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ABSTRACT: In this article we derive an unbiased expression for the expected
mean-squared error associated with continuously differentiable estimators of
the noncentrality parameter of a chi-square random variable. We then consider
the task of denoising squared-magnitude magnetic resonance image data, which
are well modeled as independent noncentral chi-square random variables on two
degrees of freedom. We consider two broad classes of linearly parameterized
shrinkage estimators that can be optimized using our risk estimate, one in the
general context of undecimated filterbank transforms, and another in the
specific case of the unnormalized Haar wavelet transform. The resultant
algorithms are computationally tractable and improve upon state-of-the-art
methods for both simulated and actual magnetic resonance image data.
06/2011;
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ABSTRACT: We propose a general methodology (PURE-LET) to design and optimize a wide class of transform-domain thresholding algorithms for denoising images corrupted by mixed Poisson-Gaussian noise. We express the denoising process as a linear expansion of thresholds (LET) that we optimize by relying on a purely data-adaptive unbiased estimate of the mean-squared error (MSE), derived in a non-Bayesian framework (PURE: Poisson-Gaussian unbiased risk estimate). We provide a practical approximation of this theoretical MSE estimate for the tractable optimization of arbitrary transform-domain thresholding. We then propose a pointwise estimator for undecimated filterbank transforms, which consists of subband-adaptive thresholding functions with signal-dependent thresholds that are globally optimized in the image domain. We finally demonstrate the potential of the proposed approach through extensive comparisons with state-of-the-art techniques that are specifically tailored to the estimation of Poisson intensities. We also present denoising results obtained on real images of low-count fluorescence microscopy.
IEEE Transactions on Image Processing 03/2011; 20(3):696-708. · 3.04 Impact Factor
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IEEE Transactions on Image Processing. 01/2011; 20:696-708.
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IEEE Trans. Circuits Syst. Video Techn. 01/2010; 20:913-919.
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ABSTRACT: We propose a novel algorithm for denoising Poisson-corrupted images, that performs a signal-adaptive thresholding of the undecimated Haar wavelet coefficients. A Poisson's unbiased MSE estimate is devised and adapted to arbitrary transform-domain pointwise processing. This prior-free quadratic measure of quality is then used to globally optimize a linearly parameterized subband-adaptive thresholding, which accounts for the signal-dependent noise variance. We demonstrate the qualitative and computational competitiveness of the resulting denoising algorithm through comprehensive comparisons with some state-of-the-art multiscale techniques specifically designed for Poisson intensity estimation. We also show promising denoising results obtained on low-count fluorescence microscopy images.
Proceedings of the International Conference on Image Processing, ICIP 2010, September 26-29, Hong Kong, China; 01/2010
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SIAM J. Scientific Computing. 01/2009; 31:3179-3194.
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ABSTRACT: We consider the problem of optimizing the parameters of a given denoising algorithm for restoration of a signal corrupted by white Gaussian noise. To achieve this, we propose to minimize Stein's unbiased risk estimate (SURE) which provides a means of assessing the true mean-squared error (MSE) purely from the measured data without need for any knowledge about the noise-free signal. Specifically, we present a novel Monte-Carlo technique which enables the user to calculate SURE for an arbitrary denoising algorithm characterized by some specific parameter setting. Our method is a black-box approach which solely uses the response of the denoising operator to additional input noise and does not ask for any information about its functional form. This, therefore, permits the use of SURE for optimization of a wide variety of denoising algorithms. We justify our claims by presenting experimental results for SURE-based optimization of a series of popular image-denoising algorithms such as total-variation denoising, wavelet soft-thresholding, and Wiener filtering/smoothing splines. In the process, we also compare the performance of these methods. We demonstrate numerically that SURE computed using the new approach accurately predicts the true MSE for all the considered algorithms. We also show that SURE uncovers the optimal values of the parameters in all cases.
IEEE Transactions on Image Processing 10/2008; 17(9):1540-54. · 3.04 Impact Factor
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IEEE Transactions on Image Processing. 01/2008; 17:482-492.
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IEEE Transactions on Signal Processing. 01/2008; 56:1055-1070.
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ABSTRACT: We propose a new approach to image denoising, based on the image-domain minimization of an estimate of the mean squared error--Stein's unbiased risk estimate (SURE). Unlike most existing denoising algorithms, using the SURE makes it needless to hypothesize a statistical model for the noiseless image. A key point of our approach is that, although the (nonlinear) processing is performed in a transformed domain--typically, an undecimated discrete wavelet transform, but we also address nonorthonormal transforms--this minimization is performed in the image domain. Indeed, we demonstrate that, when the transform is a "tight" frame (an undecimated wavelet transform using orthonormal filters), separate subband minimization yields substantially worse results. In order for our approach to be viable, we add another principle, that the denoising process can be expressed as a linear combination of elementary denoising processes--linear expansion of thresholds (LET). Armed with the SURE and LET principles, we show that a denoising algorithm merely amounts to solving a linear system of equations which is obviously fast and efficient. Quite remarkably, the very competitive results obtained by performing a simple threshold (image-domain SURE optimized) on the undecimated Haar wavelet coefficients show that the SURE-LET principle has a huge potential.
IEEE Transactions on Image Processing 12/2007; 16(11):2778-86. · 3.04 Impact Factor
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ABSTRACT: Recently, we have introduced an integrated framework that combines wavelet-based processing with statistical testing in the spatial domain. In this paper, we propose two important enhancements of the framework. First, we revisit the underlying paradigm; i.e., that the effect of the wavelet processing can be considered as an adaptive denoising step to "improve" the parameter map, followed by a statistical detection procedure that takes into account the non-linear processing of the data. With an appropriate modification of the framework, we show that it is possible to reduce the spatial bias of the method with respect to the best linear estimate, providing conservative results that are closer to the original data. Second, we propose an extension of our earlier technique that compensates for the lack of shift-invariance of the wavelet transform. We demonstrate experimentally that both enhancements have a positive effect on performance. In particular, we present a reproducibility study for multi-session data that compares WSPM against SPM with different amounts of smoothing. The full approach is available as a toolbox, named WSPM, for the SPM2 software; it takes advantage of multiple options and features of SPM such as the general linear model.
NeuroImage 11/2007; 37(4):1205-17. · 5.89 Impact Factor
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ABSTRACT: This paper introduces a new approach to orthonormal wavelet image denoising. Instead of postulating a statistical model for the wavelet coefficients, we directly parametrize the denoising process as a sum of elementary nonlinear processes with unknown weights. We then minimize an estimate of the mean square error between the clean image and the denoised one. The key point is that we have at our disposal a very accurate, statistically unbiased, MSE estimate--Stein's unbiased risk estimate--that depends on the noisy image alone, not on the clean one. Like the MSE, this estimate is quadratic in the unknown weights, and its minimization amounts to solving a linear system of equations. The existence of this a priori estimate makes it unnecessary to devise a specific statistical model for the wavelet coefficients. Instead, and contrary to the custom in the literature, these coefficients are not considered random anymore. We describe an interscale orthonormal wavelet thresholding algorithm based on this new approach and show its near-optimal performance--both regarding quality and CPU requirement--by comparing it with the results of three state-of-the-art nonredundant denoising algorithms on a large set of test images. An interesting fallout of this study is the development of a new, group-delay-based, parent-child prediction in a wavelet dyadic tree.
IEEE Transactions on Image Processing 04/2007; 16(3):593-606. · 3.04 Impact Factor
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ABSTRACT: Optical imaging techniques offer powerful solutions to capture brain networks processing in animals, especially when activity is distributed in functionally distinct spatial domains. Despite the progress in imaging techniques, the standard analysis procedures and statistical assessments for this type of data are still limited. In this paper, we perform two in vivo non-invasive optical recording techniques in the mouse olfactory bulb, using a genetically expressed activity reporter fluorescent protein (synaptopHfluorin) and intrinsic signals of the brain. For both imaging techniques, we show that the odour-triggered signals can be accurately parameterized using linear models. Fitting the models allows us to extract odour specific signals with a reduced level of noise compared to standard methods. In addition, the models serve to evaluate statistical significance, using a wavelet-based framework that exploits spatial correlation at different scales. We propose an extension of this framework to extract activation patterns at specific wavelet scales. This method is especially interesting to detect the odour inputs that segregate on the olfactory bulb in small spherical structures called glomeruli. Interestingly, with proper selection of wavelet scales, we can isolate significantly activated glomeruli and thus determine the odour map in an automated manner. Comparison against manual detection of glomeruli shows the high accuracy of the proposed method. Therefore, beyond the advantageous alternative to the existing treatments of optical imaging signals in general, our framework propose an interesting procedure to dissect brain activation patterns on multiple scales with statistical control.
NeuroImage 03/2007; 34(3):1020-35. · 5.89 Impact Factor
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ABSTRACT: Optical imaging is a powerful technique to map brain function in animals. In this study, we consider in vivo optical imaging of the murine olfactory bulb, using an intrinsic signal and a genetically expressed activity reporter fluorescent protein (synaptopHfluorin). The aim is to detect odor-evoked activations that occur in small spherical structures of the olfactory bulb called glomeruli. We propose a new way of analyzing this kind of data that combines a linear model (LM) fitting along the temporal dimension, together with a discrete wavelet transform (DWT) along the spatial dimensions. We show that relevant regressors for the LM are available for both types of optical signals. In addition, the spatial wavelet transform allows us to exploit spatial correlation at different scales, and in particular to extract activation patterns at the expected size of glomeruli. Our framework also provides a statistical significance for every pixel in the activation maps and it has strong type I error control.
Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Washington, DC, USA, April 12-16, 2007; 01/2007
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ABSTRACT: We introduce a three-dimensional (3-D) parametric active contour algorithm for the shape estimation of DNA molecules from stereo cryo-electron micrographs. We estimate the shape by matching the projections of a 3-D global shape model with the micrographs; we choose the global model as a 3-D filament with a B-spline skeleton and a specified radial profile. The active contour algorithm iteratively updates the B-spline coefficients, which requires us to evaluate the projections and match them with the micrographs at every iteration. Since the evaluation of the projections of the global model is computationally expensive, we propose a fast algorithm based on locally approximating it by elongated blob-like templates. We introduce the concept of projection-steerability and derive a projection-steerable elongated template. Since the two-dimensional projections of such a blob at any 3-D orientation can be expressed as a linear combination of a few basis functions, matching the projections of such a 3-D template involves evaluating a weighted sum of inner products between the basis functions and the micrographs. The weights are simple functions of the 3-D orientation and the inner-products are evaluated efficiently by separable filtering. We choose an internal energy term that penalizes the average curvature magnitude. Since the exact length of the DNA molecule is known a priori, we introduce a constraint energy term that forces the curve to have this specified length. The sum of these energies along with the image energy derived from the matching process is minimized using the conjugate gradients algorithm. We validate the algorithm using real, as well as simulated, data and show that it performs well.
IEEE Transactions on Image Processing 02/2006; 15(1):214-27. · 3.04 Impact Factor
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ABSTRACT: We propose here a new pointwise wavelet thresholding function that incorporates inter-scale dependencies. This non-linear function depends on a set of four linear parameters per sub-band which are set by minimizing Stein's unbiased MSE estimate (SURE). Our approach assumes additive Gaussian white noise. In order for the inter-scale dependencies to be faithfully taken into account, we also develop a rigorous feature alignment processing, that is adapted to arbitrary wavelet filters (e.g. non-symmetric filters). Finally, we demonstrate the efficiency of our denoising approach in simulations over a wide range of noise levels for a representative set of standard images
Proceedings of the International Conference on Image Processing, ICIP 2006, October 8-11, Atlanta, Georgia, USA; 01/2006
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ABSTRACT: In this paper, we use polyharmonic B-splines to build multidimensional wavelet bases. These functions are nonseparable, multidimensional basis functions that are localized versions of radial basis functions. We show that Rabut's elementary polyharmonic B-splines do not converge to a Gaussian as the order parameter increases, as opposed to their separable B-spline counterparts. Therefore, we introduce a more isotropic localization operator that guarantees this convergence, resulting into the isotropic polyharmonic B-splines. Next, we focus on the two-dimensional quincunx subsampling scheme. This configuration is of particular interest for image processing because it yields a finer scale progression than the standard dyadic approach. However, up until now, the design of appropriate filters for the quincunx scheme has mainly been done using the McClellan transform. In our approach, we start from the scaling functions, which are the polyharmonic B-splines and, as such, explicitly known, and we derive a family of polyharmonic spline wavelets corresponding to different flavors of the semi-orthogonal wavelet transform; e.g., orthonormal, B-spline, and dual. The filters are automatically specified by the scaling relations satisfied by these functions. We prove that the isotropic polyharmonic B-spline wavelet converges to a combination of four Gabor atoms, which are well separated in the frequency domain. We also show that these wavelets are nearly isotropic and that they behave as an iterated Laplacian operator at low frequencies. We describe an efficient fast Fourier transform-based implementation of the discrete wavelet transform based on polyharmonic B-splines.
IEEE Transactions on Image Processing 12/2005; 14(11):1798-813. · 3.04 Impact Factor
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ABSTRACT: This paper deals with fast image and video segmentation using active contours. Region-based active contours using level sets are powerful techniques for video segmentation, but they suffer from large computational cost. A parametric active contour method based on B-Spline interpolation has been proposed in to highly reduce the computational cost, but this method is sensitive to noise. Here, we choose to relax the rigid interpolation constraint in order to robustify our method in the presence of noise: by using smoothing splines, we trade a tunable amount of interpolation error for a smoother spline curve. We show by experiments on natural sequences that this new flexibility yields segmentation results of higher quality at no additional computational cost. Hence, real-time processing for moving objects segmentation is preserved.
IEEE Transactions on Image Processing 08/2005; 14(7):910-24. · 3.04 Impact Factor
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ABSTRACT: We introduce an integrated framework for detecting brain activity from fMRI data, which is based on a spatial discrete wavelet transform. Unlike the standard wavelet-based approach for fMRI analysis, we apply the suitable statistical test procedure in the spatial domain. For a desired significance level, this scheme has one remaining degree of freedom, characterizing the wavelet processing, which is optimized according to the principle of minimal approximation error. This allows us to determine the threshold values in a way that does not depend on data. While developing our framework, we make only conservative assumptions. Consequently, the detection of activation is based on strong evidence. We have implemented this framework as a toolbox (WSPM) for the SPM2 software, taking advantage of multiple options and functions of SPM such as the setup of the linear model and the use of the hemodynamic response function. We show by experimental results that our method is able to detect activation patterns; the results are comparable to those obtained by SPM even though statistical assumptions are more conservative.
NeuroImage 01/2005; 23(4):1472-85. · 5.89 Impact Factor
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ABSTRACT: We provide a new comparison between hexagonal and orthogonal lattices, based on approximation theory. For each of the lattices, we select the "natural" spline basis function as generator for a shift-invariant function space; i.e., the tensor-product B-splines for the orthogonal lattice and the non-separable hex-splines for the hexagonal lattice. For a given order of approximation, we compare the asymptotic constants of the error kernels, which give a very good indication of the approximation quality. We find that the approximation quality on the hexagonal lattice is consistently better, when choosing lattices with the same sampling density. The area sampling gain related to these asymptotic constants quickly converges when the order of approximation of the basis functions increases. Surprisingly, nearest-neighbor interpolation does not allow to profit from the hexagonal grid. For practical purposes, the second-order hex-spline (i.e., constituted by linear patches) appears as a particularly useful candidate to exploit the advantages of hexagonal lattices when representing images on them.
Image Processing, 2005. ICIP 2005. IEEE International Conference on; 01/2005
