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.

Quantum inspired approach for denoising with application to medical imaging.

Background noise in many fields such as medical imaging poses significant challenges for accurate diagnosis, prompting the development of denoising algorithms. Traditional methodologies, however, often struggle to address the complexities of noisy environments in high dimensional imaging systems. This paper introduces a novel quantum-inspired approach for image denoising, drawing upon principles of quantum and condensed matter physics. Our approach views medical images as amorphous structures akin to those found in condensed matter physics and we propose an algorithm that incorporates the concept of mode resolved localization directly into the denoising process. Notably, our approach eliminates the need for hyperparameter tuning. The proposed method is a standalone algorithm with minimal manual intervention, demonstrating its potential to use quantum-based techniques in classical signal denoising. Through numerical validation, we showcase the effectiveness of our approach in addressing noise-related challenges in imaging and especially medical imaging, underscoring its relevance for possible quantum computing applications.

Quantum inspired approach for denoising with application to medical imaging.

Background noise in many fields such as medical imaging poses significant challenges for accurate diagnosis, prompting the development of denoising algorithms. Traditional methodologies, however, often struggle to address the complexities of noisy environments in high dimensional imaging systems. This paper introduces a novel quantum-inspired approach for image denoising, drawing upon principles of quantum and condensed matter physics. Our approach views medical images as amorphous structures akin to those found in condensed matter physics and we propose an algorithm that incorporates the concept of mode resolved localization directly into the denoising process. Notably, our approach eliminates the need for hyperparameter tuning. The proposed method is a standalone algorithm with minimal manual intervention, demonstrating its potential to use quantum-based techniques in classical signal denoising. Through numerical validation, we showcase the effectiveness of our approach in addressing noise-related challenges in imaging and especially medical imaging, underscoring its relevance for possible quantum computing applications.

The Performance Improvement of Ultrasound Localization Microscopy (ULM) Using the Robust Principal Component Analysis (RPCA).

This paper presents an algorithm for ultrafast ultrasound localization microscopy (ULM) used for the detection, localization, accumulation, and rendering of intravenously injected ultrasound contrast agents (UCAs) enabling to yield hemodynamic maps of the brain microvasculature. It consists in integrating a robust principal component analysis (RPCA)-based approach into the ULM process for more robust tissue filtering, resulting in more accurate ULM images. Numerical experiments conducted on an in vivo rat brain perfusion dataset demonstrate the efficiency of the proposed approach compared to the most widely used state-of-the-art method.

Multi-layered adaptive neoangiogenesis Intra-Operative quantification (MANIOQ).

Quantification of vascularization volume can provide valuable information for diagnosis and prognosis in vascular pathologies. It can be adapted to inform the surgical management of gliomas, aggressive brain tumors characterized by exuberant sprouting of new blood vessels (neoangiogenesis). Filtered ultrafast Doppler data can provide two main parameters: vascularization index (VI) and fractional moving blood volume (FMBV) that clinically reflect tumor micro vascularization. Current protocols lack robust, automatic, and repeatable filtering methods. We present a filtrating method called Multi-layered Adaptive Neoangiogenesis Intra-Operative Quantification (MANIOQ). First, an adaptive clutter filtering is implemented, based on singular value decomposition (SVD) and hierarchical clustering. Second a method for noise equalization is applied, based on the subtraction of a weighted noise profile. Finally, an in vivo analysis of the periphery of the B-mode hyper signal area allows to measure the vascular infiltration extent of the brain tumors. Ninety ultrasound acquisitions were processed from 23 patients. Compared to reference methods in the literature, MANIOQ provides a more robust tissue filtering, and noise equalization allows for the first time to keep axial and lateral gain compensation (TGC and LGC). MANIOQ opens the way to an intra-operative clinical analysis of gliomas micro vascularization.

Validation of dried blood spots samples for the screening of hepatitis B virus surface by enzyme immunoassay method.

Dried Blood Spots (DBS) are blood collection carriers that facilitate the storage and transport of samples. Used for quality control during sero-epidemiological investigations, DBS eluate are not the conventional specimen indicated by manufacturers for enzyme immunoassay method (EIA) for hepatitis B virus surface (HBs antigen). The aim of our study was to evaluate DBS eluates used as a matrix for EIA of HBs antigen in a reference laboratory. This study took place from August 2016 to November 2017 at the Centre for Diagnosis and Research on AIDS and other infectious diseases (CeDReS) in Abidjan, Côte d'Ivoire. We used a panel of 149 whole blood samples from blood donors. The DBS performed with these samples were analyzed after elution with the HBsAg (version ULTRA) ELISA, Dia.Pro Diagnostic Bioprobes S.R.L., Sesto San Giovanni, Italy. The technical performance (sensitivity and specificity and kappa coefficient) of the test performed on DBS was determined for different ratios (optical density/threshold value) compared to the results obtained on the plasma used as reference. We obtained a sensitivity of 100% with DBS for all ratios. The specificity increased according to the ratio of optical density of the individual EIA reaction to the threshold value, with 6.09%, 47.0%, and 83.0%, respectively, for ratios of 1.0, 3.0, and 5.0. Best performance was observed at ratio of 10.0 with a sensitivity and specificity of 100%. In conclusion, DBS eluate can be used for the diagnosis of viral hepatitis B and would be useful for conducting sero-epidemiological investigations. However, ratio giving best performance must be determined for each enzyme immunoassay method kits.

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.

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.

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.

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 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.

Methodology for developing a high-precision ultrasound flow meter and fluid velocity profile reconstruction.

This article reports the methodology used to develop a high-precision ultrasound transit time flow meter dedicated to liquid hydrocarbons. This kind of flow meter is designed for custody transfer applications requiring accuracy better than 0.15% of reading. We focus here on certain specific points to achieve this accuracy. The transit time method needs to estimate accurately the time delay between signals received by a pair of transducers. In this study, we review different ways of estimating this time delay. We also propose a specific configuration of the flow meter paths. In particular, this configuration compensates for the swirl phenomenon, which has a significant impact on the accuracy of the flow meter. We also propose a theoretical parametric profile to reconstruct the fluid velocity profile in order to perform in situ diagnosis of the flow. The parameters of the model are estimated from the measurements of the flow meter. Simulations and experimental results showed that this method provides characterization of the flow in disturbed and undisturbed flow conditions.

Approximate Message Passing Reconstruction of Quantitative Acoustic Microscopy Images.

A novel framework for compressive sensing (CS) data acquisition and reconstruction in quantitative acoustic microscopy (QAM) is presented. Three different CS patterns, adapted to the specifics of QAM systems, were investigated as an alternative to the current raster-scanning approach. They consist of diagonal sampling, a row random, and a spiral scanning pattern and can all significantly reduce both the acquisition time and the amount of sampled data. For subsequent image reconstruction, we design and implement an innovative technique, whereby a recently proposed approximate message passing method is adapted to account for the underlying data statistics. A Cauchy maximum a posteriori image denoising algorithm is thus employed to account for the non-Gaussianity of QAM wavelet coefficients. The proposed methods were tested retrospectively on experimental data acquired with a 250- or 500-MHz QAM system. The experimental data were obtained from a human lymph node sample (250 MHz) and human cornea (500 MHz). Reconstruction results showed that the best performance is obtained using a spiral sensing pattern combined with the Cauchy denoiser in the wavelet domain. The spiral sensing matrix reduced the number of spatial samples by a factor of 2 and led to an excellent peak signal-to-noise ratio of 43.21 dB when reconstructing QAM speed-of-sound images of a human lymph node. These results demonstrate that the CS approach could significantly improve scanning time, while reducing costs of future QAM systems.

Comparison of an adaptive local thresholding method on CBCT and µCT endodontic images.

Root canal segmentation on cone beam computed tomography (CBCT) images is difficult because of the noise level, resolution limitations, beam hardening and dental morphological variations. An image processing framework, based on an adaptive local threshold method, was evaluated on CBCT images acquired on extracted teeth. A comparison with high quality segmented endodontic images on micro computed tomography (µCT) images acquired from the same teeth was carried out using a dedicated registration process. Each segmented tooth was evaluated according to volume and root canal sections through the area and the Feret's diameter. The proposed method is shown to overcome the limitations of CBCT and to provide an automated and adaptive complete endodontic segmentation. Despite a slight underestimation (-4, 08%), the local threshold segmentation method based on edge-detection was shown to be fast and accurate. Strong correlations between CBCT and µCT segmentations were found both for the root canal area and diameter (respectively 0.98 and 0.88). Our findings suggest that combining CBCT imaging with this image processing framework may benefit experimental endodontology, teaching and could represent a first development step towards the clinical use of endodontic CBCT segmentation during pulp cavity treatment.

Adaptive AR and neurofuzzy approaches: access to cerebral particle signatures.

In recent years, a relationship has been suggested between the occurrence of cerebral embolism and stroke. Ultrasound has therefore become essential in the detection of emboli when monitoring cerebral vascular disorders and forms part of ultrasound brain-imaging techniques. Such detection is based on investigating the middle cerebral artery using a TransCranial Doppler (TCD) system, and analyzing the Doppler signal of the embolism. Most of the emboli detected in practical experiments are large emboli because their signatures are easy to recognize in the TCD signal. However, detection of small emboli remains a challenge. Various approaches have been proposed to solve the problem, ranging from the exclusive use of expert human knowledge to automated collection of signal parameters. Many studies have recently been performed using time-frequency distributions and classical parameter modeling for automatic detection of emboli. It has been shown that autoregressive (AR) modeling associated with an abrupt change detection technique is one of the best methods for detection of microemboli. One alternative to this is a technique based on taking expert knowledge into account. This paper aims to unite these two approaches using AR modeling and expert knowledge through a neurofuzzy approach. The originality of this approach lies in combining these two techniques and then proposing a parameter referred to as score ranging from 0 to 1. Unlike classical techniques, this score is not only a measure of confidence of detection but also a tool enabling the final detection of the presence or absence of microemboli to be performed by the practitioner. Finally, this paper provides performance evaluation and comparison with an automated technique, i.e., AR modeling used in vitro.

Reconstruction of Enhanced Ultrasound Images From Compressed Measurements Using Simultaneous Direction Method of Multipliers.

High-resolution ultrasound (US) image reconstruction from a reduced number of measurements is of great interest in US imaging, since it could enhance both frame rate and image resolution. Compressive deconvolution (CD), combining compressed sensing and image deconvolution, represents an interesting possibility to consider this challenging task. The model of CD includes, in addition to the compressive sampling matrix, a 2-D convolution operator carrying the information on the system point spread function. Through this model, the resolution of reconstructed US images from compressed measurements mainly depends on three aspects: the acquisition setup, i.e., the incoherence of the sampling matrix, the image regularization, i.e., the sparsity prior, and the optimization technique. In this paper, we mainly focused on the last two aspects. We proposed a novel simultaneous direction method of multipliers based optimization scheme to invert the linear model, including two regularization terms expressing the sparsity of the RF images in a given basis and the generalized Gaussian statistical assumption on tissue reflectivity functions. The performance of the method is evaluated on both simulated and in vivo data.

Beamforming Through Regularized Inverse Problems in Ultrasound Medical Imaging.

Beamforming (BF) in ultrasound (US) imaging has significant impact on the quality of the final image, controlling its resolution and contrast. Despite its low spatial resolution and contrast, delay-and-sum (DAS) is still extensively used nowadays in clinical applications, due to its real-time capabilities. The most common alternatives are minimum variance (MV) method and its variants, which overcome the drawbacks of DAS, at the cost of higher computational complexity that limits its utilization in real-time applications. In this paper, we propose to perform BF in US imaging through a regularized inverse problem based on a linear model relating the reflected echoes to the signal to be recovered. Our approach presents two major advantages: 1) its flexibility in the choice of statistical assumptions on the signal to be beamformed (Laplacian and Gaussian statistics are tested herein) and 2) its robustness to a reduced number of pulse emissions. The proposed framework is flexible and allows for choosing the right tradeoff between noise suppression and sharpness of the resulted image. We illustrate the performance of our approach on both simulated and experimental data, with in vivo examples of carotid and thyroid. Compared with DAS, MV, and two other recently published BF techniques, our method offers better spatial resolution, respectively contrast, when using Laplacian and Gaussian priors.

Compressive Deconvolution in Medical Ultrasound Imaging.

The interest of compressive sampling in ultrasound imaging has been recently extensively evaluated by several research teams. Following the different application setups, it has been shown that the RF data may be reconstructed from a small number of measurements and/or using a reduced number of ultrasound pulse emissions. Nevertheless, RF image spatial resolution, contrast and signal to noise ratio are affected by the limited bandwidth of the imaging transducer and the physical phenomenon related to US wave propagation. To overcome these limitations, several deconvolution-based image processing techniques have been proposed to enhance the ultrasound images. In this paper, we propose a novel framework, named compressive deconvolution, that reconstructs enhanced RF images from compressed measurements. Exploiting an unified formulation of the direct acquisition model, combining random projections and 2D convolution with a spatially invariant point spread function, the benefit of our approach is the joint data volume reduction and image quality improvement. The proposed optimization method, based on the Alternating Direction Method of Multipliers, is evaluated on both simulated and in vivo data.