Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

Evaluation of denoising techniques to remove speckle and Gaussian noise from dermoscopy images

Computerized methods provide analyses of skin lesions from dermoscopy images automatically. However, the images acquired from dermoscopy devices are noisy and cause low accuracy in automated methods. Therefore, various methods have been applied for denoising in the literature. There are some review-type papers about these methods. However, their authors have focused on either denoising with a specific approach or denoising from other images rather than dermoscopy images, which have a different characteristic. It is not possible to determine which method is the most suitable for denoising from dermoscopy images according to the results presented in them. Therefore, a review on the denoising approaches applied with dermoscopy images is required and, according to our knowledge, there is no such a review-type paper. To fill this gap in the literature, the required review has been performed in this work. Also, in this work, the methods in the literature have been implemented using the same data sets containing images with speckle or Gaussian types of noise. The results have been analyzed not only visually but also quantitatively to compare capabilities of the techniques. Our experiments indicated that each denoising technique has its own disadvantages and advantages. The main contributions of this paper are three-fold: (i) A comprehensive review on the denoising approaches applied with dermoscopy images has been presented. (ii) The denoising techniques have been implemented with the same images for meaningful comparisons. (iii) Both visual and quantitative analyses with different metrics have been performed and comparative performance evaluations have been presented.

Automatic breast lesion segmentation in phase preserved DCE-MRIs

We offer a framework for automatically and accurately segmenting breast lesions from Dynamic Contrast Enhanced (DCE) MRI in this paper. The framework is built using max flow and min cut problems in the continuous domain over phase preserved denoised images. Three stages are required to complete the proposed approach. First, post-contrast and pre-contrast images are subtracted, followed by image registrations that benefit to enhancing lesion areas. Second, a phase preserved denoising and pixel-wise adaptive Wiener filtering technique is used, followed by max flow and min cut problems in a continuous domain. A denoising mechanism clears the noise in the images by preserving useful and detailed features such as edges. Then, lesion detection is performed using continuous max flow. Finally, a morphological operation is used as a post-processing step to further delineate the obtained results. A series of qualitative and quantitative trials employing nine performance metrics on 21 cases with two different MR image resolutions were used to verify the effectiveness of the proposed method. Performance results demonstrate the quality of segmentation obtained from the proposed method.

Effect of Denoising and Deblurring 18F-Fluorodeoxyglucose Positron Emission Tomography Images on a Deep Learning Model’s Classification Performance for Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common progressive neurodegenerative disease. 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) is widely used to predict AD using a deep learning model. However, the effects of noise and blurring on 18F-FDG PET images were not considered. The performance of a classification model trained using raw, deblurred (by the fast total variation deblurring method), or denoised (by the median modified Wiener filter) 18F-FDG PET images without or with cropping around the limbic system area using a 3D deep convolutional neural network was investigated. The classification model trained using denoised whole-brain 18F-FDG PET images achieved classification performance (0.75/0.65/0.79/0.39 for sensitivity/specificity/F1-score/Matthews correlation coefficient (MCC), respectively) higher than that with raw and deblurred 18F-FDG PET images. The classification model trained using cropped raw 18F-FDG PET images achieved higher performance (0.78/0.63/0.81/0.40 for sensitivity/specificity/F1-score/MCC) than the whole-brain 18F-FDG PET images (0.72/0.32/0.71/0.10 for sensitivity/specificity/F1-score/MCC, respectively). The 18F-FDG PET image deblurring and cropping (0.89/0.67/0.88/0.57 for sensitivity/specificity/F1-score/MCC) procedures were the most helpful for improving performance. For this model, the right middle frontal, middle temporal, insula, and hippocampus areas were the most predictive of AD using the class activation map. Our findings demonstrate that 18F-FDG PET image preprocessing and cropping improves the explainability and potential clinical applicability of deep learning models.

Performance Evaluation of Dorsal Vein Network of Hand Imaging Using Relative Total Variation-Based Regularization for Smoothing Technique in a Miniaturized Vein Imaging System: A Pilot Study

Vein puncture is commonly used for blood sampling, and accurately locating the blood vessel is an important challenge in the field of diagnostic tests. Imaging systems based on near-infrared (NIR) light are widely used for accurate human vein puncture. In particular, segmentation of a region of interest using the obtained NIR image is an important field, and research for improving the image quality by removing noise and enhancing the image contrast is being widely conducted. In this paper, we propose an effective model in which the relative total variation (RTV) regularization algorithm and contrast-limited adaptive histogram equalization (CLAHE) are combined, whereby some major edge information can be better preserved. In our previous study, we developed a miniaturized NIR imaging system using light with a wavelength of 720–1100 nm. We evaluated the usefulness of the proposed algorithm by applying it to images acquired by the developed NIR imaging system. Compared with the conventional algorithm, when the proposed method was applied to the NIR image, the visual evaluation performance and quantitative evaluation performance were enhanced. In particular, when the proposed algorithm was applied, the coefficient of variation was improved by a factor of 15.77 compared with the basic image. The main advantages of our algorithm are the high noise reduction efficiency, which is beneficial for reducing the amount of undesirable information, and better contrast. In conclusion, the applicability and usefulness of the algorithm combining the RTV approach and CLAHE for NIR images were demonstrated, and the proposed model can achieve a high image quality.

Determination of the Geographical Origin of Walnuts (Juglans regia L.) Using Near-Infrared Spectroscopy and Chemometrics

The prices of walnuts vary according to their geographical origin and, therefore, offer a financial incentive for adulteration. A reliable analysis method is required to quickly detect possible misdeclarations and thus prevent food fraud. In this study, a method to distinguish between seven geographical origins of walnuts using Fourier transform near-infrared (FT-NIR) spectroscopy combined with chemometrics as a fast, versatile, and easy to handle analytical tool was developed. NIR spectra of 212 ground and afterwards freeze-dried walnut samples, harvested in three consecutive years (2017-2019), were collected. We optimized the data pre-processing by applying and evaluating 50,545 different pre-processing combinations, followed by linear discriminant analysis (LDA) which was confirmed by nested cross-validation. The results show that in the scope of our research minimal pre-processing led to the best results: By applying just multiplicative scatter correction (MSC) and median centering, a classification accuracy of 77.00% ± 1.60% was achieved. Consequently, this complex model can be used to answer economically relevant questions e.g., to distinguish between European and Chinese walnuts. Furthermore, the great influence of the applied pre-processing methods, e.g., the selected wavenumber range, on the achieved classification accuracy is shown which underlines the importance of optimization of the pre-processing strategy.

Adaptive Processing for EM Telemetry Signal Recovery: Field Data from Sichuan Province

This paper deals with the study of multi-channel adaptive noise cancellation with a focus on its application in electromagnetic (EM) telemetry. We presented new variable step-size least mean square (LMS) techniques: regularized variable step-size LMS and regularized sigmoid variable size LMS, for electromagnetic telemetry data processing. Considering the complexity and spatial distribution of environmental noise, algorithms with multiple reference signals were used to retrieve transmitted EM signals. The feasibility of the regularized variable step size LMS algorithms with numerical simulation was analyzed and presented. The adaptive processing techniques were applied in the recovery of frequency and binary phase shift key modulated signal. The proposed multi-channel adaptive technique achieves fast convergence speed, low mean squared error and is shown to have good convergence characteristics compared to conventional methods. In addition to attaining good results from the multi-channel adaptive filter and performing the signal analysis in real-time, we implemented combined fast effective impulse noise removal techniques. The combination of median and mean filters was effective in removing a wide range of impulsive noises without distorting any other data points. Further, electromagnetic telemetry data were acquired during a drilling operation in Sichuan province, China, for real field application. Data processing workflow was designed for EM telemetry data processing based on the noise characteristics, simulation results and expected result for demodulation. To establish a comprehensive overview, a performance comparison of the acquisition array system is also provided. Conclusively, the introduced multichannel adaptive noise canceling techniques are very effective in recovering transmitted EM telemetry signals.

Preliminary study of improved median filter using adaptively mask size in light microscopic image

This study aimed to develop and evaluate an improved median filter (IMF) with an adaptive mask size for light microscope (LM) images. We acquired images of the mouse first molar using a LM at 100× magnification. The images obtained using our proposed IMF were compared with those from a conventional median filter. Several parameters such as the contrast-to-noise ratio, coefficient of variation, no-reference assessments and peak signal-to-noise ratio were employed to evaluate the image quality quantitatively. The results demonstrated that the proposed IMF could effectively de-noise the LM images and preserve the image details, achieving a better performance than the conventional median filter.

Machine Learning Analysis for Quantitative Discrimination of Dried Blood Droplets

One of the most interesting and everyday natural phenomenon is the formation of different patterns after the evaporation of liquid droplets on a solid surface. The analysis of dried patterns from blood droplets has recently gained a lot of attention, experimentally and theoretically, due to its potential application in diagnostic medicine and forensic science. This paper presents evidence that images of dried blood droplets have a signature revealing the exhaustion level of the person, and discloses an entirely novel approach to studying human dried blood droplet patterns. We took blood samples from 30 healthy young male volunteers before and after exhaustive exercise, which is well known to cause large changes to blood chemistry. We objectively and quantitatively analysed 1800 images of dried blood droplets, developing sophisticated image processing analysis routines and optimising a multivariate statistical machine learning algorithm. We looked for statistically relevant correlations between the patterns in the dried blood droplets and exercise-induced changes in blood chemistry. An analysis of the various measured physiological parameters was also investigated. We found that when our machine learning algorithm, which optimises a statistical model combining Principal Component Analysis (PCA) as an unsupervised learning method and Linear Discriminant Analysis (LDA) as a supervised learning method, is applied on the logarithmic power spectrum of the images, it can provide up to 95% prediction accuracy, in discriminating the physiological conditions, i.e., before or after physical exercise. This correlation is strongest when all ten images taken per volunteer per condition are averaged, rather than treated individually. Having demonstrated proof-of-principle, this method can be applied to identify diseases.

Applications of the Whittaker smoother in NMR spectroscopy

The Whittaker smoother, a special case of penalized least square, is a multipurpose algorithm that has proven to be very useful in many scientific fields, including image processing, chromatography, and optical spectroscopy. It shares many similarities with the Savitzky-Golay algorithm, but it is significantly faster and easier to automate. Its use in nuclear magnetic resonance, however, is not widespread although several applications have recently been published. In this review, the mathematical background of the method and its main applications in nuclear magnetic resonance spectroscopy will be discussed.

Automatic and fast segmentation of breast region-of-interest (ROI) and density in MRIs

Accurate segmentation of the breast region of interest (BROI) and breast density (BD) is a significant challenge during the analysis of breast MR images. Most of the existing methods for breast segmentation are semi-automatic and limited in their ability to achieve accurate results. This is because of difficulties in removing landmarks from noisy magnetic resonance images (MRI) due to similar intensity levels and the close connection to BROI. This study proposes an innovative, fully automatic and fast segmentation approach to identify and remove landmarks such as the heart and pectoral muscles. The BROI segmentation is carried out with a framework consisting of three major steps. Firstly, we use adaptive wiener filtering and k-means clustering to minimize the influence of noises, preserve edges and remove unwanted artefacts. The second step systematically excludes the heart area by utilizing active contour based level sets where initial contour points are determined by the maximum entropy thresholding and convolution method. Finally, a pectoral muscle is removed by using morphological operations and local adaptive thresholding on MR images. Prior to the elimination of the pectoral muscle, the MR image is sub divided into three sections: left, right, and central based on the geometrical information. Subsequently, a BD segmentation is achieved with 4 level fuzzy c-means (FCM) thresholding on the denoised BROI segmentation. The proposed method is validated using the 1350 breast images from 15 female subjects. The pixel-based quantitative analysis showed excellent segmentation results when compared with manually drawn BROI and BD. Furthermore, the presented results in terms of evaluation matrices: Acc, Sp, AUC, MR, P, Se and DSC demonstrate the high quality of segmentations using the proposed method. The average computational time for the segmentation of BROI and BD is 1 minute and 50 seconds.

A Slice-based 13C-detected NMR Spin System Forming and Resonance Assignment Method

Nuclear magnetic resonance (NMR) spectroscopy is attracting more attention in the field of computational structural biology. Till recently, ¹H-detected experiments are the dominant NMR technique used due to the high sensitivity of ¹H nuclei. However, the current availability of high magnetic fields and cryogenically cooled probe heads allow researchers to overcome the low sensitivity of ¹³C nuclei. Consequently, ¹³C-detected experiments have become a popular technique in different NMR applications especially resonance assignment and structure determination of large proteins. In this paper, we propose the first spin system forming method for ¹³C-detected NMR spectra. Our method is able to accurately form spin systems based on as few as two ¹³C-detected spectra, CBCACON, and CBCANCO. Our method picks slices from the more trusted spectrum and uses them as feedback to direct the slice picking in the less trusted one. This feedback leads to picking the accurate slices that consequently helps to form better spin systems. We tested our method on a real dataset of 'Ubiquitin' and a benchmark simulated dataset consisting of 12 proteins. We fed our spin systems as inputs to a genetic algorithm to generate the chemical shift assignment, and obtained 92 percent correct chemical shift assignment for Ubiquitin. For the simulated dataset, we obtained an average recall of 86 percent and an average precision of 88 percent. Finally, our chemical shift assignment of Ubiquitin was given as an input to CS-ROSETTA server that generated structures close to the experimentally determined structure.

"Summer Shift": A Potential Effect of Sunshine on the Time Onset of ST-Elevation Acute Myocardial Infarction

Background

ST‐elevation acute myocardial infarction (STEMI) represents one of the leading causes of death. The time of STEMI onset has a circadian rhythm with a peak during diurnal hours, and the occurrence of STEMI follows a seasonal pattern with a salient peak of cases in the winter months and a marked reduction of cases in the summer months. Scholars investigated the reason behind the winter peak, suggesting that environmental and climatic factors concur in STEMI pathogenesis, but no studies have investigated whether the circadian rhythm is modified with the seasonal pattern, in particular during the summer reduction in STEMI occurrence.

Methods and Results

Here, we provide a multiethnic and multination epidemiological study (from both hemispheres at different latitudes, n=2270 cases) that investigates whether the circadian variation of STEMI onset is altered in the summer season. The main finding is that the difference between numbers of diurnal (6:00 to 18:00) and nocturnal (18:00 to 6:00) STEMI is markedly decreased in the summer season, and this is a prodrome of a complex mechanism according to which the circadian rhythm of STEMI time onset seems season dependent.

Conclusions

The “summer shift” of STEMI to the nocturnal interval is consistent across different populations, and the sunshine duration (a measure related to cloudiness and solar irradiance) underpins this season‐dependent circadian perturbation. Vitamin D, which in our results seems correlated with this summer shift, is also primarily regulated by the sunshine duration, and future studies should investigate their joint role in the mechanisms of STEMI etiogenesis.

A fast fiducial marker tracking model for fully automatic alignment in electron tomography

Motivation

Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner.

Results

In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers.

Availability and implementation

The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the '-t' option.

Contact

xin.gao@kaust.edu.sa.

Supplementary information

Supplementary data are available at Bioinformatics online.

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review

Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image.

MatCol: a tool to measure fluorescence signal colocalisation in biological systems

Protein colocalisation is often studied using pixel intensity-based coefficients such as Pearson, Manders, Li or Costes. However, these methods cannot be used to study object-based colocalisations in biological systems. Therefore, a novel method is required to automatically identify regions of fluorescent signal in two channels, identify the co-located parts of these regions, and calculate the statistical significance of the colocalisation. We have developed MatCol to address these needs. MatCol can be used to visualise protein and/or DNA colocalisations and fine tune user-defined parameters for the colocalisation analysis, including the application of median or Wiener filtering to improve the signal to noise ratio. Command-line execution allows batch processing of multiple images. Users can also calculate the statistical significance of the observed object colocalisations compared to overlap by random chance using Student's t-test. We validated MatCol in a biological setting. The colocalisations of telomeric DNA and TRF2 protein or TRF2 and PML proteins in >350 nuclei derived from three different cell lines revealed a highly significant correlation between manual and MatCol identification of colocalisations (linear regression R2 = 0.81, P < 0.0001). MatCol has the ability to replace manual colocalisation counting, and the potential to be applied to a wide range of biological areas.