1,335 research outputs found
Mapping Topographic Structure in White Matter Pathways with Level Set Trees
Fiber tractography on diffusion imaging data offers rich potential for
describing white matter pathways in the human brain, but characterizing the
spatial organization in these large and complex data sets remains a challenge.
We show that level set trees---which provide a concise representation of the
hierarchical mode structure of probability density functions---offer a
statistically-principled framework for visualizing and analyzing topography in
fiber streamlines. Using diffusion spectrum imaging data collected on
neurologically healthy controls (N=30), we mapped white matter pathways from
the cortex into the striatum using a deterministic tractography algorithm that
estimates fiber bundles as dimensionless streamlines. Level set trees were used
for interactive exploration of patterns in the endpoint distributions of the
mapped fiber tracks and an efficient segmentation of the tracks that has
empirical accuracy comparable to standard nonparametric clustering methods. We
show that level set trees can also be generalized to model pseudo-density
functions in order to analyze a broader array of data types, including entire
fiber streamlines. Finally, resampling methods show the reliability of the
level set tree as a descriptive measure of topographic structure, illustrating
its potential as a statistical descriptor in brain imaging analysis. These
results highlight the broad applicability of level set trees for visualizing
and analyzing high-dimensional data like fiber tractography output
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An Optimized Structure-Function Design Principle Underlies Efficient Signaling Dynamics in Neurons.
Dynamic signaling on branching axons is critical for rapid and efficient communication between neurons in the brain. Efficient signaling in axon arbors depends on a trade-off between the time it takes action potentials to reach synaptic terminals (temporal cost) and the amount of cellular material associated with the wiring path length of the neuron's morphology (material cost). However, where the balance between structural and dynamical considerations for achieving signaling efficiency is, and the design principle that neurons optimize to preserve this balance, is still elusive. In this work, we introduce a novel analysis that compares morphology and signaling dynamics in axonal networks to address this open problem. We show that in Basket cell neurons the design principle being optimized is the ratio between the refractory period of the membrane, and action potential latencies between the initial segment and the synaptic terminals. Our results suggest that the convoluted paths taken by axons reflect a design compensation by the neuron to slow down signaling latencies in order to optimize this ratio. Deviations in this ratio may result in a breakdown of signaling efficiency in the cell. These results pave the way to new approaches for investigating more complex neurophysiological phenomena that involve considerations of neuronal structure-function relationships
Landmark Localization, Feature Matching and Biomarker Discovery from Magnetic Resonance Images
The work presented in this thesis proposes several methods that can be roughly divided into three different categories: I) landmark localization in medical images, II) feature matching for image registration,
and III) biomarker discovery in neuroimaging.
The first part deals with the identification of anatomical landmarks. The motivation stems from the fact that the manual identification and labeling of these landmarks is very time consuming and prone to observer errors, especially when large datasets must be analyzed. In this thesis we present three methods to tackle this challenge: A landmark descriptor based on local self-similarities (SS), a subspace building framework based on manifold learning and a sparse coding landmark descriptor based on data-specific learned dictionary basis.
The second part of this thesis deals with finding matching features between a pair of images. These matches can be used to perform a registration between them. Registration is a powerful tool that allows mapping images in a common space in order to aid in their analysis. Accurate registration can be challenging to achieve using intensity based registration algorithms. Here, a framework is proposed for learning correspondences in pairs of images by matching SS features and random sample and consensus (RANSAC) is employed as a robust model estimator to learn a deformation model based on feature matches.
Finally, the third part of the thesis deals with biomarker discovery using machine learning. In this section a framework for feature extraction from learned low-dimensional subspaces that represent inter-subject
variability is proposed. The manifold subspace is built using data-driven regions of interest (ROI). These regions are learned via sparse regression, with stability selection. Also, probabilistic distribution models for
different stages in the disease trajectory are estimated for different class populations in the low-dimensional manifold and used to construct a probabilistic scoring function.Open Acces
A Perfect Match Condition for Point-Set Matching Problems Using the Optimal Mass Transport Approach
We study the performance of optimal mass transport--based methods applied to point-set matching problems. The present study, which is based on the L2 mass transport cost, states that perfect matches always occur when the product of the point-set cardinality and the norm of the curl of the nonrigid deformation field does not exceed some constant. This analytic result is justified by a numerical study of matching two sets of pulmonary vascular tree branch points whose displacement is caused by the lung volume changes in the same human subject. The nearly perfect match performance verifies the effectiveness of this mass transport--based approach.Read More: http://epubs.siam.org/doi/abs/10.1137/12086443
3D shape matching and registration : a probabilistic perspective
Dense correspondence is a key area in computer vision and medical image analysis. It has applications in registration and shape analysis. In this thesis, we develop a technique to recover dense correspondences between the surfaces of neuroanatomical objects over heterogeneous populations of individuals. We recover dense correspondences based on 3D shape matching. In this thesis, the 3D shape matching problem is formulated under the framework of Markov Random Fields (MRFs). We represent the surfaces of neuroanatomical objects as genus zero voxel-based meshes. The surface meshes are projected into a Markov random field space. The projection carries both geometric and topological information in terms of Gaussian curvature and mesh neighbourhood from the original space to the random field space. Gaussian curvature is projected to the nodes of the MRF, and the mesh neighbourhood structure is projected to the edges. 3D shape matching between two surface meshes is then performed by solving an energy function minimisation problem formulated with MRFs. The outcome of the 3D shape matching is dense point-to-point correspondences. However, the minimisation of the energy function is NP hard. In this thesis, we use belief propagation to perform the probabilistic inference for 3D shape matching. A sparse update loopy belief propagation algorithm adapted to the 3D shape matching is proposed to obtain an approximate global solution for the 3D shape matching problem. The sparse update loopy belief propagation algorithm demonstrates significant efficiency gain compared to standard belief propagation. The computational complexity and convergence property analysis for the sparse update loopy belief propagation algorithm are also conducted in the thesis. We also investigate randomised algorithms to minimise the energy function. In order to enhance the shape matching rate and increase the inlier support set, we propose a novel clamping technique. The clamping technique is realized by combining the loopy belief propagation message updating rule with the feedback from 3D rigid body registration. By using this clamping technique, the correct shape matching rate is increased significantly. Finally, we investigate 3D shape registration techniques based on the 3D shape matching result. Based on the point-to-point dense correspondences obtained from the 3D shape matching, a three-point based transformation estimation technique is combined with the RANdom SAmple Consensus (RANSAC) algorithm to obtain the inlier support set. The global registration approach is purely dependent on point-wise correspondences between two meshed surfaces. It has the advantage that the need for orientation initialisation is eliminated and that all shapes of spherical topology. The comparison of our MRF based 3D registration approach with a state-of-the-art registration algorithm, the first order ellipsoid template, is conducted in the experiments. These show dense correspondence for pairs of hippocampi from two different data sets, each of around 20 60+ year old healthy individuals
Physiology-based simulation of the retinal vasculature enables annotation-free segmentation of OCT angiographs
Optical coherence tomography angiography (OCTA) can non-invasively image the
eye's circulatory system. In order to reliably characterize the retinal
vasculature, there is a need to automatically extract quantitative metrics from
these images. The calculation of such biomarkers requires a precise semantic
segmentation of the blood vessels. However, deep-learning-based methods for
segmentation mostly rely on supervised training with voxel-level annotations,
which are costly to obtain. In this work, we present a pipeline to synthesize
large amounts of realistic OCTA images with intrinsically matching ground truth
labels; thereby obviating the need for manual annotation of training data. Our
proposed method is based on two novel components: 1) a physiology-based
simulation that models the various retinal vascular plexuses and 2) a suite of
physics-based image augmentations that emulate the OCTA image acquisition
process including typical artifacts. In extensive benchmarking experiments, we
demonstrate the utility of our synthetic data by successfully training retinal
vessel segmentation algorithms. Encouraged by our method's competitive
quantitative and superior qualitative performance, we believe that it
constitutes a versatile tool to advance the quantitative analysis of OCTA
images.Comment: Accepted at MICCAI 202
Physiology-based simulation of the retinal vasculature enables annotation-free segmentation of OCT angiographs
Optical coherence tomography angiography (OCTA) can non-invasively image the eye's circulatory system. In order to reliably characterize the retinal vasculature, there is a need to automatically extract quantitative metrics from these images. The calculation of such biomarkers requires a precise semantic segmentation of the blood vessels. However, deep-learning-based methods for segmentation mostly rely on supervised training with voxel-level annotations, which are costly to obtain. In this work, we present a pipeline to synthesize large amounts of realistic OCTA images with intrinsically matching ground truth labels; thereby obviating the need for manual annotation of training data. Our proposed method is based on two novel components: 1) a physiology-based simulation that models the various retinal vascular plexuses and 2) a suite of physics-based image augmentations that emulate the OCTA image acquisition process including typical artifacts. In extensive benchmarking experiments, we demonstrate the utility of our synthetic data by successfully training retinal vessel segmentation algorithms. Encouraged by our method's competitive quantitative and superior qualitative performance, we believe that it constitutes a versatile tool to advance the quantitative analysis of OCTA images
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