3D early embryogenesis image filtering by nonlinear partial differential equations

We present nonlinear diffusion equations, numerical schemes to solve them and their application for filtering 3D images obtained from laser scanning microscopy (LSM) of living zebrafish embryos, with a goal to identify the optimal filtering method and its parameters. In the large scale applications dealing with analysis of 3D + time embryogenesis images, an important objective is a correct detection of the number and position of cell nuclei yielding the spatio-temporal cell lineage tree of embryogenesis. The filtering is the first and necessary step of the image analysis chain and must lead to correct results, removing the noise, sharpening the nuclei edges and correcting the acquisition errors related to spuriously connected subregions. In this paper we study such properties for the regularized Perona–Malik model and for the generalized mean curvature flow equations in the level-set formulation. A comparison with other nonlinear diffusion filters, like tensor anisotropic diffusion and Beltrami flow, is also included. All numerical schemes are based on the same discretization principles, i.e. finite volume method in space and semi-implicit scheme in time, for solving nonlinear partial differential equations. These numerical schemes are unconditionally stable, fast and naturally parallelizable. The filtering results are evaluated and compared first using the Mean Hausdorff distance between a gold standard and different isosurfaces of original and filtered data. Then, the number of isosurface connected components in a region of interest (ROI) detected in original and after the filtering is compared with the corresponding correct number of nuclei in the gold standard. Such analysis proves the robustness and reliability of the edge preserving nonlinear diffusion filtering for this type of data and lead to finding the optimal filtering parameters for the studied models and numerical schemes. Further comparisons consist in ability of splitting the very close objects which are artificially connected due to acquisition error intrinsically linked to physics of LSM. In all studied aspects it turned out that the nonlinear diffusion filter which is called geodesic mean curvature flow (GMCF) has the best performance.     

Speckles Suppression Techniques for Ultrasound Images

Most medical images have a poorer signal to noise ratio than scenes taken with a digital camera, which often leads to incorrect diagnosis. Speckles suppression from ultrasound images is one of the most important concerns in computer-aided diagnosis. This article proposes two novel, robust and efficient ultrasound images denoising techniques. The first technique is the enhanced ultrasound images denoising (EUID) technique, which estimates automatically the speckle noise amount in the ultrasound images by estimating important input parameters of the filter and then denoising the image using the sigma filter. The second technique is the ultrasound image denoising using neural network (UIDNN) that is based on the second-order difference of pixels with adaptive threshold value in order to identify random valued speckles from images to achieve high efficient image restoration. The performances of the proposed techniques are analyzed and compared with those of other image denoising techniques. The experimental results show that the proposed techniques are valuable tools for speckles suppression, being accurate, less tedious, and preventing typical human errors associated with manual tasks in addition to preserving the edges from the image. The EUID algorithm has nearly the same peak signal to noise ratio (PSNR) as Frost and speckle-reducing anisotropic diffusion 1, whereas it achieves higher gains, on average—0.4 dB higher PSNR—than the Lee, Kuan, and anisotropic diffusion filters. The UIDNN technique outperforms all the other techniques since it can determine the noisy pixels and perform filtering for these pixels only. Generally, when relatively high levels of noise are added, the proposed algorithms show better performances than the other conventional filters.     

Non-parametric geodesic active regions: method and evaluation for cerebral aneurysms segmentation in 3DRA and CTA

Segmentation of vascular structures is a difficult and challenging task. In this article, we present an algorithm devised for the segmentation of such structures. Our technique consists in a geometric deformable model with associated energy functional that incorporates high-order multiscale features in a non-parametric statistical framework. Although the proposed segmentation method is generic, it has been applied to the segmentation of cerebral aneurysms in 3DRA and CTA. An evaluation study over 10 clinical datasets indicate that the segmentations obtained by our method present a high overlap index with respect to the ground-truth (91.13% and 73.31%, respectively) and that the mean error distance from the surface to the ground truth is close to the in-plane resolution (0.40 and 0.38 mm, respectively). Besides, our technique favorably compares to other alternative techniques based on deformable models, namely parametric geodesic active regions and active contours without edges.     

Image filtering via generalized scale

In medical imaging, low signal-to-noise ratio (SNR) and/or contrast-to-noise ratio (CNR) often cause many image processing algorithms to perform poorly. Postacquisition image filtering is an important off-line image processing approach widely employed to enhance the SNR and CNR. A major drawback of many filtering techniques is image degradation by diffusing/blurring edges and/or fine structures. In this paper, we introduce a scale-based filtering method that employs scale-dependent diffusion conductance to perform filtering. This approach utilizes novel object scale information via a concept called generalized scale, which imposes no shape, size, or anisotropic constraints unlike previously published ball scale-based filtering strategies. The object scale allows us to better control the filtering process by constraining smoothing in regions with fine details and in the vicinity of boundaries while permitting effective smoothing in the interior of homogeneous regions. A new quantitative evaluation strategy that captures the SNR to CNR trade-off behavior of filtering methods is presented. The evaluations based on the Brainweb data sets show superior performance of generalized scale-based diffusive filtering over two existing methods, namely, ball scale-based and nonlinear complex diffusion processes. Qualitative experiments based on both phantom and patient magnetic resonance images demonstrate that the generalized scale-based approach leads to better preservation of fine details and edges.     

A comparison of two algorithms for automated stone detection in clinical B-mode ultrasound images of the abdomen

Ultrasound (US) imaging is an indispensible technique for detection of abdominal stones which are a serious health hazard. Segmentation of stones from abdominal ultrasound images presents a unique challenge because these images contain strong speckle noise and attenuated artifacts. In clinical situations where a large number of stones must be identified, traditional methods such as manual identification become tedious and lack reproducibility too. The necessity of obtaining high reproducibility and the need to increase efficiency motivates the development of automated and fast procedures that segment out stones of all sizes and shapes in medical images by applying image segmentation techniques. In this paper we present and compare two fully automatic and unsupervised methods for robust stone detection in B-mode ultrasound images of the abdomen. Our approaches are based on the marker controlled watershed segmentation, along with some pre-processing and post-processing procedures that eliminate the inherent problems associated with medical ultrasound images. The first algorithm (Algorithm I) utilizes the advantage of the Speckle reducing anisotropic diffusion (SRAD) technique, along with unsharp filtering and histo- gram equalization for removal of speckle noise, and the second algorithm (Algorithm II) is based on the log decompression model which too serves as a tool for minimization of speckle. Experimental results obtained from processing a set of 50 ultrasound images ensure the robustness of both the proposed algorithms. Comparative results of both the algorithms based on efficiency and relative error in stone area have been provided.     

PerceptFlow: Real-Time Ultrafast Doppler Image Enhancement Using Deep Convolutional Neural Network and Perceptual Loss

Ultrafast ultrasound is an emerging imaging modality derived from standard medical ultrasound. It allows for a high spatial resolution of 100 μm and a temporal resolution in the millisecond range with techniques such as ultrafast Doppler imaging. Ultrafast Doppler imaging has become a priceless tool for neuroscience, especially for visualizing functional vascular structures and navigating the brain in real time. Yet, the quality of a Doppler image strongly depends on experimental conditions and is easily subject to artifacts and deterioration, especially with transcranial imaging, which often comes at the cost of higher noise and lower sensitivity to small blood vessels. A common solution to better visualize brain vasculature is either accumulating more information, integrating the image over several seconds or using standard filter-based enhancement techniques, which often over-smooth the image, thus failing both to preserve sharp details and to improve our perception of the vasculature. In this study we propose combining the standard Doppler accumulation process with a real-time enhancement strategy, based on deep-learning techniques, using perceptual loss (PerceptFlow). With our perceptual approach, we bypass the need for long integration times to enhance Doppler images. We applied and evaluated our proposed method on transcranial Doppler images of mouse brains, outperforming state-of-the-art filters. We found that, in comparison to standard filters such as the Gaussian filter (GF) and block-matching and 3-D filtering (BM3D), PerceptFlow was capable of reducing background noise with a significant increase in contrast and contrast-to-noise ratio, as well as better preserving details without compromising spatial resolution.     

Characterization of changes in blood vessel width and tortuosity in retinopathy of prematurity using image analysis

Many retinal diseases are characterised by changes to retinal vessels. For example, a common condition associated with retinopathy of prematurity (ROP) is so-called plus disease, characterised by increased vascular dilation and tortuosity. This paper presents a general technique for segmenting out vascular structures in retinal images, and characterising the segmented blood vessels. The segmentation technique consists of several steps. Morphological preprocessing is used to emphasise linear structures such as vessels. A second derivative operator is used to further emphasise thin vascular structures, and is followed by a final morphological filtering stage. Thresholding of this image is used to provide a segmented vascular mask. Skeletonisation of this mask allows identification of points in the image where vessels cross (bifurcations and crossing points) and allows the width and tortuosity of vessel segments to be calculated. The accuracy of the segmentation stage is quite dependent on the parameters used, particularly at the thresholding stage. However, reliable measurements of vessel width and tortuosity were shown using test images. Using these tools, a set of images drawn from 23 subjects being screened for the presence of threshold ROP disease is considered. Of these subjects, 11 subsequently required treatment for ROP, 9 had no evidence of ROP, and 3 had spontaneously regressed ROP. The average vessel width and tortuosity for the treated subjects was 96.8 microm and 1.125. The corresponding figures for the non-treated cohort were 86.4 microm and 1.097. These differences were statistically significant at the 99% and 95% significance level, respectively. Subjects who progressed to threshold disease during the course of screening showed an average increase in vessel width of 9.6 microm and in tortuosity of +0.008. Only the change in width was statistically significant. Applying a simple retrospective screening paradigm based solely on vessel width and tortuosity yields a screening test with a sensitivity and specificity of 82% and 75%. Factors confounding a more accurate test include poor image quality, inaccuracies in vessel segmentation, inaccuracies in measurement of vessel width and tortuosity, and limitations inherent in screening based solely on examination of the posterior pole.     

基于各向异性扩散和小波变换的磁共振图像降噪和增强方法

降噪是医学图像处理中一个非常重要的问题,传统去噪方法在降低噪声的同时会模糊图像的边缘,各向异性扩散滤波在降低图像噪声的同时能够使图像的边缘得到保持.利用小波变换可以对图像进行多尺度分解,使我们可以在不同尺度上对图像进行处理.本文利用各向异性扩散滤波对MRI图像进行降噪,然后利用平稳小波变换对图像进行增强处理.实验结果表明,该方法在有效去除噪声的同时能够增强图像的细节,有效地提高了图像的质量.     

Linear regression with spatial constraint to generate parametric images of ligand-receptor dynamic PET studies with a simplified reference tissue model

For the quantitative analysis of ligand-receptor dynamic positron emission tomography (PET) studies, it is often desirable to apply reference tissue methods that eliminate the need for arterial blood sampling. A common technique is to apply a simplified reference tissue model (SRTM). Applications of this method are generally based on an analytical solution of the SRTM equation with parameters estimated by nonlinear regression. In this study, we derive, based on the same assumptions used to derive the SRTM, a new set of operational equations of integral form with parameters directly estimated by conventional weighted linear regression (WLR). In addition, a linear regression with spatial constraint (LRSC) algorithm is developed for parametric imaging to reduce the effects of high noise levels in pixel time activity curves that are typical of PET dynamic data. For comparison, conventional weighted nonlinear regression with the Marquardt algorithm (WNLRM) and nonlinear ridge regression with spatial constraint (NLRRSC) were also implemented using the nonlinear analytical solution of the SRTM equation. In contrast to the other three methods, LRSC reduces the percent root mean square error of the estimated parameters, especially at higher noise levels. For estimation of binding potential (BP), WLR and LRSC show similar variance even at high noise levels, but LRSC yields a smaller bias. Results from human studies demonstrate that LRSC produces high-quality parametric images. The variance of R(1) and k(2) images generated by WLR, WNLRM, and NLRRSC can be decreased 30%-60% by using LRSC. The quality of the BP images generated by WLR and LRSC is visually comparable, and the variance of BP images generated by WNLRM can be reduced 10%-40% by WLR or LRSC. The BP estimates obtained using WLR are 3%-5% lower than those estimated by LRSC. We conclude that the new linear equations yield a reliable, computationally efficient, and robust LRSC algorithm to generate parametric images of ligand-receptor dynamic PET studies.     

Breast Ultrasound Despeckling Using Anisotropic Diffusion Guided by Texture Descriptors

Breast ultrasound (BUS) is considered the most important adjunct method to mammography for diagnosing cancer. However, this image modality suffers from an intrinsic artifact called speckle noise, which degrades spatial and contrast resolution and obscures the screened anatomy. Hence, it is necessary to reduce speckle artifacts before performing image analysis by means of computer-aided diagnosis systems, for example. In addition, the trade-off between smoothing level and preservation of lesion contour details should be addressed by speckle reduction schemes. In this scenario, we propose a BUS despeckling method based on anisotropic diffusion guided by Log–Gabor filters (ADLG). Because we assume that different breast tissues have distinct textures, in our approach we perform a multichannel decomposition of the BUS image using Log–Gabor filters. Next, the conduction coefficient of anisotropic diffusion filtering is computed using texture responses instead of intensity values as stated originally. The proposed algorithm is validated using both synthetic and real breast data sets, with 900 and 50 images, respectively. The performance measures are compared with four existing speckle reduction schemes based on anisotropic diffusion: conventional anisotropic diffusion filtering (CADF), speckle-reducing anisotropic diffusion (SRAD), texture-oriented anisotropic diffusion (TOAD), and interference-based speckle filtering followed by anisotropic diffusion (ISFAD). The validity metrics are the Pratt’s figure of merit, for synthetic images, and the mean radial distance (in pixels), for real sonographies. Figure of merit and mean radial distance indices should tend toward ‘1’ and ‘0’, respectively, to indicate adequate edge preservation. The results suggest that ADLG outperforms the four speckle removal filters compared with respect to simulated and real BUS images. For each method—ADLG, CADF, SRAD, TOAD and ISFAD—the figure of merit median values are 0.83, 0.40, 0.39, 0.51 and 0.59, and the mean radial distance median results are 4.19, 6.29, 6.39, 6.43 and 5.88.     

Using nonlinear diffusion and mean shift to detect and connect cross-sections of axons in 3D optical microscopy images

The morphology of neuronal axons has been actively investigated by researchers to understand functionalities of neuronal networks, for example, in developmental neurology. Today's optical microscope and labeling techniques allow us to obtain high-resolution images about axons in three dimensions (3D), however, it remains challenging to segment and reconstruct the 3D morphology of axons. These include differentiating adjacent axons and detecting the axon branches. In this paper we present a method to track axons in 3D by identifying cross-sections of axons on 2D images and connecting the cross-sections over a series of 2D images to reconstruct the 3D morphology. The method can separate adjacent axons and detect the split and merge of axons. The method consists of three steps, modified nonlinear diffusion to remove noise and enhance edges in 2D, morphological operations to detect edges of the cross-sections of axons in 2D, and mean shift to track the cross-sections of axons in 3D. Performance of the method is demonstrated by processing real data acquired by confocal laser scanning microscopy.     

k-means based hybrid wavelet and curvelet transform approach for denoising of remotely sensed images

This article presents a new technique for denoising of remotely sensed images based on multi-resolution analysis (MRA). Multi-resolution techniques provide a coarse-to-fine and scale-invariant decomposition of images for image processing and analysis. The multi-resolution image analysis methods have the ability to analyse the image in an adaptive manner, capturing local as well as global information. Further, noise, as one of the biggest obstacles for image analysis and for further processing, is effectively handled by multi-resolution methods. The article aims at the analysis of noise filtering of image using wavelets and curvelets methods on multispectral images acquired by the QuickBird and medium-resolution Landsat Thematic Mapper satellite systems. To improve the performance of noise filtering, an iterative thresholding scheme and a hybrid approach based on wavelet and curvelet transforms are proposed for restoring the image from its noisy version. Two comparative measures are used for evaluation of the performance of the methods for denoising. One of them is the peak signal-to-noise ratio and the second is the ability of the noise filtering scheme to preserve the sharpness of the edges. By both of these comparative measures, the hybrid approach of curvelet and wavelet for heterogeneous and homogeneous areas with iterative threshold has proved to be better than the others. Results are illustrated using QuickBird and Landsat images for proposed methods and compared with wavelets and curvelet-based denoising.     

Filtering and segmentation of 3D angiographic data: Advances based on mathematical morphology

In the last 20 years, 3D angiographic imaging has proven its usefulness in the context of various clinical applications. However, angiographic images are generally difficult to analyse due to their size and the complexity of the data that they represent, as well as the fact that useful information is easily corrupted by noise and artifacts. Therefore, there is an ongoing necessity to provide tools facilitating their visualisation and analysis, while vessel segmentation from such images remains a challenging task. This article presents new vessel segmentation and filtering techniques, relying on recent advances in mathematical morphology. In particular, methodological results related to spatially variant mathematical morphology and connected filtering are stated, and included in an angiographic data processing framework. These filtering and segmentation methods are evaluated on real and synthetic 3D angiographic data.     

Robust strain-estimation algorithm using combined radiofrequency and envelope cross-correlation with diffusion filtering

In ultrasound elastography, the strain in compressed tissue due to external deformation is estimated and is smaller in harder than softer tissue. With increased stress, the nonaxial motions of tissue elements increase and result in noisier strain images. At high strain, the envelope of the rf signal exhibits robustness to signal decorrelation. However, the precision of strain estimates using envelope signals is much worse compared to that using the rf signals. In this paper, we propose a novel approach for robust strain estimation by combining weighted rf cross-correlation and envelope cross-correlation functions. An applied strain-dependent piecewise-linear-weight is used for this purpose. In addition, we introduce nonlinear diffusion filtering to further enhance the resulting strain image. The results of our algorithm are demonstrated for up to 10% applied strain using a finite-element modelling (FEM) simulation phantom. It reveals that the elastographic signal-to-noise ratio (SNRe) and the elastographic contrast-to-noise ratio (CNRe) of the strain images can be improved more significantly than with other algorithms used in this paper. In addition, comparative results in terms of the mean structural similarity (MSSIM) using in vivo breast data show that the strain image quality can be improved noticeably by the proposed method than with the techniques employed in this work.     

基于区域生长超声图像分割血管边界反映血管病变

背景:通过分析超声血管图像能反映血管的病变情况。目的:采用区域生长理论对超声图像进行图像分割,分析边界点的相对位移。方法:先对视频图像分帧,将动态图像转换为静态图像,采用Gabor滤波、自适应直方图量化去除超声图像噪声,然后运用区域生长法对图像做分割,接着通过开闭运算、sobel算子检测图像边界,最后提取出两条血管边界。结果与结论:通过Gabor滤波、区域生长法等手段,得到了比较好的分割结果。区域生长法在处理速度上满足了实时性要求,具有一定的通用性。并且通过分析边界点的相对位移曲线,一定程度上反映血管的病变。     

B-mode compound imaging in mice

Cross-sectional B-mode images were obtained from a dead mouse for a 360 degrees scan around the mouse using a 12-MHz linear array. For each cross-section, a set of aligned images was obtained after rotation about the isocenter, which were added to produce a single compound image. The compound images demonstrated a substantial improvement over single B-mode images, with uniform image quality, low noise and improved visualization of structures. This technique may be of interest in forming the basis for a new 3-D in vivo technique in the abdomen and pelvic regions, providing high-quality ultrasound images that are not dependent on operator skill. A further development worth pursuing for improved spatial resolution is reconstruction-based tomography.     

Efficient workflow for automatic segmentation of the right heart based on 2D echocardiography

The present study aimed to present a workflow algorithm for automatic processing of 2D echocardiography images. The workflow was based on several sequential steps. For each step, we compared different approaches. Epicardial 2D echocardiography datasets were acquired during various open-chest beating-heart surgical procedures in three porcine hearts. We proposed a metric called the global index that is a weighted average of several accuracy coefficients, indices and the mean processing time. This metric allows the estimation of the speed and accuracy for processing each image. The global index ranges from 0 to 1, which facilitates comparison between different approaches. The second step involved comparison among filtering, sharpening and segmentation techniques. During the noise reduction step, we compared the median filter, total variation filter, bilateral filter, curvature flow filter, non-local means filter and mean shift filter. To clarify the endocardium borders of the right heart, we used the linear sharpen. Lastly, we applied watershed segmentation, clusterisation, region-growing, morphological segmentation, image foresting segmentation and isoline delineation. We assessed all the techniques and identified the most appropriate workflow for echocardiography image segmentation of the right heart. For successful processing and segmentation of echocardiography images with minimal error, we found that the workflow should include the total variation filter/bilateral filter, linear sharpen technique, isoline delineation/region-growing segmentation and morphological post-processing. We presented an efficient and accurate workflow for the precise diagnosis of cardiovascular diseases. We introduced the global index metric for image pre-processing and segmentation estimation.     

Real-time MR diffusion tensor and Q-ball imaging using Kalman filtering

Diffusion magnetic resonance imaging (dMRI) has become an established research tool for the investigation of tissue structure and orientation. In this paper, we present a method for real-time processing of diffusion tensor and Q-ball imaging. The basic idea is to use Kalman filtering framework to fit either the linear tensor or Q-ball model. Because the Kalman filter is designed to be an incremental algorithm, it naturally enables updating the model estimate after the acquisition of any new diffusion-weighted volume. Processing diffusion models and maps during ongoing scans provides a new useful tool for clinicians, especially when it is not possible to predict how long a subject may remain still in the magnet. First, we introduce the general linear models corresponding to the two diffusion tensor and analytical Q-ball models of interest. Then, we present the Kalman filtering framework and we focus on the optimization of the diffusion orientation sets in order to speed up the convergence of the online processing. Last, we give some results on a healthy volunteer for the online tensor and the Q-ball model, and we make some comparisons with the conventional offline techniques used in the literature. We could achieve full real-time for diffusion tensor imaging and deferred time for Q-ball imaging, using a single workstation.     

Gaussianization of Diffusion MRI Data Using Spatially Adaptive Filtering

Diffusion MRI magnitude data, typically Rician or noncentral $\chi$ distributed, is affected by the noise floor, which falsely elevates signal, reduces image contrast, and biases estimation of diffusion parameters. Noise floor can be avoided by extracting real-valued Gaussian-distributed data from complex diffusion-weighted images via phase correction, which is performed by rotating each complex diffusion-weighted image based on its phase so that the actual image content resides in the real part. The imaginary part can then be discarded, leaving only the real part to form a Gaussian-noise image that is not confounded by the noise floor. The effectiveness of phase correction depends on the estimation of the background phase associated with factors such as brain motion, cardiac pulsation, perfusion, and respiration. Most existing smoothing techniques, applied to the real and imaginary images for phase estimation, assume spatially-stationary noise. This assumption does not necessarily hold in real data. In this paper, we introduce an adaptive filtering approach, called multi-kernel filter (MKF), for image smoothing catering to spatially-varying noise. Inspired by the mechanisms of human vision, MKF employs a bilateral filter with spatially-varying kernels. Extensive experiments demonstrate that MKF significantly improves spatial adaptivity and outperforms various state-of-the-art filters in signal Gaussianization.     

Comparison of regularization methods for human cardiac diffusion tensor MRI

Diffusion tensor MRI (DT-MRI) is an imaging technique that is gaining importance in clinical applications. However, there is very little work concerning the human heart. When applying DT-MRI to in vivo human hearts, the data have to be acquired rapidly to minimize artefacts due to cardiac and respiratory motion and to improve patient comfort, often at the expense of image quality. This results in diffusion weighted (DW) images corrupted by noise, which can have a significant impact on the shape and orientation of tensors and leads to diffusion tensor (DT) datasets that are not suitable for fibre tracking. This paper compares regularization approaches that operate either on diffusion weighted images or on diffusion tensors. Experiments on synthetic data show that, for high signal-to-noise ratio (SNR), the methods operating on DW images produce the best results; they substantially reduce noise error propagation throughout the diffusion calculations. However, when the SNR is low, Rician Cholesky and Log-Euclidean DT regularization methods handle the bias introduced by Rician noise and ensure symmetry and positive definiteness of the tensors. Results based on a set of sixteen ex vivo human hearts show that the different regularization methods tend to provide equivalent results.