arXiv subjects

R. Duits

Publications and source records attributed to R. Duits.

8 recordsLinked to original sources

arXiv2017

Design and Processing of Invertible Orientation Scores of 3D Images for Enhancement of Complex Vasculature

The enhancement and detection of elongated structures in noisy image data is relevant for many biomedical imaging applications. To handle complex crossing structures in 2D images, 2D orientation scores $U: \mathbb{R} ^ 2\times S ^ 1 \rightarrow \mathbb{C}$ were introduced, which already showed their use in a variety of applications. Here we extend this work to 3D orientation scores $U: \mathbb{R} ^ 3 \times S ^ 2\rightarrow \mathbb{C}$. First, we construct the orientation score from a given dataset, which is achieved by an invertible coherent state type of transform. For this transformation we introduce 3D versions of the 2D cake-wavelets, which are complex wavelets that can simultaneously detect oriented structures and oriented edges. Here we introduce two types of cake-wavelets, the first uses a discrete Fourier transform, the second is designed in the 3D generalized Zernike basis, allowing us to calculate analytical expressions for the spatial filters. Finally, we show two applications of the orientation score transformation. In the first application we propose an extension of crossing-preserving coherence enhancing diffusion via our invertible orientation scores of 3D images which we apply to real medical image data. In the second one we develop a new tubularity measure using 3D orientation scores and apply the tubularity measure to both artificial and real medical data.

cs.CV↗

arXiv2017

Vessel Tracking via Sub-Riemannian Geodesics on $\mathbb{R}^2 \times P^{1}$

We study a data-driven sub-Riemannian (SR) curve optimization model for connecting local orientations in orientation lifts of images. Our model lives on the projective line bundle $\mathbb{R}^{2} \times P^{1}$, with $P^{1}=S^{1}/_{\sim}$ with identification of antipodal points. It extends previous cortical models for contour perception on $\mathbb{R}^{2} \times P^{1}$ to the data-driven case. We provide a complete (mainly numerical) analysis of the dynamics of the 1st Maxwell-set with growing radii of SR-spheres, revealing the cut-locus. Furthermore, a comparison of the cusp-surface in $\mathbb{R}^{2} \times P^{1}$ to its counterpart in $\mathbb{R}^{2} \times S^{1}$ of a previous model, reveals a general and strong reduction of cusps in spatial projections of geodesics. Numerical solutions of the model are obtained by a single wavefront propagation method relying on a simple extension of existing anisotropic fast-marching or iterative morphological scale space methods. Experiments show that the projective line bundle structure greatly reduces the presence of cusps. Another advantage of including $\mathbb{R}^2 \times P^{1}$ instead of $\mathbb{R}^{2} \times S^{1}$ in the wavefront propagation is reduction of computational time.

math.OC↗

arXiv2016

New Exact and Numerical Solutions of the (Convection-)Diffusion Kernels on SE(3)

We consider hypo-elliptic diffusion and convection-diffusion on $\mathbb{R}^3 \rtimes S^2$, the quotient of the Lie group of rigid body motions SE(3) in which group elements are equivalent if they are equal up to a rotation around the reference axis. We show that we can derive expressions for the convolution kernels in terms of eigenfunctions of the PDE, by extending the approach for the SE(2) case. This goes via application of the Fourier transform of the PDE in the spatial variables, yielding a second order differential operator. We show that the eigenfunctions of this operator can be expressed as (generalized) spheroidal wave functions. The same exact formulas are derived via the Fourier transform on SE(3). We solve both the evolution itself, as well as the time-integrated process that corresponds to the resolvent operator. Furthermore, we have extended a standard numerical procedure from SE(2) to SE(3) for the computation of the solution kernels that is directly related to the exact solutions. Finally, we provide a novel analytic approximation of the kernels that we briefly compare to the exact kernels.

math.AP↗

arXiv2016

Tracking of Lines in Spherical Images via Sub-Riemannian Geodesics on SO(3)

In order to detect salient lines in spherical images, we consider the problem of minimizing the functional $\int \limits_0^l C(\gamma(s)) \sqrt{\xi^2 + k_g^2(s)} \, {\rm d}s$ for a curve $\gamma$ on a sphere with fixed boundary points and directions. The total length $l$ is free, $s$ denotes the spherical arclength, and $k_g$ denotes the geodesic curvature of $\gamma$. Here the smooth external cost $C\geq \delta>0$ is obtained from spherical data. We lift this problem to the sub-Riemannian (SR) problem in Lie group $SO(3)$ and show that the spherical projection of certain SR geodesics provides a solution to our curve optimization problem. In fact, this holds only for the geodesics whose spherical projection does not exhibit a cusp. The problem is a spherical extension of a well-known contour perception model, where we extend the model by Boscain and Rossi to the general case $\xi > 0$, $C \neq 1$. For $C=1$, we derive SR geodesics and evaluate the first cusp time. We show that these curves have a simpler expression when they are parameterized by spherical arclength rather than by sub-Riemannian arclength. For case $C \neq 1$ (data-driven SR geodesics), we solve via a SR Fast Marching method. Finally, we show an experiment of vessel tracking in a spherical image of the retina and study the effect of including the spherical geometry in analysis of vessels curvature.

math.OC↗

arXiv2015

Improving Fiber Alignment in HARDI by Combining Contextual PDE Flow with Constrained Spherical Deconvolution

We propose two strategies to improve the quality of tractography results computed from diffusion weighted magnetic resonance imaging (DW-MRI) data. Both methods are based on the same PDE framework, defined in the coupled space of positions and orientations, associated with a stochastic process describing the enhancement of elongated structures while preserving crossing structures. In the first method we use the enhancement PDE for contextual regularization of a fiber orientation distribution (FOD) that is obtained on individual voxels from high angular resolution diffusion imaging (HARDI) data via constrained spherical deconvolution (CSD). Thereby we improve the FOD as input for subsequent tractography. Secondly, we introduce the fiber to bundle coherence (FBC), a measure for quantification of fiber alignment. The FBC is computed from a tractography result using the same PDE framework and provides a criterion for removing the spurious fibers. We validate the proposed combination of CSD and enhancement on phantom data and on human data, acquired with different scanning protocols. On the phantom data we find that PDE enhancements improve both local metrics and global metrics of tractography results, compared to CSD without enhancements. On the human data we show that the enhancements allow for a better reconstruction of crossing fiber bundles and they reduce the variability of the tractography output with respect to the acquisition parameters. Finally, we show that both the enhancement of the FODs and the use of the FBC measure on the tractography improve the stability with respect to different stochastic realizations of probabilistic tractography. This is shown in a clinical application: the reconstruction of the optic radiation for epilepsy surgery planning.

cs.CV↗

arXiv2015

New Approximation of a Scale Space Kernel on SE(3) and Applications in Neuroimaging

We provide a new, analytic kernel for scale space filtering of dMRI data. The kernel is an approximation for the Green's function of a hypo-elliptic diffusion on the 3D rigid body motion group SE(3), for fiber enhancement in dMRI. The enhancements are described by linear scale space PDEs in the coupled space of positions and orientations embedded in SE(3). As initial condition for the evolution we use either a Fiber Orientation Distribution (FOD) or an Orientation Density Function (ODF). Explicit formulas for the exact kernel do not exist. Although approximations well-suited for fast implementation have been proposed in literature, they lack important symmetries of the exact kernel. We introduce techniques to include these symmetries in approximations based on the logarithm on SE(3), resulting in an improved kernel. Regarding neuroimaging applications, we apply our enhancement kernel (a) to improve dMRI tractography results and (b) to quantify coherence of obtained streamline bundles.

math.AP↗

arXiv2015

Locally Adaptive Frames in the Roto-Translation Group and their Applications in Medical Imaging

Locally adaptive differential frames (gauge frames) are a well-known effective tool in image analysis, used in differential invariants and PDE-flows. However, at complex structures such as crossings or junctions, these frames are not well-defined. Therefore, we generalize the notion of gauge frames on images to gauge frames on data representations $U:\mathbb{R}^{d} \rtimes S^{d-1} \to \mathbb{R}$ defined on the extended space of positions and orientations, which we relate to data on the roto-translation group $SE(d)$, $d=2,3$. This allows to define multiple frames per position, one per orientation. We compute these frames via exponential curve fits in the extended data representations in $SE(d)$. These curve fits minimize first or second order variational problems which are solved by spectral decomposition of, respectively, a structure tensor or Hessian of data on $SE(d)$. We include these gauge frames in differential invariants and crossing preserving PDE-flows acting on extended data representation $U$ and we show their advantage compared to the standard left-invariant frame on $SE(d)$. Applications include crossing-preserving filtering and improved segmentations of the vascular tree in retinal images, and new 3D extensions of coherence-enhancing diffusion via invertible orientation scores.

math.GR↗

arXiv2013

Left-invariant evolutions of wavelet transforms on the Similitude Group

Enhancement of multiple-scale elongated structures in noisy image data is relevant for many biomedical applications but commonly used PDE-based enhancement techniques often fail at crossings in an image. To get an overview of how an image is composed of local multiple-scale elongated structures we construct a multiple scale orientation score, which is a continuous wavelet transform on the similitude group, SIM(2). Our unitary transform maps the space of images onto a reproducing kernel space defined on SIM(2), allowing us to robustly relate Euclidean (and scaling) invariant operators on images to left-invariant operators on the corresponding continuous wavelet transform. Rather than often used wavelet (soft-)thresholding techniques, we employ the group structure in the wavelet domain to arrive at left-invariant evolutions and flows (diffusion), for contextual crossing preserving enhancement of multiple scale elongated structures in noisy images. We present experiments that display benefits of our work compared to recent PDE techniques acting directly on the images and to our previous work on left-invariant diffusions on orientation scores defined on Euclidean motion group.

math.AP↗