200 research outputs found
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 defined on the extended space of positions and
orientations, which we relate to data on the roto-translation group ,
. 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 . 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 . We include
these gauge frames in differential invariants and crossing preserving PDE-flows
acting on extended data representation and we show their advantage compared
to the standard left-invariant frame on . 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
Nilpotent Approximations of Sub-Riemannian Distances for Fast Perceptual Grouping of Blood Vessels in 2D and 3D
We propose an efficient approach for the grouping of local orientations
(points on vessels) via nilpotent approximations of sub-Riemannian distances in
the 2D and 3D roto-translation groups and . In our distance
approximations we consider homogeneous norms on nilpotent groups that locally
approximate , and which are obtained via the exponential and logarithmic
map on . In a qualitative validation we show that the norms provide
accurate approximations of the true sub-Riemannian distances, and we discuss
their relations to the fundamental solution of the sub-Laplacian on .
The quantitative experiments further confirm the accuracy of the
approximations. Quantitative results are obtained by evaluating perceptual
grouping performance of retinal blood vessels in 2D images and curves in
challenging 3D synthetic volumes. The results show that 1) sub-Riemannian
geometry is essential in achieving top performance and 2) that grouping via the
fast analytic approximations performs almost equally, or better, than
data-adaptive fast marching approaches on and .Comment: 18 pages, 9 figures, 3 tables, in review at JMI
Total Variation and Mean Curvature PDEs on
Total variation regularization and total variation flows (TVF) have been
widely applied for image enhancement and denoising. To include a generic
preservation of crossing curvilinear structures in TVF we lift images to the
homogeneous space of positions and
orientations as a Lie group quotient in SE(d). For d = 2 this is called 'total
roto-translation variation' by Chambolle & Pock. We extend this to d = 3, by a
PDE-approach with a limiting procedure for which we prove convergence. We also
include a Mean Curvature Flow (MCF) in our PDE model on M. This was first
proposed for d = 2 by Citti et al. and we extend this to d = 3. Furthermore,
for d = 2 we take advantage of locally optimal differential frames in
invertible orientation scores (OS). We apply our TVF and MCF in the
denoising/enhancement of crossing fiber bundles in DW-MRI. In comparison to
data-driven diffusions, we see a better preservation of bundle boundaries and
angular sharpness in fiber orientation densities at crossings. We support this
by error comparisons on a noisy DW-MRI phantom. We also apply our TVF and MCF
in enhancement of crossing elongated structures in 2D images via OS, and
compare the results to nonlinear diffusions (CED-OS) via OS.Comment: Submission to the Seventh International Conference on Scale Space and
Variational Methods in Computer Vision (SSVM 2019). (v2) Typo correction in
lemma 1. (v3) Typo correction last paragraph page
Geodesic Tracking via New Data-driven Connections of Cartan Type for Vascular Tree Tracking
We introduce a data-driven version of the plus Cartan connection on the
homogeneous space of 2D positions and orientations. We formulate
a theorem that describes all shortest and straight curves (parallel velocity
and parallel momentum, respectively) with respect to this new data-driven
connection and corresponding Riemannian manifold. Then we use these shortest
curves for geodesic tracking of complex vasculature in multi-orientation image
representations defined on . The data-driven Cartan connection
characterizes the Hamiltonian flow of all geodesics. It also allows for
improved adaptation to curvature and misalignment of the (lifted) vessel
structure that we track via globally optimal geodesics. We compute these
geodesics numerically via steepest descent on distance maps on
that we compute by a new modified anisotropic fast-marching method.
Our experiments range from tracking single blood vessels with fixed endpoints
to tracking complete vascular trees in retinal images. Single vessel tracking
is performed in a single run in the multi-orientation image representation,
where we project the resulting geodesics back onto the underlying image. The
complete vascular tree tracking requires only two runs and avoids prior
segmentation, placement of extra anchor points, and dynamic switching between
geodesic models.
Altogether we provide a geodesic tracking method using a single, flexible,
transparent, data-driven geodesic model providing globally optimal curves which
correctly follow highly complex vascular structures in retinal images.
All experiments in this article can be reproduced via documented Mathematica
notebooks available at GitHub
(https://github.com/NickyvdBerg/DataDrivenTracking)
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.Comment: 40 page
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
Invertible Orientation Scores of 3D Images
The enhancement and detection of elongated structures in noisy image data is
relevant for many biomedical applications. To handle complex crossing
structures in 2D images, 2D orientation scores were introduced, which already
showed their use in a variety of applications. Here we extend this work to 3D
orientation scores. 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. For efficient implementation of the different steps in the
wavelet creation we use a spherical harmonic transform. Finally, we show some
first results of practical applications of 3D orientation scores.Comment: ssvm 2015 published version in LNCS contains a mistake (a switch
notation spherical angles) that is corrected in this arxiv versio
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