arXiv subjects

Oleg Michailovich

Publications and source records attributed to Oleg Michailovich.

15 recordsLinked to original sources

arXiv2021

PILOT: Physics-Informed Learned Optimized 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 relative 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 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 a 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 back-propagation operators. We demonstrate its effectiveness on image reconstruction and image segmentation tasks, reporting substantial improvements in terms of acceleration factors as well as the quality of these tasks.

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arXiv2020

Towards a quantitative assessment of neurodegeneration in Alzheimer's disease

Alzheimer's disease (AD) is an irreversible neurodegenerative disorder that progressively destroys memory and other cognitive domains of the brain. While effective therapeutic management of AD is still in development, it seems reasonable to expect their prospective outcomes to depend on the severity of baseline pathology. For this reason, substantial research efforts have been invested in the development of effective means of non-invasive diagnosis of AD at its earliest possible stages. In pursuit of the same objective, the present paper addresses the problem of the quantitative diagnosis of AD by means of Diffusion Magnetic Resonance Imaging (dMRI). In particular, the paper introduces the notion of a pathology specific imaging contrast (PSIC), which, in addition to supplying a valuable diagnostic score, can serve as a means of visual representation of the spatial extent of neurodegeneration. The values of PSIC are computed by a dedicated deep neural network (DNN), which has been specially adapted to the processing of dMRI signals. Once available, such values can be used for several important purposes, including stratification of study subjects. In particular, experiments confirm the DNN-based classification can outperform a wide range of alternative approaches in application to the basic problem of stratification of cognitively normal (CN) and AD subjects. Notwithstanding its preliminary nature, this result suggests a strong rationale for further extension and improvement of the explorative methodology described in this paper.

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arXiv2020

Towards learned optimal q-space sampling in diffusion MRI

Fiber tractography is an important tool of computational neuroscience that enables reconstructing the spatial connectivity and organization of white matter of the brain. Fiber tractography takes advantage of diffusion Magnetic Resonance Imaging (dMRI) which allows measuring the apparent diffusivity of cerebral water along different spatial directions. Unfortunately, collecting such data comes at the price of reduced spatial resolution and substantially elevated acquisition times, which limits the clinical applicability of dMRI. This problem has been thus far addressed using two principal strategies. Most of the efforts have been extended towards improving the quality of signal estimation for any, yet fixed sampling scheme (defined through the choice of diffusion-encoding gradients). On the other hand, optimization over the sampling scheme has also proven to be effective. Inspired by the previous results, the present work consolidates the above strategies into a unified estimation framework, in which the optimization is carried out with respect to both estimation model and sampling design {\it concurrently}. The proposed solution offers substantial improvements in the quality of signal estimation as well as the accuracy of ensuing analysis by means of fiber tractography. While proving the optimality of the learned estimation models would probably need more extensive evaluation, we nevertheless claim that the learned sampling schemes can be of immediate use, offering a way to improve the dMRI analysis without the necessity of deploying the neural network used for their estimation. We present a comprehensive comparative analysis based on the Human Connectome Project data. Code and learned sampling designs aviliable at https://github.com/tomer196/Learned_dMRI.

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arXiv2020

Learning beamforming in ultrasound imaging

Medical ultrasound (US) is a widespread imaging modality owing its popularity to cost efficiency, portability, speed, and lack of harmful ionizing radiation. In this paper, we demonstrate that replacing the traditional ultrasound processing pipeline with a data-driven, learnable counterpart leads to significant improvement in image quality. Moreover, we demonstrate that greater improvement can be achieved through a learning-based design of the transmitted beam patterns simultaneously with learning an image reconstruction pipeline. We evaluate our method on an in-vivo first-harmonic cardiac ultrasound dataset acquired from volunteers and demonstrate the significance of the learned pipeline and transmit beam patterns on the image quality when compared to standard transmit and receive beamformers used in high frame-rate US imaging. We believe that the presented methodology provides a fundamentally different perspective on the classical problem of ultrasound beam pattern design.

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arXiv2020

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.

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arXiv2020

High-fidelity, accelerated whole-brain submillimeter in-vivo diffusion MRI using gSlider-Spherical Ridgelets (gSlider-SR)

Purpose: To develop an accelerated, robust, and accurate diffusion MRI acquisition and reconstruction technique for submillimeter whole human brain in-vivo scan on a clinical scanner. Methods: We extend the ultra-high resolution diffusion MRI acquisition technique, gSlider, by allowing under-sampling in q-space and Radio-Frequency (RF)-encoded data, thereby accelerating the total acquisition time of conventional gSlider. The novel method, termed gSlider-SR, compensates for the lack of acquired information by exploiting redundancy in the dMRI data using a basis of Spherical Ridgelets (SR), while simultaneously enhancing the signal-to-noise ratio. Using Monte-Carlo simulation with realistic noise levels and several acquisitions of in-vivo human brain dMRI data (acquired on a Siemens Prisma 3T scanner), we demonstrate the efficacy of our method using several quantitative metrics. Results: For high-resolution dMRI data with realistic noise levels (synthetically added), we show that gSlider-SR can reconstruct high-quality dMRI data at different acceleration factors preserving both signal and angular information. With in-vivo data, we demonstrate that gSlider-SR can accurately reconstruct 860 $μm$ diffusion MRI data (64 diffusion directions at b = 2000 $s/ {mm}^2$), at comparable quality as that obtained with conventional gSlider with four averages, thereby providing an eight-fold reduction in scan time (from 1 h 20 min to 10 min). Conclusion: gSlider-SR enables whole-brain high angular resolution dMRI at a submillimeter spatial resolution with a dramatically reduced acquisition time, making it feasible to use the proposed scheme on existing clinical scanners.

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arXiv2019

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:\textit{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).

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arXiv2018

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 \textit{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 \textit{single-line transmission} (SLT) data. Experimental evaluation demonstrates significant 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 different patients and anatomies on real and phantom data.

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arXiv2018

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.

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arXiv2011

Image Deblurring Using Derivative Compressed Sensing for Optical Imaging Application

Reconstruction of multidimensional signals from the samples of their partial derivatives is known to be a standard problem in inverse theory. Such and similar problems routinely arise in numerous areas of applied sciences, including optical imaging, laser interferometry, computer vision, remote sensing and control. Though being ill-posed in nature, the above problem can be solved in a unique and stable manner, provided proper regularization and relevant boundary conditions. In this paper, however, a more challenging setup is addressed, in which one has to recover an image of interest from its noisy and blurry version, while the only information available about the imaging system at hand is the amplitude of the generalized pupil function (GPF) along with partial observations of the gradient of GPF's phase. In this case, the phase-related information is collected using a simplified version of the Shack-Hartmann interferometer, followed by recovering the entire phase by means of derivative compressed sensing. Subsequently, the estimated phase can be combined with the amplitude of the GPF to produce an estimate of the point spread function (PSF), whose knowledge is essential for subsequent image deconvolution. In summary, the principal contribution of this work is twofold. First, we demonstrate how to simplify the construction of the Shack-Hartmann interferometer so as to make it less expensive and hence more accessible. Second, it is shown by means of numerical experiments that the above simplification and its associated solution scheme produce image reconstructions of the quality comparable to those obtained using dense sampling of the GPF phase.

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arXiv2010

Spatially regularized compressed sensing of diffusion MRI data

The present paper introduces a method for substantial reduction of the number of diffusion encoding gradients required for reliable reconstruction of HARDI signals. The method exploits the theory of compressed sensing (CS), which establishes conditions on which a signal of interest can be recovered from its under-sampled measurements, provided that the signal admits a sparse representation in the domain of a linear transform. In the case at hand, the latter is defined to be spherical ridgelet transformation, which excels in sparsifying HARDI signals. What makes the resulting reconstruction procedure even more accurate is a combination of the sparsity constraints in the diffusion domain with additional constraints imposed on the estimated diffusion field in the spatial domain. Accordingly, the present paper describes a novel way to combine the diffusion- and spatial-domain constraints to achieve a maximal reduction in the number of diffusion measurements, while sacrificing little in terms of reconstruction accuracy. Finally, details are provided on a particularly efficient numerical scheme which can be used to solve the aforementioned reconstruction problem by means of standard and readily available estimation tools. The paper is concluded with experimental results which support the practical value of the proposed reconstruction methodology.

cs.IT↗

arXiv2010

Image Segmentation Using Weak Shape Priors

The problem of image segmentation is known to become particularly challenging in the case of partial occlusion of the object(s) of interest, background clutter, and the presence of strong noise. To overcome this problem, the present paper introduces a novel approach segmentation through the use of "weak" shape priors. Specifically, in the proposed method, an segmenting active contour is constrained to converge to a configuration at which its geometric parameters attain their empirical probability densities closely matching the corresponding model densities that are learned based on training samples. It is shown through numerical experiments that the proposed shape modeling can be regarded as "weak" in the sense that it minimally influences the segmentation, which is allowed to be dominated by data-related forces. On the other hand, the priors provide sufficient constraints to regularize the convergence of segmentation, while requiring substantially smaller training sets to yield less biased results as compared to the case of PCA-based regularization methods. The main advantages of the proposed technique over some existing alternatives is demonstrated in a series of experiments.

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arXiv2010

Regularized Richardson-Lucy Algorithm for Sparse Reconstruction of Poissonian Images

Restoration of digital images from their degraded measurements has always been a problem of great theoretical and practical importance in numerous applications of imaging sciences. A specific solution to the problem of image restoration is generally determined by the nature of degradation phenomenon as well as by the statistical properties of measurement noises. The present study is concerned with the case in which the images of interest are corrupted by convolutional blurs and Poisson noises. To deal with such problems, there exists a range of solution methods which are based on the principles originating from the fixed-point algorithm of Richardson and Lucy (RL). In this paper, we provide conceptual and experimental proof that such methods tend to converge to sparse solutions, which makes them applicable only to those images which can be represented by a relatively small number of non-zero samples in the spatial domain. Unfortunately, the set of such images is relatively small, which restricts the applicability of RL-type methods. On the other hand, virtually all practical images admit sparse representations in the domain of a properly designed linear transform. To take advantage of this fact, it is therefore tempting to modify the RL algorithm so as to make it recover representation coefficients, rather than the values of their associated image. Such modification is introduced in this paper. Apart from the generality of its assumptions, the proposed method is also superior to many established reconstruction approaches in terms of estimation accuracy and computational complexity. This and other conclusions of this study are validated through a series of numerical experiments.

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arXiv2009

An Iterative Shrinkage Approach to Total-Variation Image Restoration

The problem of restoration of digital images from their degraded measurements plays a central role in a multitude of practically important applications. A particularly challenging instance of this problem occurs in the case when the degradation phenomenon is modeled by an ill-conditioned operator. In such a case, the presence of noise makes it impossible to recover a valuable approximation of the image of interest without using some a priori information about its properties. Such a priori information is essential for image restoration, rendering it stable and robust to noise. Particularly, if the original image is known to be a piecewise smooth function, one of the standard priors used in this case is defined by the Rudin-Osher-Fatemi model, which results in total variation (TV) based image restoration. The current arsenal of algorithms for TV-based image restoration is vast. In the present paper, a different approach to the solution of the problem is proposed based on the method of iterative shrinkage (aka iterated thresholding). In the proposed method, the TV-based image restoration is performed through a recursive application of two simple procedures, viz. linear filtering and soft thresholding. Therefore, the method can be identified as belonging to the group of first-order algorithms which are efficient in dealing with images of relatively large sizes. Another valuable feature of the proposed method consists in its working directly with the TV functional, rather then with its smoothed versions. Moreover, the method provides a single solution for both isotropic and anisotropic definitions of the TV functional, thereby establishing a useful connection between the two formulae.

cs.CV↗

arXiv2009

Information tracking approach to segmentation of ultrasound imagery of prostate

The size and geometry of the prostate are known to be pivotal quantities used by clinicians to assess the condition of the gland during prostate cancer screening. As an alternative to palpation, an increasing number of methods for estimation of the above-mentioned quantities are based on using imagery data of prostate. The necessity to process large volumes of such data creates a need for automatic segmentation tools which would allow the estimation to be carried out with maximum accuracy and efficiency. In particular, the use of transrectal ultrasound (TRUS) imaging in prostate cancer screening seems to be becoming a standard clinical practice due to the high benefit-to-cost ratio of this imaging modality. Unfortunately, the segmentation of TRUS images is still hampered by relatively low contrast and reduced SNR of the images, thereby requiring the segmentation algorithms to incorporate prior knowledge about the geometry of the gland. In this paper, a novel approach to the problem of segmenting the TRUS images is described. The proposed approach is based on the concept of distribution tracking, which provides a unified framework for modeling and fusing image-related and morphological features of the prostate. Moreover, the same framework allows the segmentation to be regularized via using a new type of "weak" shape priors, which minimally bias the estimation procedure, while rendering the latter stable and robust.

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