Marmoset brain segmentation from deconvolved magnetic resonance images and estimated label maps.

PURPOSE: The proposed method aims to create label maps that can be used for the segmentation of animal brain MR images without the need of a brain template. This is achieved by performing a joint deconvolution and segmentation of the brain MR images. METHODS: It is based on modeling locally the image statistics using a generalized Gaussian distribution (GGD) and couples the deconvolved image and its corresponding labels map using the GGD-Potts model. Because of the complexity of the resulting Bayesian estimators of the unknown model parameters, a Gibbs sampler is used to generate samples following the desired posterior probability. RESULTS: The performance of the proposed algorithm is assessed on simulated and real MR images by the segmentation of enhanced marmoset brain images into its main compartments using the corresponding label maps created. Quantitative assessment showed that this method presents results that are comparable to those obtained with the classical method-registering the volumes to a brain template. CONCLUSION: The proposed method of using labels as prior information for brain segmentation provides a similar or a slightly better performance compared with the classical reference method based on a dedicated template.

Towards an automatic early stress recognition system for office environments based on multimodal measurements: A review.

Stress is a major problem of our society, as it is the cause of many health problems and huge economic losses in companies. Continuous high mental workloads and non-stop technological development, which leads to constant change and need for adaptation, makes the problem increasingly serious for office workers. To prevent stress from becoming chronic and provoking irreversible damages, it is necessary to detect it in its early stages. Unfortunately, an automatic, continuous and unobtrusive early stress detection method does not exist yet. The multimodal nature of stress and the research conducted in this area suggest that the developed method will depend on several modalities. Thus, this work reviews and brings together the recent works carried out in the automatic stress detection looking over the measurements executed along the three main modalities, namely, psychological, physiological and behavioural modalities, along with contextual measurements, in order to give hints about the most appropriate techniques to be used and thereby, to facilitate the development of such a holistic system.

Efficient Stratified 3-D Scatterer Sampling for Freehand Ultrasound Simulation.

Ultrasound image simulation is a well-explored field with the main objective of generating realistic synthetic images, further used as ground truth for computational imaging algorithms or for radiologists' training. Several ultrasound simulators are already available, most of them consisting in similar steps: 1) generate a collection of tissue mimicking individual scatterers with random spatial positions and random amplitudes; 2) model the ultrasound probe and the emission and reception schemes; and 3) generate the radio frequency (RF) signals resulting from the interaction between the scatterers and the propagating ultrasound waves. This article is focused on the first step. To ensure fully developed speckle, a few tens of scatterers by resolution cell are needed, demanding to handle high amounts of data (especially in 3-D) and resulting into important computational time. The objective of this work is to explore new scatterer spatial distributions, with application to multiple coherent 2-D slice simulations from 3-D volumes. More precisely, lazy evaluation of pseudorandom schemes proves them to be highly computationally efficient compared with uniform random distribution commonly used. We also propose an end-to-end method from the 3-D tissue volume to resulting ultrasound images using coherent and 3-D-aware scatterer generation and usage in a real-time context.

An inverse method using Cross spectral Matrix Fitting for passive cavitation imaging.

High intensity focused ultrasound (HIFU) can produce cavitation, which requires monitoring for specific applications such as sonoporation, targeted drug delivery or histotripsy. Passive acoustic mapping has been proposed in the literature as a method for monitoring cavitation, but it lacks spatial resolution, primarily in the axial direction, due to the absence of a time reference. This is a common issue with passive imaging compared to standard pulse-echo ultrasound. In order to improve the axial resolution, we propose an adaptation of the Cross spectral Matrix Fitting (CMF) method for passive cavitation imaging, which is based on the resolution of an inverse problem with different regularizations that promote sparsity in the reconstructed cavitation maps: Elastic Net (CMF-ElNet) and sparse Total Variation (CMF-spTV). The results from both simulated and experimental data are presented and compared to state-of-the-art approaches, such as the frequential Delay-and-Sum (DAS) and the frequential Robust Capon Beamformer (RCB). We show the interest of the method for improving the axial resolution, with an axial Full Width Half Maximum (FWHM) divided by 3 and 5 compared to RCB and DAS, respectively. Moreover, CMF based methods improve Contrast-to-Noise Ratio (CNR) by more than 15 dB in experimental conditions compared to RCB. We also show the advantage of the sparse Total Variation prior over Elastic Net when dealing with cloud shaped cavitation sources, that can be assumed as sparse grouped sources.

Simultaneous imaging of ultrasonic relative backscatter and attenuation coefficients for quantitative liver steatosis assessment.

Prevalence of liver disease is continuously increasing and nonalcoholic fatty liver disease (NAFLD) is the most common etiology. We present an approach to detect the progression of liver steatosis based on quantitative ultrasound (QUS) imaging. This study was performed on a group of 55 rats that were subjected to a control or methionine and choline deficient (MCD) diet known to induce NAFLD. Ultrasound (US) measurements were performed at 2 and 6 weeks. Thereafter, animals were humanely euthanized and livers excised for histological analysis. Relative backscatter and attenuation coefficients were simultaneously estimated from the US data and envelope signal-to-noise ratio was calculated to train a regression model for: (1) fat fraction percentage estimation and (2) performing classification according to Brunt's criteria in grades (0 <5%; 1, 5-33%; 2, >33-66%; 3, >66%) of liver steatosis. The trained regression model achieved an [Formula: see text] of 0.97 (p-value < 0.01) and a RMSE of 3.64. Moreover, the classification task reached an accuracy of 94.55%. Our results suggest that in vivo QUS is a promising noninvasive imaging modality for the early assessment of NAFLD.

Adaptive noise reduction for power Doppler imaging using SVD filtering in the channel domain and coherence weighting of pixels.

Objective. Ultrafast power Doppler (UPD) is an ultrasound method that can image blood flow at several thousands of frames per second. In particular, the high number of data provided by UPD enables the use of singular value decomposition (SVD) as a clutter filter for suppressing tissue signal. Notably, is has been demonstrated in various applications that SVD filtering increases significantly the sensitivity of UPD to microvascular flows. However, UPD is subjected to significant depth-dependent electronic noise and an optimal denoising approach is still being sought.Approach. In this study, we propose a new denoising method for UPD imaging: the Coherence Factor Mask (CFM). This filter is first based on filtering the ultrasound time-delayed data using SVD in the channel domain to remove clutter signal. Then, a spatiotemporal coherence mask that exploits coherence information between channels for identifying noisy pixels is computed. The mask is finally applied to beamformed images to decrease electronic noise before forming the power Doppler image. We describe theoretically how to filter channel data using a single SVD. Then, we evaluate the efficiency of the CFM filter for denoisingin vitroandin vivoimages and compare its performances with standard UPD and with three existing denoising approaches.Main results. The CFM filter gives gains in signal-to-noise ratio and contrast-to-noise ratio of up to 22 dB and 20 dB, respectively, compared to standard UPD and globally outperforms existing methods for reducing electronic noise. Furthermore, the CFM filter has the advantage over existing approaches of being adaptive and highly efficient while not requiring a cut-off for discriminating noise and blood signals nor for determining an optimal coherence lag.Significance. The CFM filter has the potential to help establish UPD as a powerful modality for imaging microvascular flows.

Inverse Problem of Ultrasound Beamforming With Denoising-Based Regularized Solutions.

During the past few years, inverse problem formulations of ultrasound beamforming have attracted growing interest. They usually pose beamforming as a minimization problem of a fidelity term resulting from the measurement model plus a regularization term that enforces a certain class on the resulting image. Here, we take advantage of alternating direction method of multipliers to propose a flexible framework in which each term is optimized separately. Furthermore, the proposed beamforming formulation is extended to replace the regularization term with a denoising algorithm, based on the recent approaches called plug-and-play (PnP) and regularization by denoising (RED). Such regularizations are shown in this work to better preserve speckle texture, an important feature in ultrasound imaging, than sparsity-based approaches previously proposed in the literature. The efficiency of the proposed methods is evaluated on simulations, real phantoms, and in vivo data available from a plane-wave imaging challenge in medical ultrasound. Furthermore, a comprehensive comparison with existing ultrasound beamforming methods is also provided. These results show that the RED algorithm gives the best image quality in terms of contrast index while preserving the speckle statistics.

CX-DaGAN: Domain Adaptation for Pneumonia Diagnosis on a Small Chest X-Ray Dataset.

Recent advances in deep learning led to several algorithms for the accurate diagnosis of pneumonia from chest X-rays. However, these models require large training medical datasets, which are sparse, isolated, and generally private. Furthermore, these models in medical imaging are known to over-fit to a particular data domain source, i.e., these algorithms do not conserve the same accuracy when tested on a dataset from another medical center, mainly due to image distribution discrepancies. In this work, a domain adaptation and classification technique is proposed to overcome the over-fit challenges on a small dataset. This method uses a private-small dataset (target domain), a public-large labeled dataset from another medical center (source domain), and consists of three steps. First, it performs a data selection of the source domain's most representative images based on similarity constraints through principal component analysis subspaces. Second, the selected samples from the source domain are fit to the target distribution through an image to image translation based on a cycle-generative adversarial network. Finally, the target train dataset and the adapted images from the source dataset are used within a convolutional neural network to explore different settings to adjust the layers and perform the classification of the target test dataset. It is shown that fine-tuning a few specific layers together with the selected-adapted images increases the sorting accuracy while reducing the trainable parameters. The proposed approach achieved a notable increase in the target dataset's overall classification accuracy, reaching up to 97.78 % compared to 90.03 % by standard transfer learning.

Ultrasound Image Deconvolution Using Fundamental and Harmonic Images.

Ultrasound (US) image restoration from radio frequency (RF) signals is generally addressed by deconvolution techniques mitigating the effect of the system point spread function (PSF). Most of the existing methods estimate the tissue reflectivity function (TRF) from the so-called fundamental US images, based on an image model assuming the linear US wave propagation. However, several human tissues or tissues with contrast agents have a nonlinear behavior when interacting with US waves leading to harmonic images. This work takes this nonlinearity into account in the context of TRF restoration, by considering both fundamental and harmonic RF signals. Starting from two observation models (for the fundamental and harmonic images), TRF estimation is expressed as the minimization of a cost function defined as the sum of two data fidelity terms and one sparsity-based regularization stabilizing the solution. The high attenuation with a depth of harmonic echoes is integrated into the direct model that relates the observed harmonic image to the TRF. The interest of the proposed method is shown through synthetic and in vivo results and compared with other restoration methods.

Joint Blind Deconvolution and Robust Principal Component Analysis for Blood Flow Estimation in Medical Ultrasound Imaging.

This article addresses the problem of high-resolution Doppler blood flow estimation from an ultrafast sequence of ultrasound images. Formulating the separation of clutter and blood components as an inverse problem has been shown in the literature to be a good alternative to spatio-temporal singular value decomposition (SVD)-based clutter filtering. In particular, a deconvolution step has recently been embedded in such a problem to mitigate the influence of the point spread function (PSF) of the imaging system. Deconvolution was shown in this context to improve the accuracy of the blood flow reconstruction. However, the PSF needs to be measured experimentally, and measuring it requires nontrivial experimental setups. To overcome this limitation, we propose herein a blind deconvolution method able to estimate both the blood component and the PSF from Doppler data. Numerical experiments conducted on simulated and in vivo data demonstrate qualitatively and quantitatively the effectiveness of the proposed approach in comparison with the previous method based on experimentally measured PSF and two other state-of-the-art approaches.

Assessment of root canal transportation of 2Shape and ProTaper gold in mandibular molar mesial canals: A micro-computed tomographic study.

The aim of this study was to compare shaping abilities of Protaper Gold® (PTG) and 2Shape® (TS) by using a new automatic process and micro-computed tomography (Micro-CT). 32 first mandibular molars with two separate mesial canals were selected. Only mesial roots were prepared with PTG and TS. Pre- and post-operative scans were performed using Micro-CT to provide volumes with a voxel size of 20 µm. Volumes, non-instrumented area, amount of transportation and centering ability in coronal, middle and apical third shaping time and procedural errors were recorded. TS and PTG increased the endodontic volume of 2.98 mm3 (±1.56) and 3.21 mm3 (±1.78) respectively with no statistical difference (p = .168) and no procedural errors. No significant difference was found concerning canal transportation among groups but only within the same group PTG (p value < .001) and TS (p value < .001). The mean centering ratio was significantly different only between the section levels for PTG (p value < .001) and TS (p value = .01); it was significantly reduced in the cervical third. The percentage of untouched canal walls ranged between 29.78% (±15.145) and 36.60% (±11.968) respectively for PTG and TS with no statistical difference among groups (p value = .168). TS and PTG with post machining heat treatment were able to produce centered preparations with no significant difference or procedural errors. TS system provided a shorter preparation time than PTG files.

Detection of Line Artifacts in Lung Ultrasound Images of COVID-19 Patients Via Nonconvex Regularization.

In this article, we present a novel method for line artifacts quantification in lung ultrasound (LUS) images of COVID-19 patients. We formulate this as a nonconvex regularization problem involving a sparsity-enforcing, Cauchy-based penalty function, and the inverse Radon transform. We employ a simple local maxima detection technique in the Radon transform domain, associated with known clinical definitions of line artifacts. Despite being nonconvex, the proposed technique is guaranteed to convergence through our proposed Cauchy proximal splitting (CPS) method, and accurately identifies both horizontal and vertical line artifacts in LUS images. To reduce the number of false and missed detection, our method includes a two-stage validation mechanism, which is performed in both Radon and image domains. We evaluate the performance of the proposed method in comparison to the current state-of-the-art B-line identification method, and show a considerable performance gain with 87% correctly detected B-lines in LUS images of nine COVID-19 patients.

Fusion of Magnetic Resonance and Ultrasound Images for Endometriosis Detection.

This paper introduces a new fusion method for magnetic resonance (MR) and ultrasound (US) images, which aims at combining the advantages of each modality, i.e., good contrast and signal to noise ratio for the MR image and good spatial resolution for the US image. The proposed algorithm is based on two inverse problems, performing a super-resolution of the MR image and a denoising of the US image. A polynomial function is introduced to model the relationships between the gray levels of the two modalities. The resulting inverse problem is solved using a proximal alternating linearized minimization framework. The accuracy and the interest of the fusion algorithm are shown quantitatively and qualitatively via evaluations on synthetic and experimental phantom data.

Investigation of PVA cryogel Young's modulus stability with time, controlled by a simple reliable technique.

We describe a quasistatic method for mechanical characterization of tissue-mimicking material used in elastography. We demonstrate that it is possible to assess the elasticity modulus with a reasonable reproducibility using simple and easy tools and methods. Possessing a simple relevant technique with evaluated relative error to assess Young's modulus of these phantoms could deeply improve the quality of the research in the field of elastography. The method was tested and validated with four samples of polyvinyl alcohol (PVA) cryogel with different elasticity values corresponding to those of stiffer soft biological tissues. Young's moduli, varying from 70 to 180 kPa depending on the number of freeze-thaw cycles (two to five), were measured within strict measurement conditions and found to have a reproducibility varying from 4% to 8%. Relative error, estimated as the ratio between observed and reference values, varied from 16% to 32%. Besides, measurement stability over 4 months was evaluated. The method demonstrated good feasibility and acceptable reproducibility for mechanically characterizing and controlled over time phantoms used for validating new potential ultrasound imaging techniques in the field of elastography. Nevertheless, in this study, investigation was performed on gel possessing young's modulus values ranging from 80 to 215 kPa. Some tissue values of Young'modulus were reported to be lower, ranging from 0.6 to 28 kPa as liver or glandular values. Consequently, further validation of this static method for mechanical characterization of phantom gels should be performed using softer PVA cryogel.

Analytic estimation of subsample spatial shift using the phases of multidimensional analytic signals.

In this correspondence, a method of analytic subsample spatial shift estimation based on an a priori n-D signal model is proposed. The estimation uses the linear phases of n analytic signals defined with the multidimensional Hilbert transform. This estimation proposes: i) an analytic solution to the n-D shift estimation and ii) an estimation without processing complex cross-correlation function or cross-spectra between signals contrary to most phase shift estimators. The method provides better performance in estimating subsample shifts than two classical estimators, one using the maximum of cross-correlation function and the other seeking the zero of the complex correlation function phase. Two delay estimators using the in-phase and quadrature-phase components of signals are also compared to our estimator. Like most estimators using the complex signal phases, the estimator proposed herein presents the advantage of unaltered accuracy when low sampled signals are used. Moreover, we show that this method can be applied to motion tracking with ultrasound images. Thus, included in a block-based motion estimation method and tested with ultrasound data, this estimator provides an analytical solution to the translation estimation problem.

On Single-Image Super-Resolution in 3D Brain Magnetic Resonance Imaging.

The objective of this work is to apply 3D super resolution (SR) techniques to brain magnetic resonance (MR) image restoration. Two 3D SR methods are considered following different trends: one recently proposed tensor-based approach and one inverse problem algorithm based on total variation and low rank regularization. The evaluation of their effectiveness is assessed through the segmentation of brain compartments: gray matter, white matter and cerebrospinal fluid. The two algorithms are qualitatively and quantitatively evaluated on simulated images with ground truth available and on experimental data. The originality of this work is to consider the SR methods as an initial step towards the final segmentation task. The results show the ability of both methods to overcome the loss of spatial resolution and to facilitate the segmentation of brain structures with improved accuracy compared to native low-resolution MR images. Both algorithms achieved almost equivalent results with a highly reduced computational time cost for the tensor-based approach.

A Convolutional Neural Network for 250-MHz Quantitative Acoustic-microscopy Resolution Enhancement.

Quantitative acoustic microscopy (QAM) permits the formation of quantitative two-dimensional (2D) maps of acoustic and mechanical properties of soft tissues at microscopic resolution. The 2D maps formed using our custom SAM systems employing a 250-MHz and a 500-MHz single-element transducer have a nominal resolution of 7 µm and 4µm, respectively. In a previous study, the potential of single-image super-resolution (SR) image post-processing to enhance the spatial resolution of 2D SAM maps was demonstrated using a forward model accounting for blur, decimation, and noise. However, results obtained when the SR method was applied to soft tissue data were not entirely satisfactory because of the limitation of the convolution model considered and by the difficulty of estimating the system point spread function and designing the appropriate regularization term. Therefore, in this study, a machine learning approach based on convolutional neural networks was implemented. For training, data acquired on the same samples at 250 and 500 MHz were used. The resulting trained network was tested on 2D impedance maps (2DZMs) of human lymph nodes acquired from breast-cancer patients. Visual inspection of the reconstructed enhanced 2DZMs were found similar to the 2DZMs obtained at 500 MHz which were used as ground truth. In addition, the enhanced 250-MHz 2DZMs obtained from the proposed method yielded better peak signal to noise ratio and normalized mean square error than those obtained with the previous SR method. This improvement was also demonstrated by the statistical analyses. This pioneering work could significantly reduce challenges and costs associated with current very high-frequency SAM systems while providing enhanced spatial resolution.

Robust Optical Flow Estimation in Cardiac Ultrasound Images Using a Sparse Representation.

This paper introduces a robust 2-D cardiac motion estimation method. The problem is formulated as an energy minimization with an optical flow-based data fidelity term and two regularization terms imposing spatial smoothness and the sparsity of the motion field in an appropriate cardiac motion dictionary. Robustness to outliers, such as imaging artefacts and anatomical motion boundaries, is introduced using robust weighting functions for the data fidelity term as well as for the spatial and sparse regularizations. The motion fields and the weights are computed jointly using an iteratively re-weighted minimization strategy. The proposed robust approach is evaluated on synthetic data and realistic simulation sequences with available ground-truth by comparing the performance with state-of-the-art algorithms. Finally, the proposed method is validated using two sequences of in vivo images. The obtained results show the interest of the proposed approach for 2-D cardiac ultrasound imaging.

Motion Compensated Dynamic MRI Reconstruction With Local Affine Optical Flow Estimation.

This paper proposes a novel framework to reconstruct dynamic magnetic resonance imaging (DMRI) with motion compensation (MC). Specifically, by combining the intensity-based optical flow constraint with the traditional compressed sensing scheme, we are able to jointly reconstruct the DMRI sequences and estimate the interframe motion vectors. Then, the DMRI reconstruction can be refined through MC with the estimated motion field. By employing the coarse-to-fine multi-scale resolution strategy, we are able to update the motion field in different spatial scales. The estimated motion vectors need to be interpolated to the finest resolution scale to compensate the DMRI reconstruction. Moreover, the proposed framework is capable of handling a wide class of prior information (regularizations) for DMRI reconstruction, such as sparsity, low rank, and total variation. The formulated optimization problem is solved by a primal-dual algorithm with linesearch due to its efficiency when dealing with non-differentiable problems. Experiments on various DMRI datasets validate the reconstruction quality improvement using the proposed scheme in comparison to several state-of-the-art algorithms.

A Tensor Factorization Method for 3-D Super Resolution With Application to Dental CT.

Available super-resolution techniques for 3-D images are either computationally inefficient prior-knowledge-based iterative techniques or deep learning methods which require a large database of known low-resolution and high-resolution image pairs. A recently introduced tensor-factorization-based approach offers a fast solution without the use of known image pairs or strict prior assumptions. In this paper, this factorization framework is investigated for single image resolution enhancement with an offline estimate of the system point spread function. The technique is applied to 3-D cone beam computed tomography for dental image resolution enhancement. To demonstrate the efficiency of our method, it is compared to a recent state-of-the-art iterative technique using low-rank and total variation regularizations. In contrast to this comparative technique, the proposed reconstruction technique gives a 2-order-of-magnitude improvement in running time-2 min compared to 2 h for a dental volume of 282×266×392 voxels. Furthermore, it also offers slightly improved quantitative results (peak signal-to-noise ratio and segmentation quality). Another advantage of the presented technique is the low number of hyperparameters. As demonstrated in this paper, the framework is not sensitive to small changes in its parameters, proposing an ease of use.