Dr. Michael Zibulevsky
PILOT: Physics-Informed Learned Optimal Trajectories for accelerated MRI
Magnetic Resonance Imaging (MRI) has long been considered to be among “the gold standards” of diagnostic medical imaging. The long acquisition times, however, render MRI prone to motion artifacts, let alone their adverse contribution to the relatively high costs of MRI examination. Over the last few decades, multiple studies have focused on the development of both physical and post-processing methods for accelerated acquisition of MRI scans. These two approaches, however, have so far been addressed separately. On the other hand, recent works in optical computational imaging have demonstrated growing success of the concurrent learning-based design of data acquisition and image reconstruction schemes. Such schemes have already demonstrated substantial effectiveness, leading to considerably shorter acquisition times and improved quality of image reconstruction. Inspired by this initial success, in this work, we propose a novel approach to the learning of optimal schemes for conjoint acquisition and reconstruction of MRI scans, with the optimization, carried out simultaneously with respect to the time-efficiency of data acquisition and the quality of resulting reconstructions. To be of practical value, the schemes are encoded in the form of general k-space trajectories, whose associated magnetic gradients are constrained to obey a set of predefined hardware requirements (as defined in terms of, e.g., peak currents and maximum slew rates of magnetic gradients). With this proviso in mind, we propose a novel algorithm for the end-to-end training of a combined acquisition-reconstruction pipeline using a deep neural network with differentiable forward- and backpropagation operators. We also demonstrate the effectiveness of the proposed solution in application to both image reconstruction and image segmentation, reporting substantial improvements in terms of acceleration factors as well as the quality of these end tasks.
Learning beamforming in ultrasound imaging
Joint learning of Cartesian undersampling and reconstruction for accelerated MRI
Magnetic Resonance Imaging (MRI) is considered today the golden-standard modality for soft tissues. The long acquisition times, however, make it more prone to motion artifacts as well as contribute to the relatively high costs of this examination. Over the years, multiple studies concentrated on designing reduced measurement schemes and image reconstruction schemes for MRI, however, these problems have been so far addressed separately. On the other hand, recent works in optical computational imaging have demonstrated growing success of the simultaneous learning-based design of the acquisition and reconstruction schemes manifesting significant improvement in the reconstruction quality with a constrained time budget. Inspired by these successes, in this work, we propose to learn accelerated MR acquisition schemes (in the form of Cartesian trajectories) jointly with the image reconstruction operator. To this end, we propose an algorithm for training the combined acquisition-reconstruction pipeline end-to-end in a differentiable way. We demonstrate the significance of using the learned Cartesian trajectories at different speed up rates.
Self-supervised learning of inverse problem solvers in medical imaging
In the past few years, deep learning-based methods have demonstrated enormous success for solving inverse problems in medical imaging. In this work, we address the following question: Given a set of measurements obtained from real imaging experiments, what is the best way to use a learnable model and the physics of the modality to solve the inverse problem and reconstruct the latent image? Standard supervised learning based methods approach this problem by collecting data sets of known latent images and their corresponding measurements. However, these methods are often impractical due to the lack of availability of appropriately sized training sets, and, more generally, due to the inherent difficulty in measuring the “groundtruth” latent image. In light of this, we propose a self-supervised approach to training inverse models in medical imaging in the absence of aligned data. Our method only requiring access to the measurements and the forward model at training. We showcase its effectiveness on inverse problems arising in accelerated magnetic resonance imaging (MRI).
High frame-rate cardiac ultrasound imaging with deep learning
Cardiac ultrasound imaging requires a high frame rate in order to capture rapid motion. This can be achieved by multi-line acquisition (MLA), where several narrow-focused received lines are obtained from each wide-focused transmitted line. This shortens the acquisition time at the expense of introducing block artifacts. In this paper, we propose a data-driven learning-based approach to improve the MLA image quality. We train an end-to-end convolutional neural network on pairs of real ultrasound cardiac data, acquired through MLA and the corresponding single-line acquisition (SLA). The network achieves a significant improvement in image quality for both 5- and 7-line MLA resulting in a decorrelation measure similar to that of SLA while having the frame rate of MLA.
High quality ultrasonic multi-line transmission through deep learning
Frame rate is a crucial consideration in cardiac ultrasound imaging and 3D sonography. Several methods have been proposed in the medical ultrasound literature aiming at accelerating the image acquisition. In this paper, we consider one such method called multi-line transmission (MLT), in which several evenly separated focused beams are transmitted simultaneously. While MLT reduces the acquisition time, it comes at the expense of a heavy loss of contrast due to the interactions between the beams (cross-talk artifact). In this paper, we introduce a data-driven method to reduce the artifacts arising in MLT. To this end, we propose to train an end-to-end convolutional neural network consisting of correction layers followed by a constant apodization layer. The network is trained on pairs of raw data obtained through MLT and the corresponding single-line transmission (SLT) data. Experimental evaluation demonstrates signicant improvement both in the visual image quality and in objective measures such as contrast ratio and contrast-to-noise ratio, while preserving resolution unlike traditional apodization-based methods. We show that the proposed method is able to generalize
well across dierent patients and anatomies on real and phantom data.
Towards CT-quality ultrasound imaging using deep learning
The cost-effectiveness and practical harmlessness of ultra- sound imaging have made it one of the most widespread tools for medical diagnosis. Unfortunately, the beam-forming based image formation produces granular speckle noise, blur- ring, shading and other artifacts. To overcome these effects, the ultimate goal would be to reconstruct the tissue acoustic properties by solving a full wave propagation inverse prob- lem. In this work, we make a step towards this goal, using Multi-Resolution Convolutional Neural Networks (CNN). As a result, we are able to reconstruct CT-quality images from the reflected ultrasound radio-frequency(RF) data obtained by simulation from real CT scans of a human body. We also show that CNN is able to imitate existing computationally heavy despeckling methods, thereby saving orders of magni- tude in computations and making them amenable to real-time applications.
On separation of semitransparent dynamic images from static background
Presented here is the problem of recovering a dynamic image superimposed on a static background. Such a problem is ill-posed and may arise e.g. in imaging through semireflective media, in separation of an illumination image from a reflectance image, in imaging with diffraction phenomena, etc. In this work we study regularization of this problem in spirit of Total Variation and general sparsifying transformations.
Quasi maximum likelihood blind deconvolution: super- an sub-Gaussianity versus consistency
In this note we consider the problem of MIMO quasi maximum likelihood (QML) blind deconvolution. We examine two classes of estimators, which are commonly believed to be suitable for super- and sub-Gaussian sources. We state the consistency conditions and demonstrate a distribution, for which the studied estimators are unsuitable, in the sense that they are asymptotically unstable
Relative optimization for blind deconvolution
We propose a relative optimization framework for quasi-maximum likelihood (QML) blind deconvolution and the relative Newton method as its particular instance. The special Hessian structure allows fast Newton system construction and solution, resulting in a fast-convergent algorithm with iteration complexity comparable to that of gradient methods. We also propose the use of rational IIR restoration kernels, which constitute a richer family of filters than the traditionally used FIR kernels. We discuss different choices of non-linear functions suitable for deconvolution of super- and sub-Gaussian sources and formulate the conditions, under which the QML estimation is stable. Simulation results demonstrate the efficiency of the proposed methods.
Blind deconvolution of images using optimal sparse representations
The relative Newton algorithm, previously proposed for quasi-maximum likelihood blind source separation and blind deconvolution of one-dimensional signals is generalized for blind deconvolution of images. Smooth approximation of the absolute value is used in modeling the log probability density function, which is suitable for sparse sources. In addition, we propose a method of sparsification, which allows blind deconvolution of sources with arbitrary distribution, and show how to find optimal sparsifying transformations by training.
Unmixing tissues: sparse component analysis in multi-contrast MRI
We pose the problem of tissue classification in MRI as a blind source separation (BSS) problem and solve it by means of sparse component analysis (SCA). Assuming that most MR images can be sparsely represented, we consider their optimal sparse representation. Sparse components define a physically-meaningful feature space for classification. We demonstrate our approach on simulated and real multi-contrast MRI data. The proposed framework is general in that it is applicable to other modalities of medical imaging as well, whenever the linear mixing model is applicable.
Sparse ICA for blind separation of transmitted and reflected images
We address the problem of recovering a scene recorded through a semi-reflecting medium (i.e. planar lens), with a virtual reflected image being superimposed on the image of the scene transmitted through the semi-reflective lens. Recent studies propose imaging through a linear polarizer at several orientations to estimate the reflected and the transmitted components in the scene. In this stud,y we extend the sparse ICA (SPICA) technique and apply it to the problem of separating the image of the scene without having any a priori knowledge about its structure or statistics. Recent novel advances in the SPICA approach are discussed. Simulation and experimental results demonstrate the efficacy of the proposed methods.
Optimal sparse representations for blind source separation and blind deconvolution: a learning approach
We present a generic approach, which allows to adapt sparse blind deconvolution and blind source separation algorithms to arbitrary sources. The key idea is to bring the problem to the case in which the underlying sources are sparse by applying a sparsifying transformation on the mixtures. We present simulation results and show that such transformation can be found by training. Properties of the optimal sparsifying transformation are highlighted by an example with aerial images.
Fast relative Newton algorithm for blind deconvolution of images
We present an efficient Newton-like algorithm for quasi-maximum likelihood (QML) blind deconvolution of images. This algorithm exploits the sparse structure of the Hessian. An optimal distribution-shaping approach by means of sparsification allows one to use simple and convenient sparsity prior for processing of a wide range of natural images. Simulation results demonstrate the efficiency of the proposed method.
Blind source separation using block-coordinate relative Newton method
Presented here is a generalization of the relative Newton method, recently proposed for quasi maximum likelihood blind source separation. Special structure of the Hessian matrix allows performing block-coordinate Newton descent, which significantly reduces the algorithm computational complexity and boosts its performance. Simulations based on artificial and real data showed that the separation quality using the proposed algorithm is superior compared to other accepted blind source separation methods.
Blind source separation using the block-coordinate relative Newton method
Presented here is a generalization of the modified relative Newton method, recently proposed by Zibulevsky for quasi-maximum likelihood blind source separation. The special structure of the Hessian matrix allows to perform block-coordinate Newton descent, which significantly reduces the algorithm computational complexity and boosts its performance. Simulations based on artificial and real data show that the separation quality using the proposed algorithm outperforms other accepted blind source separation methods.
QML blind deconvolution: asymptotic analysis
Blind deconvolution is considered as a problem of quasi-maximum likelihood (QML) estimation of the restoration kernel. Simple closed-form expressions for the asymptotic estimation error are derived. The asymptotic performance bounds coincide with the Cramér-Rao bounds, when the true ML estimator is used. Conditions for asymptotic stability of the QML estimator are derived. Special cases when the estimator is super-efficient are discussed.
Optimal sparse representations for blind deconvolution of images
The relative Newton algorithm, previously proposed for quasi-maximum likelihood blind source separation and blind deconvolution of one-dimensional signals is generalized for blind deconvolution of images. Smooth approximation of the absolute value is used in modeling the log probability density function, which is suitable for sparse sources. We propose a method of sparsification, which allows blind deconvolution of sources with arbitrary distribution, and show how to find optimal sparsifying transformations by training.
Quasi maximum likelihood blind deconvolution of images acquired through scattering media
We address the problem of restoration of images obtained through a scattering medium. We present an efficient quasi-maximum likelihood blind deconvolution approach based on the fast relative Newton algorithm and optimal distribution shaping approach (sparsification), which allows to use simple and convenient sparsity prior for a wide class of images. Simulation results prove the efficiency of the proposed method.
Optimal nonlinear line-of-flight estimation in positron emission tomography
We consider detection of high-energy photons in PET using thick scintillation crystals. Parallax effect and multiple Compton interactions such crystals significantly reduce the accuracy of conventional detection methods. In order to estimate the photon line of flight based on photomultiplier responses, we use asymptotically optimal nonlinear techniques, implemented by feedforward and radial basis function (RBF) neural networks. Incorporation of information about angles of incidence of photons significantly improves the accuracy of estimation. The proposed estimators are fast enough to perform detection, using conventional computers. Monte-Carlo simulation results show that our approach significantly outperforms the conventional Anger algorithm.
Separation of semireflective layers using Sparse ICA
We address the problem of Blind Source Separation (BSS) of superimposed images and, in particular, consider the recovery of a scene recorded through a semi-refective medium (e.g. glass windshield) from its mixture with a virtual reflected image. We extend the Sparse ICA (SPICA) approach to BSS and apply it to the separation of the desired image from the superimposed images, without having any a priori knowledge about its structure and/or statistics. Advances in the SPICA approach are discussed. Simulations and experimental results illustrate the efficiency of the proposed approach, and of its specific implementation in a simple algorithm of a low computational cost. The approach and the algorithm are generic in that they can be adapted and applied to a wide range of BSS problems involving one-dimensional signals or images.
Reconstruction in ultrasound diffraction tomography using non-uniform FFT
We show an iterative reconstruction framework for diffraction ultrasound tomography. The use of broadband illumination allows a significant reduction of the number of projections compared to straight ray tomography. The proposed algorithm makes use of the forward nonuniform fast Fourier transform (NUFFT) for iterative Fourier inversion. Incorporation of total variation regularization allows the reduction of noise and Gibbs phenomena while preserving the edges. The complexity of the NUFFT-based reconstruction is comparable to the frequency domain interpolation (gridding) algorithm, whereas the reconstruction accuracy (in sense of the L2 and the L∞ norm) is better.
Iterative reconstruction in diffraction tomography using non-uniform fast Fourier transform
We show an iterative reconstruction framework for diffraction ultrasound tomography. The use of broadband illumination allows the number of projections to be reduced significantly compared to straight ray tomography. The proposed algorithm makes use of fast forward non-uniform Fourier transform (NUFFT) for iterative Fourier inversion. Incorporation of total variation regularization allows noise and Gibbs phenomena to be reduced whilst preserving the edges.
Optimal nonlinear estimation of photon coordinates in PET
We consider detection of high-energy photons in PET using thick scintillation crystals. Parallax effect and multiple Compton interactions in this type of crystals significantly reduce the accuracy of conventional detection methods. In order to estimate the scintillation point coordinates based on photomultiplier responses, we use asymptotically optimal nonlinear techniques, implemented by feed-forward neural networks, radial basis functions (RBF) networks, and neuro-fuzzy systems. Incorporation of information about angles of incidence of photons significantly improves the accuracy of estimation. The proposed estimators are fast enough to perform detection using conventional computers.