Wavelet/shearlet hybridized neural networks for biomedical image restoration

Recently, new programming paradigms have emerged that combine parallelism and numerical computations with algorithmic differentiation. This approach allows for the hybridization of neural network techniques for inverse imaging problems with more traditional methods such as wavelet-based sparsity modelling techniques. The benefits are twofold: on the one hand traditional methods with well-known properties can be integrated in neural networks, either as separate layers or tightly integrated in the network, on the other hand, parameters in traditional methods can be trained end-to-end from datasets in a neural network "fashion" (e.g., using Adagrad or Adam optimizers). In this paper, we explore these hybrid neural networks in the context of shearlet-based regularization for the purpose of biomedical image restoration. Due to the reduced number of parameters, this approach seems a promising strategy especially when dealing with small training data sets

The SURE-LET approach to image denoising

Denoising is an essential step prior to any higher-level image-processing tasks such as segmentation or object tracking, because the undesirable corruption by noise is inherent to any physical acquisition device. When the measurements are performed by photosensors, one usually distinguish between two main regimes: in the first scenario, the measured intensities are sufficiently high and the noise is assumed to be signal-independent. In the second scenario, only few photons are detected, which leads to a strong signal-dependent degradation. When the noise is considered as signal-independent, it is often modeled as an additive independent (typically Gaussian) random variable, whereas, otherwise, the measurements are commonly assumed to follow independent Poisson laws, whose underlying intensities are the unknown noise-free measures. We first consider the reduction of additive white Gaussian noise (AWGN). Contrary to most existing denoising algorithms, our approach does not require an explicit prior statistical modeling of the unknown data. Our driving principle is the minimization of a purely data-adaptive unbiased estimate of the mean-squared error (MSE) between the processed and the noise-free data. In the AWGN case, such a MSE estimate was first proposed by Stein, and is known as "Stein's unbiased risk estimate" (SURE). We further develop the original SURE theory and propose a general methodology for fast and efficient multidimensional image denoising, which we call the SURE-LET approach. While SURE allows the quantitative monitoring of the denoising quality, the flexibility and the low computational complexity of our approach are ensured by a linear parameterization of the denoising process, expressed as a linear expansion of thresholds (LET).We propose several pointwise, multivariate, and multichannel thresholding functions applied to arbitrary (in particular, redundant) linear transformations of the input data, with a special focus on multiscale signal representations. We then transpose the SURE-LET approach to the estimation of Poisson intensities degraded by AWGN. The signal-dependent specificity of the Poisson statistics leads to the derivation of a new unbiased MSE estimate that we call "Poisson's unbiased risk estimate" (PURE) and requires more adaptive transform-domain thresholding rules. In a general PURE-LET framework, we first devise a fast interscale thresholding method restricted to the use of the (unnormalized) Haar wavelet transform. We then lift this restriction and show how the PURE-LET strategy can be used to design and optimize a wide class of nonlinear processing applied in an arbitrary (in particular, redundant) transform domain. We finally apply some of the proposed denoising algorithms to real multidimensional fluorescence microscopy images. Such in vivo imaging modality often operates under low-illumination conditions and short exposure time; consequently, the random fluctuations of the measured fluorophore radiations are well described by a Poisson process degraded (or not) by AWGN. We validate experimentally this statistical measurement model, and we assess the performance of the PURE-LET algorithms in comparison with some state-of-the-art denoising methods. Our solution turns out to be very competitive both qualitatively and computationally, allowing for a fast and efficient denoising of the huge volumes of data that are nowadays routinely produced in biomedical imaging

A nonlinear Stein based estimator for multichannel image denoising

The use of multicomponent images has become widespread with the improvement of multisensor systems having increased spatial and spectral resolutions. However, the observed images are often corrupted by an additive Gaussian noise. In this paper, we are interested in multichannel image denoising based on a multiscale representation of the images. A multivariate statistical approach is adopted to take into account both the spatial and the inter-component correlations existing between the different wavelet subbands. More precisely, we propose a new parametric nonlinear estimator which generalizes many reported denoising methods. The derivation of the optimal parameters is achieved by applying Stein's principle in the multivariate case. Experiments performed on multispectral remote sensing images clearly indicate that our method outperforms conventional wavelet denoising technique

Wavelet Shrinkage Based Image Denoising using Soft Computing

Noise reduction is an open problem and has received considerable attention in the literature for several decades. Over the last two decades, wavelet based methods have been applied to the problem of noise reduction and have been shown to outperform the traditional Wiener filter, Median filter, and modified Lee filter in terms of root mean squared error (MSE), peak signal noise ratio (PSNR) and other evaluation methods. In this research, two approaches for the development of high performance algorithms for de-noising are proposed, both based on soft computing tools, such as fuzzy logic, neural networks, and genetic algorithms. First, an improved additive noise reduction method for digital grey scale nature images, which uses an interval type-2 fuzzy logic system to shrink wavelet coefficients, is proposed. This method is an extension of a recently published approach for additive noise reduction using a type-1 fuzzy logic system based wavelet shrinkage. Unlike the type-1 fuzzy logic system based wavelet shrinkage method, the proposed approach employs a thresholding filter to adjust the wavelet coefficients according to the linguistic uncertainty in neighborhood values, inter-scale dependencies and intra-scale correlations of wavelet coefficients at different resolutions by exploiting the interval type-2 fuzzy set theory. Experimental results show that the proposed approach can efficiently and rapidly remove additive noise from digital grey scale images. Objective analysis and visual observations show that the proposed approach outperforms current fuzzy non-wavelet methods and fuzzy wavelet based methods, and is comparable with some recent but more complex wavelet methods, such as Hidden Markov Model based additive noise de-noising method. The main differences between the proposed approach and other wavelet shrinkage based approaches and the main improvements of the proposed approach are also illustrated in this thesis. Second, another improved method of additive noise reduction is also proposed. The method is based on fusing the results of different filters using a Fuzzy Neural Network (FNN). The proposed method combines the advantages of these filters and has outstanding ability of smoothing out additive noise while preserving details of an image (e.g. edges and lines) effectively. A Genetic Algorithm (GA) is applied to choose the optimal parameters of the FNN. The experimental results show that the proposed method is powerful for removing noise from natural images, and the MSE of this approach is less, and the PSNR of is higher, than that of any individual filters which are used for fusion. Finally, the two proposed approaches are compared with each other from different point of views, such as objective analysis in terms of mean squared error(MSE), peak signal to noise ratio (PSNR), image quality index (IQI) based on quality assessment of distorted images, and Information Theoretic Criterion (ITC) based on a human vision model, computational cost, universality, and human observation. The results show that the proposed FNN based algorithm optimized by GA has the best performance among all testing approaches. Important considerations for these proposed approaches and future work are discussed

Wavelet-based noise reduction of cDNA microarray images

The advent of microarray imaging technology has lead to enormous progress in the life sciences by allowing scientists to analyze the expression of thousands of genes at a time. For complementary DNA (cDNA) microarray experiments, the raw data are a pair of red and green channel images corresponding to the treatment and control samples. These images are contaminated by a high level of noise due to the numerous noise sources affecting the image formation. A major challenge of microarray image analysis is the extraction of accurate gene expression measurements from the noisy microarray images. A crucial step in this process is denoising, which consists of reducing the noise in the observed microarray images while preserving the signal information as much as possible. This thesis deals with the problem of developing novel methods for reducing noise in cDNA microarray images for accurate estimation of the gene expression levels. Denoising methods based on the wavelet transform have shown significant success when applied to natural images. However, these methods are not very efficient for reducing noise in cDNA microarray images. An important reason for this is that existing methods are only capable of processing the red and green channel images separately. In doing so. they ignore the signal correlation as well as the noise correlation that exists between the wavelet coefficients of the two channels. The primary objective of this research is to design efficient wavelet-based noise reduction algorithms for cDNA microarray images that take into account these inter-channel dependencies by 'jointly' estimating the noise-free coefficients in both the channels. Denoising algorithms are developed using two types of wavelet transforms, namely, the frequently-used discrete wavelet transform (DWT) and the complex wavelet transform (CWT). The main advantage of using the DWT for denoising is that this transform is computationally very efficient. In order to obtain a better denoising performance for microarray images, however, the CWT is preferred to DWT because the former has good directional selectivity properties that are necessary for better representation of the circular edges of spots. The linear minimum mean squared error and maximum a posteriori estimation techniques are used to develop bivariate estimators for the noise-free coefficients of the two images. These estimators are derived by utilizing appropriate joint probability density functions for the image coefficients as well as the noise coefficients of the two channels. Extensive experimentations are carried out on a large set of cDNA microarray images to evaluate the performance of the proposed denoising methods as compared to the existing ones. Comparisons are made using standard metrics such as the peak signal-to-noise ratio (PSNR) for measuring the amount of noise removed from the pixels of the images, and the mean absolute error for measuring the accuracy of the estimated log-intensity ratios obtained from the denoised version of the images. Results indicate that the proposed denoising methods that are developed specifically for the microarray images do, indeed, lead to more accurate estimation of gene expression levels. Thus, it is expected that the proposed methods will play a significant role in improving the reliability of the results obtained from practical microarray experiments

Adaptive Edge-guided Block-matching and 3D filtering (BM3D) Image Denoising Algorithm

Image denoising is a well studied field, yet reducing noise from images is still a valid challenge. Recently proposed Block-matching and 3D filtering (BM3D) is the current state of the art algorithm for denoising images corrupted by Additive White Gaussian noise (AWGN). Though BM3D outperforms all existing methods for AWGN denoising, still its performance decreases as the noise level increases in images, since it is harder to find proper match for reference blocks in the presence of highly corrupted pixel values. It also blurs sharp edges and textures. To overcome these problems we proposed an edge guided BM3D with selective pixel restoration. For higher noise levels it is possible to detect noisy pixels form its neighborhoods gray level statistics. We exploited this property to reduce noise as much as possible by applying a pre-filter. We also introduced an edge guided pixel restoration process in the hard-thresholding step of BM3D to restore the sharpness of edges and textures. Experimental results confirm that our proposed method is competitive and outperforms the state of the art BM3D in all considered subjective and objective quality measurements, particularly in preserving edges, textures and image contrast