-posed conditions of limited detection view and bandwidth yield low image contrast and severe structure loss in most instances. In this paper, we propose a practical reconstruction method based on a deep convolutional neural network (CNN) to overcome those problem…
Low dose CT is of great interest in these days. Dose reduction raises noise level in projections and decrease image quality in reconstructions. Model based image reconstruction can combine statistical noise model together with prior knowledge into an Bayesian optimization problem so that significantly reduce noise and artefacts. In this work, we propose a model-base deep learning for CT reconstruction so that a reconstruction network can be trained with no ground-truth images needed. Instead of minimizing cost function for each image, the network learns to minimize an ensemble cost function fo…
United Imaging Intelligence（联影智能）；UIH America, Inc.（联影美国公司）；United Imaging Healthcare（上海联影医疗科技股份有限公司）
Multi-contrast MRI images provide complementary contrast information about the characteristics of anatomical structures and are commonly used in clinical practice. Recently, a multi-flip-angle (FA) and multi-echo GRE method (MULTIPLEX MRI) has been developed to simultaneously acquire multiple parametric images with just one single scan. However, it poses two challenges for MULTIPLEX to be used in the 3D high-resolution setting: a relatively long scan time and the huge amount of 3D multi-contrast data for reconstruction. Currently, no DL based method has been proposed for 3D MULTIPLEX data reco…
Deep unrolling is an emerging deep learning-based image reconstruction methodology that bridges the gap between model-based and purely deep learning-based image reconstruction methods. Although deep unrolling methods achieve state-of-the-art performance for imaging problems and allow the incorporation of the observation model into the reconstruction process, they do not provide any uncertainty information about the reconstructed image, which severely limits their use in practice, especially for safety-critical imaging applications. In this paper, we propose a learning-based image reconstructio…
