nils-herrmann/clean_scirepeval huggingface dataset:
Extended depth-of-focus for multi-channel microscopy images: a complex wavelet approach

Microscopy imaging often suffers from limited depth-of-focus. However, the specimen can be 'optically sectioned' by moving the object along the optical axis; different areas appear in focus in different images. Extended depth-of-focus is a fusion algorithm that combines those images into one single sharp composite. One promising method is based on the wavelet transform. In this paper, we show how the wavelet-based image fusion technique can be improved and easily extended to multi-channel data. First, we propose the use of complex-valued wavelet bases, which seem to outperform traditional real-valued wavelet transforms. Second, we introduce a way to apply this technique for multi-channel images that suppresses artifacts and does not introduce false colors, an important requirement for multi-channel fluorescence microscopy imaging. We evaluate our method on simulated image stacks and give results relevant to biological imaging.
Generalized smoothing splines and the optimal discretization of the Wiener filter

We introduce an extended class of cardinal L/sup */L-splines, where L is a pseudo-differential operator satisfying some admissibility conditions. We show that the L/sup */L-spline signal interpolation problem is well posed and that its solution is the unique minimizer of the spline energy functional /spl par/Ls/spl par//sub L2//sup 2/, subject to the interpolation constraint. Next, we consider the corresponding regularized least squares estimation problem, which is more appropriate for dealing with noisy data. The criterion to be minimized is the sum of a quadratic data term, which forces the solution to be close to the input samples, and a "smoothness" term that privileges solutions with small spline energies. Here, too, we find that the optimal solution, among all possible functions, is a cardinal L/sup */L-spline. We show that this smoothing spline estimator has a stable representation in a B-spline-like basis and that its coefficients can be computed by digital filtering of the input signal. We describe an efficient recursive filtering algorithm that is applicable whenever the transfer function of L is rational (which corresponds to the case of exponential splines). We justify these algorithms statistically by establishing an equivalence between L/sup */L smoothing splines and the minimum mean square error (MMSE) estimation of a stationary signal corrupted by white Gaussian noise. In this model-based formulation, the optimum operator L is the whitening filter of the process, and the regularization parameter is proportional to the noise variance. Thus, the proposed formalism yields the optimal discretization of the classical Wiener filter, together with a fast recursive algorithm. It extends the standard Wiener solution by providing the optimal interpolation space. We also present a Bayesian interpretation of the algorithm.
A Fast Multilevel Algorithm for Wavelet-Regularized Image Restoration

We present a multilevel extension of the popular ldquothresholded Landweberrdquo algorithm for wavelet-regularized image restoration that yields an order of magnitude speed improvement over the standard fixed-scale implementation. The method is generic and targeted towards large-scale linear inverse problems, such as 3-D deconvolution microscopy. The algorithm is derived within the framework of bound optimization. The key idea is to successively update the coefficients in the various wavelet channels using fixed, subband-adapted iteration parameters (step sizes and threshold levels). The optimization problem is solved efficiently via a proper chaining of basic iteration modules. The higher level description of the algorithm is similar to that of a multigrid solver for PDEs, but there is one fundamental difference: the latter iterates though a sequence of multiresolution versions of the original problem, while, in our case, we cycle through the wavelet subspaces corresponding to the difference between successive approximations. This strategy is motivated by the special structure of the problem and the preconditioning properties of the wavelet representation. We establish that the solution of the restoration problem corresponds to a fixed point of our multilevel optimizer. We also provide experimental evidence that the improvement in convergence rate is essentially determined by the (unconstrained) linear part of the algorithm, irrespective of the type of wavelet. Finally, we illustrate the technique with some image deconvolution examples, including some real 3-D fluorescence microscopy data.
Compressibility of Deterministic and Random Infinite Sequences

We introduce a definition of the notion of compressibility for infinite deterministic and i.i.d. random sequences which is based on the asymptotic behavior of truncated subsequences. For this purpose, we use asymptotic results regarding the distribution of order statistics for heavy-tail distributions and their link with α -stable laws for 1 <; α <; 2 . In many cases, our proposed definition of compressibility coincides with intuition. In particular, we prove that heavy-tail (polynomial decaying) distributions fulfill the requirements of compressibility. On the other hand, exponential decaying distributions like Laplace and Gaussian do not. The results are such that two compressible distributions can be compared with each other in terms of their degree of compressibility.
Multiframe sure-let denoising of timelapse fluorescence microscopy images

Due to the random nature of photon emission and the various internal noise sources of the detectors, real timelapse fluorescence microscopy images are usually modeled as the sum of a Poisson process plus some Gaussian white noise. In this paper, we propose an adaptation of our SURE-LET denoising strategy to take advantage of the potentially strong similarities between adjacent frames of the observed image sequence. To stabilize the noise variance, we first apply the generalized Anscombe transform using suitable parameters automatically estimated from the observed data. With the proposed algorithm, we show that, in a reasonable computation time, real fluorescence timelapse microscopy images can be denoised with higher quality than conventional algorithms.
Smoothing B-spline active contour for fast and robust image and video segmentation

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 hut they suffer from large computational cost. A parametric active contour method based on B-Spline interpolation has been proposed in F. Precioso (2002) 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.
3D Steerable Wavelets in Practice

We introduce a systematic and practical design for steerable wavelet frames in 3D. Our steerable wavelets are obtained by applying a 3D version of the generalized Riesz transform to a primary isotropic wavelet frame. The novel transform is self-reversible (tight frame) and its elementary constituents (Riesz wavelets) can be efficiently rotated in any 3D direction by forming appropriate linear combinations. Moreover, the basis functions at a given location can be linearly combined to design custom (and adaptive) steerable wavelets. The features of the proposed method are illustrated with the processing and analysis of 3D biomedical data. In particular, we show how those wavelets can be used to characterize directional patterns and to detect edges by means of a 3D monogenic analysis. We also propose a new inverse-problem formalism along with an optimization algorithm for reconstructing 3D images from a sparse set of wavelet-domain edges. The scheme results in high-quality image reconstructions which demonstrate the feature-reduction ability of the steerable wavelets as well as their potential for solving inverse problems.
Fast Haar-wavelet denoising of multidimensional fluorescence microscopy data

We propose a novel denoising algorithm to reduce the Poisson noise that is typically dominant in fluorescence microscopy data. To process large datasets at a low computational cost, we use the unnormalized Haar wavelet transform. Thanks to some of its appealing properties, independent unbiased MSE estimates can be derived for each subband. Based on these Poisson unbiased MSE estimates, we then optimize linearly parametrized interscale thresholding. Correlations between adjacent images of the multidimensional data are accounted for through a sliding window approach. Experiments on simulated and real data show that the proposed solution is qualitatively similar to a state-of-the-art multiscale method, while being orders of magnitude faster.
Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy

The imaging of proteins within macromolecular complexes has been limited by the low axial resolution of optical microscopes. To overcome this problem, we propose a novel computational reconstruction method that yields isotropic resolution in fluorescence imaging. The guiding principle is to reconstruct a single volume from the observations of multiple rotated particles. Our new operational framework detects particles, estimates their orientation, and reconstructs the final volume. The main challenge comes from the absence of initial template and a priori knowledge about the orientations. We formulate the estimation as a blind inverse problem, and propose a block-coordinate stochastic approach to solve the associated non-convex optimization problem. The reconstruction is performed jointly in multiple channels. We demonstrate that our method is able to reconstruct volumes with 3D isotropic resolution on simulated data. We also perform isotropic reconstructions from real experimental data of doubly labeled purified human centrioles. Our approach revealed the precise localization of the centriolar protein Cep63 around the centriole microtubule barrel. Overall, our method offers new perspectives for applications in biology that require the isotropic mapping of proteins within macromolecular assemblies.
Spline-Based Deforming Ellipsoids for Interactive 3D Bioimage Segmentation

We present a new fast active-contour model (a.k.a. snake) for image segmentation in 3D microscopy. We introduce a parametric design that relies on exponential B-spline bases and allows us to build snakes that are able to reproduce ellipsoids. We design our bases to have the shortest-possible support, subject to some constraints. Thus, computational efficiency is maximized. The proposed 3D snake can approximate blob-like objects with good accuracy and can perfectly reproduce spheres and ellipsoids, irrespective of their position and orientation. The optimization process is remarkably fast due to the use of Gauss' theorem within our energy computation scheme. Our technique yields successful segmentation results, even for challenging data where object contours are not well defined. This is due to our parametric approach that allows one to favor prior shapes. In addition, this paper provides a software that gives full control over the snakes via an intuitive manipulation of few control points.
A primal-dual reconstruction algorithm for fluorescence and bioluminescence tomography

We introduce a new primal-dual reconstruction algorithm for fluorescence and bioluminescence tomography. As often in optical tomography, image reconstruction is performed by optimizing a multi-term convex cost function. Current reconstruction methods employed in the field are usually limited to cost functions with a smooth data fidelity term; quadratic in general. In addition, the use of a composite regularization term (a sum of multiple terms) requires a substantial adaptation of these methods. Typically one would have to solve a subproblem via a primal-dual method at each iteration. The primal-dual scheme presented here is designed to handle directly cost functions composed of multiple, possibly non-smooth, terms. This allows more freedom for the design of tailored cost functions leading to enhanced reconstructions. We illustrate the method on two cases. First, we use a cost function composed of ℓ1 fidelity and regularization terms. We compare to the reconstructions obtained with the quadratic fidelity counterpart. Second, we employ a cost function composed of three terms : ℓ1 for data fidelity, total-variation plus (2,1)-mixed norms for regularization.
Fresnelets: new multiresolution wavelet bases for digital holography

We propose a construction of new wavelet-like bases that are well suited for the reconstruction and processing of optically generated Fresnel holograms recorded on CCD-arrays. The starting point is a wavelet basis of L2 to which we apply a unitary Fresnel transform. The transformed basis functions are shift-invariant on a level-by-level basis but their multiresolution properties are governed by the special form that the dilation operator takes in the Fresnel domain. We derive a Heisenberg-like uncertainty relation that relates the localization of Fresnelets with that of their associated wavelet basis. According to this criterion, the optimal functions for digital hologram processing turn out to be Gabor functions, bringing together two separate aspects of the holography inventor's work. We give the explicit expression of orthogonal and semi-orthogonal Fresnelet bases corresponding to polynomial spline wavelets. This special choice of Fresnelets is motivated by their near-optimal localization properties and their approximation characteristics. We then present an efficient multiresolution Fresnel transform algorithm, the Fresnelet transform. This algorithm allows for the reconstruction (backpropagation) of complex scalar waves at several user-defined, wavelength-independent resolutions. Furthermore, when reconstructing numerical holograms, the subband decomposition of the Fresnelet transform naturally separates the image to reconstruct from the unwanted zero-order and twin image terms. This greatly facilitates their suppression. We show results of experiments carried out on both synthetic (simulated) data sets as well as on digitally acquired holograms.
Design of steerable filters for the detection of micro-particles

This paper presents two contributions. We first introduce a continuous-domain version of Principal-Component Analysis (PCA) for designing steerable filters so that they best approximate a given set of image templates. We exploit the fact that steerability does not need to be enforced explicitly if one extends the set of templates by incorporating all their rotations. Our results extend previous work by Perona to multiple templates. We then apply our framework to the automatic detection and classification of micro-particles that carry biochemical probes for molecular diagnostics. Our continuous-domain PCA formalism is particularly well adapted in this context because the geometry of the carriers is known analytically. In addition, the steerable structure of our filters allows for a fast FFT-based recognition of the type of probe.
Statistical optimality of Hermite splines

Hermite splines are commonly used for interpolating data when samples of the derivative are available, in a scheme called Hermite interpolation. Assuming a suitable statistical model, we demonstrate that this method is actually optimal for reconstructing random signals in Papoulis' generalized sampling framework. We focus on second-order Lévy processes - the integrated version of Lévy processes - and rely on cubic Hermite splines to approximate the original continuous-time signal from its samples and its derivatives at integer values. We statistically justify the use of this reconstruction scheme by demonstrating the equivalence between cubic Hermite interpolation and the linear minimum mean-square error (LMMSE) estimation of a second-order Lévy process. We finally illustrate the cubic Hermite reconstruction scheme on an example of a discrete sequence sampled from the realization of a stochastic process.
Sum and Difference Histograms for Texture Classification

The sum and difference of two random variables with same variances are decorrelated and define the principal axes of their associated joint probability function. Therefore, sum and difference histograms are introduced as an alternative to the usual co-occurrence matrices used for texture analysis. Two maximum likelihood texture classifiers are presented depending on the type of object used for texture characterization (sum and difference histograms or some associated global measures). Experimental results indicate that sum and difference histograms used conjointly are nearly as powerful as cooccurrence matrices for texture discrimination. The advantage of the proposed texture analysis method over the conventional spatial gray level dependence method is the decrease in computation time and memory storage.
Variational decomposition of vector fields in the presence of noise

We present a variational framework, and an algorithm based on the alternating method of multipliers (ADMM), for the problem of decomposing a vector field into its curl- and divergence-free components (Helmholtz decomposition) in the presence of noise. We provide experimental confirmation of the effectiveness of our approach by separating vector fields consisting of a curl-free gradient field super-imposed on a divergence-free laminar flow corrupted by noise, as well as suppressing non-zero divergence distortions in a computational fluid dynamics simulation of blood flow in the thoracic aorta. The methods developed and presented here can be used in the analysis of flow-field images and in their correction and enhancement by enforcing suitable physical constraints such as zero divergence.
Wavelet Steerability and the Higher-Order Riesz Transform

Our main goal in this paper is to set the foundations of a general continuous-domain framework for designing steerable, reversible signal transformations (a.k.a. frames) in multiple dimensions (d ¿ 2). To that end, we introduce a self-reversible, Nth-order extension of the Riesz transform. We prove that this generalized transform has the following remarkable properties: shift-invariance, scale-invariance, inner-product preservation, and steerability. The pleasing consequence is that the transform maps any primary wavelet frame (or basis) of L 2( \BBR d) into another ¿steerable¿ wavelet frame, while preserving the frame bounds. The concept provides a functional counterpart to Simoncelli's steerable pyramid whose construction was primarily based on filterbank design. The proposed mechanism allows for the specification of wavelets with any order of steerability in any number of dimensions; it also yields a perfect reconstruction filterbank algorithm. We illustrate the method with the design of a novel family of multidimensional Riesz-Laplace wavelets that essentially behave like the N th-order partial derivatives of an isotropic Gaussian kernel.
MMSE denoising of sparse and non-Gaussian AR(1) processes

We propose two minimum-mean-square-error (MMSE) estimation methods for denoising non-Gaussian first-order autoregressive (AR(1)) processes. The first one is based on the message passing framework and gives the exact theoretic MMSE estimator. The second is an iterative algorithm that combines standard wavelet-based thresholding with an optimized non-linearity and cycle-spinning. This method is more computationally efficient than the former and appears to provide the same optimal denoising results in practice. We illustrate the superior performance of both methods through numerical simulations by comparing them with other well-known denoising schemes.
Statistics of wavelet coefficients for sparse self-similar images

We study the statistics of wavelet coefficients of non-Gaussian images, focusing mainly on the behaviour at coarse scales. We assume that an image can be whitened by a fractional Laplacian operator, which is consistent with an ∥ω∥-γ spectral decay. In other words, we model images as sparse and self-similar stochastic processes within the framework of generalised innovation models. We show that the wavelet coefficients at coarse scales are asymptotically Gaussian even if the prior model for fine scales is sparse. We further refine our analysis by deriving the theoretical evolution of the cumulants of wavelet coefficients across scales. Especially, the evolution of the kurtosis supplies a theoretical prediction for the Gaussianity level at each scale. Finally, we provide simulations and experiments that support our theoretical predictions.
Efficient image reconstruction under sparsity constraints with application to MRI and bioluminescence tomography

Most bioimaging modalities rely on indirect measurements of the quantity under investigation. The image is obtained as the result of an optimization problem involving a physical model of the measurement system. Due to the ill-posedness of the above problem, the impact of the noise on the reconstructed images must be controlled. The recent emphasis in biomedical image reconstruction is on regularization schemes that favor sparse solutions, which renders the optimization problem nonsmooth. In this work, we show how step-size adaptation can be used to speed up the most recent multi-step algorithms (e.g. FISTA) employed in sparse image recovery. We present experiments in MRI and Fluorescence Molecular Tomography with specifically tailored step-adaptation strategies. Our results demonstrate the possibility of an order-of-magnitude speed enhancement over state-of-the-art algorithms.
Texture discrimination using wavelets

A new approach to the characterization of texture properties at multiple scales using an overcomplete wavelet transform is described. It is shown that this representation constitutes a tight frame of l/sub 2/, and that it has a fast iterative algorithm. A texture is characterized by a set of channel variances estimated at the output of the corresponding filter-bank. Classification experiments with 12 Brodatz textures indicate that the discrete wavelet frame (DWF) approach is superior to a standard (critically sampled) wavelet transform feature extraction. This result also suggests that this approach should perform better than most traditional single resolution techniques (co-occurrences, local linear transform, etc. . .). A detailed comparison of the classification performance of various orthogonal and biorthogonal wavelet transforms is provided. The DWF feature extraction technique is incorporated into a simple multiple-component texture segmentation algorithm. Some examples are presented.<<ETX>>
Near optimal geometric image scaling using oblique projection operators

We propose to re-size images using an oblique projection operator instead of the orthogonal one in order to obtain faster, simpler, and more general algorithms. The main advantage is that it becomes perfectly feasible to use higher order models (e.g., splines of degree n/spl ges/3). We develop the theoretical background and present a simple and practical implementation procedure that uses B-splines. Experiments show that the proposed algorithm consistently outperforms the standard interpolation method and that it essentially provides the same performance as the optimal procedure (least squares solution) with considerably less computations.