A Fast Image Alignment Approach for 2D Classification of Cryo-EM Images Using Spectral Clustering

Three-dimensional (3D) reconstruction in single-particle cryo-electron microscopy (cryo-EM) is a significant technique for recovering the 3D structure of proteins or other biological macromolecules from their two-dimensional (2D) noisy projection images taken from unknown random directions. Class averaging in single-particle cryo-EM is an important procedure for producing high-quality initial 3D structures, where image alignment is a fundamental step. In this paper, an efficient image alignment algorithm using 2D interpolation in the frequency domain of images is proposed to improve the estimation accuracy of alignment parameters of rotation angles and translational shifts between the two projection images, which can obtain subpixel and subangle accuracy. The proposed algorithm firstly uses the Fourier transform of two projection images to calculate a discrete cross-correlation matrix and then performs the 2D interpolation around the maximum value in the cross-correlation matrix. The alignment parameters are directly determined according to the position of the maximum value in the cross-correlation matrix after interpolation. Furthermore, the proposed image alignment algorithm and a spectral clustering algorithm are used to compute class averages for single-particle 3D reconstruction. The proposed image alignment algorithm is firstly tested on a Lena image and two cryo-EM datasets. Results show that the proposed image alignment algorithm can estimate the alignment parameters accurately and efficiently. The proposed method is also used to reconstruct preliminary 3D structures from a simulated cryo-EM dataset and a real cryo-EM dataset and to compare them with RELION. Experimental results show that the proposed method can obtain more high-quality class averages than RELION and can obtain higher reconstruction resolution than RELION even without iteration.     

Alignment of two-dimensional electrophoresis gels

Two-dimensional electrophoresis is a major separating technique for proteins in proteomics. Alignment of gel images is critical for intra-laboratory or even more difficult inter-laboratory gel comparisons. In the paper, we propose a novel iterative closest point (ICP) method for 2D-gel electrophoresis image alignment. The paper seeks to introduce an information theoretic measure as one part of distance metric to gel image alignment. We combine intensity information of spots with geometric information of landmarks by applying information potential idea. The proposed method has been applied to both synthetic and real gel images accessible in public 2D-electrophoresis gel protein databases. The high accuracy and robustness of the algorithm indicate that it is promising for gel image alignment.     

Registration accuracy and quality of real-life images

Background

A common registration problem for the application of consumer device is to align all the acquired image sequences into a complete scene. Image alignment requires a registration algorithm that will compensate as much as possible for geometric variability among images. However, images captured views from a real scene usually produce different distortions. Some are derived from the optic characteristics of image sensors, and others are caused by the specific scenes and objects.

Methodology/Principal Findings

An image registration algorithm considering the perspective projection is proposed for the application of consumer devices in this study. It exploits a multiresolution wavelet-based method to extract significant features. An analytic differential approach is then proposed to achieve fast convergence of point matching. Finally, the registration accuracy is further refined to obtain subpixel precision by a feature-based modified Levenberg-Marquardt method. Due to its feature-based and nonlinear characteristic, it converges considerably faster than most other methods. In addition, vignette compensation and color difference adjustment are also performed to further improve the quality of registration results.

Conclusions/Significance

The performance of the proposed method is evaluated by testing the synthetic and real images acquired by a hand-held digital still camera and in comparison with two registration techniques in terms of the squared sum of intensity differences (SSD) and correlation coefficient (CC). The results indicate that the proposed method is promising in registration accuracy and quality, which are statistically significantly better than other two approaches.     

Correction of inhomogeneous magnetic resonance images using multiscale retinex for segmentation accuracy improvement

The purpose of this study was to improve the accuracy of tissue segmentation on brain magnetic resonance (MR) images preprocessed by multiscale retinex (MSR), segmented with a combined boosted decision tree (BDT) and MSR algorithm (hereinafter referred to as the MSRBDT algorithm). Simulated brain MR (SBMR) T1-weighted images of different noise levels and RF inhomogeneities were adopted to evaluate the outcome of the proposed method; the MSRBDT algorithm was used to identify the gray matter (GM), white matter (WM), and cerebral-spinal fluid (CSF) in the brain tissues. The accuracy rates of GM, WM, and CSF segmentation, with spatial features (G, x, y, r, θ), were respectively greater than 0.9805, 0.9817, and 0.9871. In addition, images segmented with the MSRBDT algorithm were better than those obtained with the expectation maximization (EM) algorithm; brain tissue segmentation in MR images was significantly more precise. The proposed MSRBDT algorithm could be beneficial in clinical image segmentation.     

Measuring alignment of the hindfoot

In subtalar arthrodesis operations, correction of the hindfoot alignment is performed in about half of the cases. To improve the quality of the operation, a measurement system was developed which reliably measures the hindfoot angle pre-, per-, and postoperatively. This device was evaluated by measuring subjects in standing weightbearing position and in prone nonweightbearing position. The results were compared with hindfoot angles constructed on posterior photographic images. The results are similar to other studies (all maximum values): intratester accuracy 1.4 degrees, intertester accuracy 2.2 degrees, intratester reliability 0.9, and intertester reliability 0.74. The proposed device will improve the quality of correction, because it enables peroperative measurement of hindfoot alignment.     

A Practical Approach Based on Analytic Deformable Algorithm for Scenic Image Registration

Background

Image registration is to produce an entire scene by aligning all the acquired image sequences. A registration algorithm is necessary to tolerance as much as possible for intensity and geometric variation among images. However, captured image views of real scene usually produce unexpected distortions. They are generally derived from the optic characteristics of image sensors or caused by the specific scenes and objects.

Methods and Findings

An analytic registration algorithm considering the deformation is proposed for scenic image applications in this study. After extracting important features by the wavelet-based edge correlation method, an analytic registration approach is then proposed to achieve deformable and accurate matching of point sets. Finally, the registration accuracy is further refined to obtain subpixel precision by a feature-based Levenberg-Marquardt (FLM) method. It converges evidently faster than most other methods because of its feature-based characteristic.

Conclusions

We validate the performance of proposed method by testing with synthetic and real image sequences acquired by a hand-held digital still camera (DSC) and in comparison with an optical flow-based motion technique in terms of the squared sum of intensity differences (SSD) and correlation coefficient (CC). The results indicate that the proposed method is satisfactory in the registration accuracy and quality of DSC images.     

Alignment error envelopes for single particle analysis

To determine the structure of a biological particle to high resolution by electron microscopy, image averaging is required to combine information from different views and to increase the signal-to-noise ratio. Starting from the number of noiseless views necessary to resolve features of a given size, four general factors are considered that increase the number of images actually needed: (1) the physics of electron scattering introduces shot noise, (2) thermal motion and particle inhomogeneity cause the scattered electrons to describe a mixture of structures, (3) the microscope system fails to usefully record all the information carried by the scattered electrons, and (4) image misalignment leads to information loss through incoherent averaging. The compound effect of factors 2-4 is approximated by the product of envelope functions. The problem of incoherent image averaging is developed in detail through derivation of five envelope functions that account for small errors in 11 "alignment" parameters describing particle location, orientation, defocus, magnification, and beam tilt. The analysis provides target error tolerances for single particle analysis to near-atomic (3.5 A) resolution, and this prospect is shown to depend critically on image quality, defocus determination, and microscope alignment.     

温室白粉虱自动计数技术研究初报

应用计算机视觉技术对温室白粉虱自动计数技术进行了研究。采用胶卷照相机和家用摄像机对田间温室白粉虱等生的叶片进行拍摄,以获得其数字图象,对白粉虱图象的分割采用Ｊohannsen基于熵的分割算法,对分割后的二值图象利用区域标记算法得到白粉虱个体的数量。对叶片挨在一起的白粉虱个体采用数学形态学算法进行了分离。用１９个虫叶片样本的统计结果表明,直接利用分割图象进行白粉虱个体计数的累积准确率达９１．９９％,而分离处理的算法则需要改进,因此,这一技术具有进一步在生态研究和ＩＰＭ实践中推广的可能性,这将使田间微小昆虫的种群数量监测和测查的工作量大幅度降低,而铉得到显著提高。     

An Active Contour Model for the Segmentation of Images with Intensity Inhomogeneities and Bias Field Estimation

Intensity inhomogeneity causes many difficulties in image segmentation and the understanding of magnetic resonance (MR) images. Bias correction is an important method for addressing the intensity inhomogeneity of MR images before quantitative analysis. In this paper, a modified model is developed for segmenting images with intensity inhomogeneity and estimating the bias field simultaneously. In the modified model, a clustering criterion energy function is defined by considering the difference between the measured image and estimated image in local region. By using this difference in local region, the modified method can obtain accurate segmentation results and an accurate estimation of the bias field. The energy function is incorporated into a level set formulation with a level set regularization term, and the energy minimization is conducted by a level set evolution process. The proposed model first appeared as a two-phase model and then extended to a multi-phase one. The experimental results demonstrate the advantages of our model in terms of accuracy and insensitivity to the location of the initial contours. In particular, our method has been applied to various synthetic and real images with desirable results.     

Automatic signal classification in fluorescence in situ hybridization images

BACKGROUND: Previous systems for dot (signal) counting in fluorescence in situ hybridization (FISH) images have relied on an auto-focusing method for obtaining a clearly defined image. Because signals are distributed in three dimensions within the nucleus and artifacts such as debris and background fluorescence can attract the focusing method, valid signals can be left unfocused or unseen. This leads to dot counting errors, which increase with the number of probes. METHODS: The approach described here dispenses with auto-focusing, and instead relies on a neural network (NN) classifier that discriminates between in and out-of-focus images taken at different focal planes of the same field of view. Discrimination is performed by the NN, which classifies signals of each image as valid data or artifacts (due to out of focusing). The image that contains no artifacts is the in-focus image selected for dot count proportion estimation. RESULTS: Using an NN classifier and a set of features to represent signals improves upon previous discrimination schemes that are based on nonadaptable decision boundaries and single-feature signal representation. Moreover, the classifier is not limited by the number of probes. Three classification strategies, two of them hierarchical, have been examined and found to achieve each between 83% and 87% accuracy on unseen data. Screening, while performing dot counting, of in and out-of-focus images based on signal classification suggests an accurate and efficient alternative to that obtained using an auto-focusing mechanism.     

Bionic Mosaic Method of Panoramic Image Based on Compound Eye of Fly

To satisfy the requirements of real-time and high quality mosaics,a bionic compound eye visual system was designed by simulating the visual mechanism of a fly compound eye.Several CCD cameras were used in this system to imitate the small eyes of a compound eye.Based on the optical analysis of this system,a direct panoramic image mosaic algorithm was proposed.Several sub-images were collected by the bionic compound eye visual system,and then the system obtained the overlapping proportions of these sub-images and cut the overlap sections of the neighboring images.Thus,a panoramic image with a large field of view was directly mosaicked,which expanded the field and guaranteed the high resolution.The experimental results show that the time consumed by the direct mosaic algorithm is only 2.2％ of that by the traditional image mosaic algorithm while guaranteeing mosaic quality.Furthermore,the proposed method effectively solved the problem of misalignment of the mosaic image and eliminated mosaic cracks as a result of the illumination factor and other factors.This method has better real-time properties compared to other methods.     

基于邻域最大差值与区域合并的油茶毒蛾幼虫图像分割

【目的】油茶树害虫的种类较多,其中油茶毒蛾Euproctis pseudoconspersa幼虫是危害较大的害虫之一。为完成油茶毒蛾幼虫的自动检测需要对其图像进行分割,油茶毒蛾幼虫图像的分割效果直接影响到图像的自动识别。【方法】本文提出了基于邻域最大差值与区域合并的油茶毒蛾幼虫图像分割算法,该方法主要是对相邻像素RGB的3个分量进行差值运算,最大差值若为0,则进行相邻像素合并得出初始的分割图像,根据合并准则进一步合并,得到最终分割结果。【结果】实验结果表明,该算法可以快速有效地将油茶毒蛾幼虫图像中的背景和虫体分割开来。【结论】使用JSEG分割算法、K均值聚类分割算法、快速几何可变形分割算法和本文算法对油茶毒蛾幼虫图像进行分割,将结果进行对比发现本文方法的分割效果最佳,且处理时间较短。     

An iterative region-growing process for cell image segmentation based on local color similarity and global shape criteria

An image segmentation process was derived from an image model that assumed that cell images represent objects having characteristic relationships, limited shape properties and definite local color features. These assumptions allowed the design of a region-growing process in which the color features were used to iteratively aggregate image points in alternation with a test of the convexity of the aggregate obtained. The combination of both local and global criteria allowed the self-adaptation of the algorithm to segmentation difficulties and led to a self-assessment of the adequacy of the final segmentation result. The quality of the segmentation was evaluated by visual control of the match between cell images and the corresponding segmentation masks proposed by the algorithm. A comparison between this region-growing process and the conventional gray-level thresholding is illustrated. A field test involving 700 bone marrow cells, randomly selected from May-Grünwald-Giemsa-stained smears, allowed the evaluation of the efficiency, effectiveness and confidence of the algorithm: 96% of the cells were evaluated as correctly segmented by the algorithm's self-assessment of adequacy, with a 98% confidence. The principles of the other major segmentation algorithms are also reviewed.     

Computer vision technique for freshness estimation from segmented eye of fish image

Preserving the quality of fish is a challenging task. Several different cooling methods and materials are used during their storage, transportation purpose. These are responsible factors that decide the freshness of a post harvested fish. In this proposed algorithm, a computer vision-based technique is developed to predict the freshness level of fish from its image. Eyes of the fish are considered as the region of interest, as a good correlation has been observed between the colour of the eye and different duration of storage day. It is segmented from the image of a fish sample and then a strategic framework is used for extraction of the discriminatory features. These extracted features show a degradation pattern which acts as an indicative parameter to determine the level of freshness of sample of fish. The proposed method provides a recognition accuracy of 96.67%. The experimental results indicate that this is an efficient and non-destructive methodology for detecting the fish freshness. The high accuracy of freshness detection and low computation time makes this non-destructive methodology efficient for real-world usage in the fish industry and market.     

Normalization of multicolor fluorescence in situ hybridization (M-FISH) images for improving color karyotyping.

BACKGROUND: Multiplex or multicolor fluorescence in situ hybridization (M-FISH) is a recently developed cytogenetic technique for cancer diagnosis and research on genetic disorders. By simultaneously viewing the multiply labeled specimens in different color channels, M-FISH facilitates the detection of subtle chromosomal aberrations. The success of this technique largely depends on the accuracy of pixel classification (color karyotyping). Improvements in classifier performance would allow the elucidation of more complex and more subtle chromosomal rearrangements. Normalization of M-FISH images has a significant effect on the accuracy of classification. In particular, misalignment or misregistration across multiple channels seriously affects classification accuracy. Image normalization, including automated registration, must be done before pixel classification. METHODS AND RESULTS: We studied several image normalization approaches that affect image classification. In particular, we developed an automated registration technique to correct misalignment across the different fluor images (caused by chromatic aberration and other factors). This new registration algorithm is based on wavelets and spline approximations that have computational advantages and improved accuracy. To evaluate the performance improvement brought about by these data normalization approaches, we used the downstream pixel classification accuracy as a measurement. A Bayesian classifier assumed that each of 24 chromosome classes had a normal probability distribution. The effects that this registration and other normalization steps have on subsequent classification accuracy were evaluated on a comprehensive M-FISH database established by Advanced Digital Imaging Research (http://www.adires.com/05/Project/MFISH_DB/MFISH_DB.shtml). CONCLUSIONS: Pixel misclassification errors result from different factors. These include uneven hybridization, spectral overlap among fluors, and image misregistration. Effective preprocessing of M-FISH images can decrease the effects of those factors and thereby increase pixel classification accuracy. The data normalization steps described in this report, such as image registration and background flattening, can significantly improve subsequent classification accuracy. An improved classifier in turn would allow subtle DNA rearrangements to be identified in genetic diagnosis and cancer research.     

不同光谱类型对银川平原土壤含盐量反演精度的影响与校正

土壤盐渍化是导致土壤质量下降、耕地减产的重要因素之一。为准确快速评价银川平原土壤含盐量,本研究对野外高光谱数据和室内高光谱数据进行一阶微分(FDR)变换,逐步回归(SR)筛选特征波段,利用偏最小二乘回归(PLSR)与支持向量机(SVM)进行建模,明确适用于本地区土壤含盐量准确反演的光谱类型,并对较差光谱类型进行分段校正与全局校正,尝试提高土壤含盐量反演精度。结果表明: 基于野外光谱的土壤含盐量反演模型精度比室内光谱平均高58.9%;对室内光谱进行分段校正、全局校正后反演精度均有提高,其中,PLSR以分段校正精度更高,建模决定系数(R_c²)、验证决定系数(R_p²)和相对分析误差(RPD)分别为0.790、0.633和1.64,而SVM以全局校正精度更高,R_c²、R_p²和RPD分别为0.927、0.947和3.87;SVM模型的反演精度高于PLSR,其中,野外光谱建模效果最佳,室内全局校正光谱与室内分段校正光谱次之,室内光谱最差。因此,野外高光谱可实现对银川平原土壤表层含盐量的定量反演,经校正的室内光谱对土壤含盐量反演精度显著提升,均可为粮食安全与生态环境高质量发展提供保障。     

Multiphase method for automatic alignment of transmission electron microscope images using markers

In order to successfully perform the 3D reconstruction in electron tomography, transmission electron microscope images must be accurately aligned or registered. So far, the problem is solved by either manually showing the corresponding fiducial markers from the set of images or automatically using simple correlation between the images on several rotations and scales. The present solutions, however, share the problem of being inefficient and/or inaccurate. We therefore propose a method in which the registration is automated using conventional colloidal gold particles as reference markers between images. We approach the problem from the computer vision viewpoint; hence, the alignment problem is divided into several subproblems: (1) finding initial matches from successive images, (2) estimating the epipolar geometry between consecutive images, (3) finding and localizing the gold particles with subpixel accuracy in each image, (4) predicting the probable matching gold particles using the epipolar constraint and its uncertainty, (5) matching and tracking the gold beads through the tilt series, and (6) optimizing the transformation parameters for the whole image set. The results show not only the reliability of the suggested method but also a high level of accuracy in alignment, since practically all the visible gold markers can be used.     

A Modified DWT-SVD Algorithm for T1-w Brain MR Images Contrast Enhancement

BackgroundImage contrast enhancement is considered as the most useful technique permitting a better appearance of the low contrast images. This paper presents a modified Discret Wavelet Transform - Singular Value Decomposition (DWT-SVD) approach for the enhancement of low contrast Brain MR Images used for brain tissues exploration.MethodsThe proposed technique is processed as follows: first of all, we consider low contrast T1-weighted MRI slices as input images (A1) on which we apply General Histogram Equalization (GHE) algorithm to have equalized images referred as (A2) having zero as mean and one as variance. Secondly, by using the Discrete Wavelet Transform (DWT) algorithm, both (A1) and (A2) are divided into low and high frequency sub-bands. On the low frequency (LL1) and (LL2) sub-bands, SVD is processed in order to generate three matrix factorization (U, V and Σ) where the maximums of (U) and (V) matrix are used for the estimation of a correction coefficient (ξ). Our contribution in this paper is to estimate the new singular value matrix (New Σ) using a weighted sum of both original and equalized singular value matrix thanks to an adjustable parameter (μ) for the targeted low contrast images. This parameter, ranged between 0.05 and 0.95, is determined empirically according to the input low contrast image. Finally, the enhanced resulting image is easily reconstructed using the Inverse SVD (ISVD) and the Inverse DWT (IDWT) processes.ResultsThe database considered in our research consisted of 120 MR brain images where T1-weighted MR brain modality are selected for the contrast enhancement process. Considering the qualitative results, our proposed contrast enhancement method have shown better distinction between brain tissues and have preserved all White Matter (WM), Gray Matter (GM) and Cerebro-Spinal Fluid (CSF) pixel edges. In fact, histogram plots of images enhanced by proposed method covered all the gray level intensities. For the quantitative results, proposed method gives the highest PSNR, QRCM, SSIM, FSIM and EME values and the lowest AMBE values for (μ) equal to 0.65 as comparing to the rest of methods. These results signifies that proposed contrast enhancement method have provided greater image quality with preservation of image structure, feature and brightness.ConclusionProposed method improved performance of contrast enhancement image without creating unwanted artifact and without destroying image edge information or affecting the specificities of brain tissues. This is due to the use of an empirically (μ) parameter adjustable according to the input MR images. Hence, the proposed approach is appropriate for enhancing contrast of huge type of low contrast images.     

Color image analysis for quantifying renal tumor angiogenesis

OBJECTIVE: To segment and quantify microvessels in renal tumor angiogenesis based on a color image analysis method and to improve the accuracy and reproducibility of quantifying microvessel density. STUDY DESIGN: The segmentation task was based on a supervised learning scheme. First, 12 color features (RGB, HSI, I1I2I3 and L*a*b*) were extracted from a training set. The feature selection procedure selected I2L*S features as the best color feature vector. Then we segmented microvessels using the discriminant function made using the minimum error rate classification rule of Bayesian decision theory. In the quantification step, after applying a connected component-labeling algorithm, microvessels with discontinuities were connected and touching microvessels separated. We tested the proposed method on 23 images. RESULTS: The results were evaluated by comparing them with manual quantification of the same images. The comparison revealed that our computerized microvessel counting correlated highly with manual counting by an expert (r = 0.95754). The association between the number of microvessels after the initial segmentation and manual quantification was also assessed using Pearson's correlation coefficient (r = 0.71187). The results indicate that our method is better than conventional computerized image analysis methods. CONCLUSION: Our method correlated highly with quantification by an expert and could become a way to improve the accuracy, feasibility and reproducibility of quantifying microvessel density. We anticipate that it will become a useful diagnostic tool for angiogenesis studies.