Mathews Jacob

Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images

For the investigation of the molecular mechanisms involved in neurite outgrowth and differentiation, accurate and reproducible segmentation and quantification of neuronal processes are a prerequisite. To facilitate this task, we developed a semiautomatic neurite tracing technique. This article describes the design and validation of the technique.

Design of steerable filters for feature detection using canny-like criteria

We propose a general approach for the design of 2D feature detectors from a class of steerable functions based on the optimization of a Canny-like criterion. In contrast with previous computational designs, our approach is truly 2D and provides filters that have closed-form expressions. It also yields operators that have a better orientation selectivity than the classical gradient or Hessian-based detectors. We illustrate the method with the design of operators for edge and ridge detection. We present some experimental results that demonstrate the performance improvement of these new feature detectors. We propose computationally efficient local optimization algorithms for the estimation of feature orientation. We also introduce the notion of shape-adaptable feature detection and use it for the detection of image corners.

Accelerated Dynamic MRI Exploiting Sparsity and Low-Rank Structure: k-t SLR

We introduce a novel algorithm to reconstruct dynamic magnetic resonance imaging (MRI) data from under-sampled k-t space data. In contrast to classical model based cine MRI schemes that rely on the sparsity or banded structure in Fourier space, we use the compact representation of the data in the Karhunen Louve transform (KLT) domain to exploit the correlations in the dataset. The use of the data-dependent KL transform makes our approach ideally suited to a range of dynamic imaging problems, even when the motion is not periodic. In comparison to current KLT-based methods that rely on a two-step approach to first estimate the basis functions and then use it for reconstruction, we pose the problem as a spectrally regularized matrix recovery problem. By simultaneously determining the temporal basis functions and its spatial weights from the entire measured data, the proposed scheme is capable of providing high quality reconstructions at a range of accelerations. In addition to using the compact representation in the KLT domain, we also exploit the sparsity of the data to further improve the recovery rate. Validations using numerical phantoms and in vivo cardiac perfusion MRI data demonstrate the significant improvement in performance offered by the proposed scheme over existing methods.

Efficient energies and algorithms for parametric snakes

Parametric active contour models are one of the preferred approaches for image segmentation because of their computational efficiency and simplicity. However, they have a few drawbacks which limit their performance. In this paper, we identify some of these problems and propose efficient solutions to get around them. The widely-used gradient magnitude-based energy is parameter dependent; its use will negatively affect the parametrization of the curve and, consequently, its stiffness. Hence, we introduce a new edge-based energy that is independent of the parameterization. It is also more robust since it takes into account the gradient direction as well. We express this energy term as a surface integral, thus unifying it naturally with the region-based schemes. The unified framework enables the user to tune the image energy to the application at hand. We show that parametric snakes can guarantee low curvature curves, but only if they are described in the curvilinear abscissa. Since normal curve evolution do not ensure constant arc-length, we propose a new internal energy term that will force this configuration. The curve evolution can sometimes give rise to closed loops in the contour, which will adversely interfere with the optimization algorithm. We propose a curve evolution scheme that prevents this condition.

Higher Degree Total Variation (HDTV) Regularization for Image Recovery

We introduce novel image regularization penalties to overcome the practical problems associated with the classical total variation (TV) scheme. Motivated by novel reinterpretations of the classical TV regularizer, we derive two families of functionals involving higher degree partial image derivatives; we term these families as isotropic and anisotropic higher degree TV (HDTV) penalties, respectively. The isotropic penalty is the mixed norm of the directional image derivatives, while the anisotropic penalty is the separable norm of directional derivatives. These functionals inherit the desirable properties of standard TV schemes such as invariance to rotations and translations, preservation of discontinuities, and convexity. The use of mixed norms in isotropic penalties encourages the joint sparsity of the directional derivatives at each pixel, thus encouraging isotropic smoothing. In contrast, the fully separable norm in the anisotropic penalty ensures the preservation of discontinuities, while continuing to smooth along the line like features; this scheme thus enhances the linenlike image characteristics analogous to standard TV. We also introduce efficient majorize-minimize algorithms to solve the resulting optimization problems. The numerical comparison of the proposed scheme with classical TV penalty, current second-degree methods, and wavelet algorithms clearly demonstrate the performance improvement. Specifically, the proposed algorithms minimize the staircase and ringing artifacts that are common with TV and wavelet schemes, while better preserving the singularities. We also observe that anisotropic HDTV penalty provides consistently improved reconstructions compared with the isotropic HDTV penalty.

Blind Compressive Sensing Dynamic MRI

We propose a novel blind compressive sensing (BCS) frame work to recover dynamic magnetic resonance images from undersampled measurements. This scheme models the dynamic signal as a sparse linear combination of temporal basis functions, chosen from a large dictionary. In contrast to classical compressed sensing, the BCS scheme simultaneously estimates the dictionary and the sparse coefficients from the undersampled measurements. Apart from the sparsity of the coefficients, the key difference of the BCS scheme with current low rank methods is the nonorthogonal nature of the dictionary basis functions. Since the number of degrees-of-freedom of the BCS model is smaller than that of the low-rank methods, it provides improved reconstructions at high acceleration rates. We formulate the reconstruction as a constrained optimization problem; the objective function is the linear combination of a data consistency term and sparsity promoting l1 prior of the coefficients. The Frobenius norm dictionary constraint is used to avoid scale ambiguity. We introduce a simple and efficient majorize-minimize algorithm, which decouples the original criterion into three simpler subproblems. An alternating minimization strategy is used, where we cycle through the minimization of three simpler problems. This algorithm is seen to be considerably faster than approaches that alternates between sparse coding and dictionary estimation, as well as the extension of K-SVD dictionary learning scheme. The use of the l1 penalty and Frobenius norm dictionary constraint enables the attenuation of insignificant basis functions compared to the l0 norm and column norm constraint assumed in most dictionary learning algorithms; this is especially important since the number of basis functions that can be reliably estimated is restricted by the available measurements. We also observe that the proposed scheme is more robust to local minima compared to K-SVD method, which relies on greedy sparse coding. Our phase transition experiments demonstrate that the BCS scheme provides much better recovery rates than classical Fourier-based CS schemes, while being only marginally worse than the dictionary aware setting. Since the overhead in additionally estimating the dictionary is low, this method can be very useful in dynamic magnetic resonance imaging applications, where the signal is not sparse in known dictionaries. We demonstrate the utility of the BCS scheme in accelerating contrast enhanced dynamic data. We observe superior reconstruction performance with the BCS scheme in comparison to existing low rank and compressed sensing schemes.

Quantitative Comparison of Reconstruction Methods for Intra-Voxel Fiber Recovery From Diffusion MRI

Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the “HARDI reconstruction challenge” organized in the context of the “ISBI 2012” conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies.

Nonlocal Regularization of Inverse Problems: A Unified Variational Framework

We introduce a unifying energy minimization framework for nonlocal regularization of inverse problems. In contrast to the weighted sum of square differences between image pixels used by current schemes, the proposed functional is an unweighted sum of inter-patch distances. We use robust distance metrics that promote the averaging of similar patches, while discouraging the averaging of dissimilar patches. We show that the first iteration of a majorize-minimize algorithm to minimize the proposed cost function is similar to current nonlocal methods. The reformulation thus provides a theoretical justification for the heuristic approach of iterating nonlocal schemes, which re-estimate the weights from the current image estimate. Thanks to the reformulation, we now understand that the widely reported alias amplification associated with iterative nonlocal methods are caused by the convergence to local minimum of the nonconvex penalty. We introduce an efficient continuation strategy to overcome this problem. The similarity of the proposed criterion to widely used nonquadratic penalties (e.g., total variation and lp semi-norms) opens the door to the adaptation of fast algorithms developed in the context of compressive sensing; we introduce several novel algorithms to solve the proposed nonlocal optimization problem. Thanks to the unifying framework, these fast algorithms are readily applicable for a large class of distance metrics.

A Fast Majorize–Minimize Algorithm for the Recovery of Sparse and Low-Rank Matrices

We introduce a novel algorithm to recover sparse and low-rank matrices from noisy and undersampled measurements. We pose the reconstruction as an optimization problem, where we minimize a linear combination of data consistency error, nonconvex spectral penalty, and nonconvex sparsity penalty. We majorize the nondifferentiable spectral and sparsity penalties in the criterion by quadratic expressions to realize an iterative three-step alternating minimization scheme. Since each of these steps can be evaluated either analytically or using fast schemes, we obtain a computationally efficient algorithm. We demonstrate the utility of the algorithm in the context of dynamic magnetic resonance imaging (MRI) reconstruction from sub-Nyquist sampled measurements. The results show a significant improvement in signal-to-noise ratio and image quality compared with classical dynamic imaging algorithms. We expect the proposed scheme to be useful in a range of applications including video restoration and multidimensional MRI.

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.